Proteins and Protein Structure

Kurochkina, Natalya

doi:10.1007/978-981-13-6601-7_1

Natalya Kurochkina²

1346 Accesses

Abstract

Proteins such as enzymes, channels, signaling molecules and adaptors carry out important functions in living organisms. Fibrous and globular proteins comprise two large groups. Long stretches of coiled coil α-helices in fibers and fibrils, triple helices of collagen , and globular heme binding subunits of hemoglobin give us main representatives and show how diverse these molecules are. Protein polypeptide chain exhibits left-handed and right handed, parallel and antiparallel arrangements of secondary structure elements such as alpha, 3₁₀ , polyproline, gamma and pi helices, strands and turns. This chapter describes structural principles of protein molecule, its conformation and relationships between primary, secondary, tertiary, and quaternary structure.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Chapter: USD 29.95; Price excludes VAT (USA)

eBook: USD 149.00; Price excludes VAT (USA)

Softcover Book: USD 189.00; Price excludes VAT (USA)

Hardcover Book: USD 199.99; Price excludes VAT (USA)

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

Adam A, Haberhauer G, Wölper C (2017) Bio-inspired herringbone foldamers: strategy for changing the structure of helices. J Org Chem 82(8):4203–4215. https://doi.org/10.1021/acs.joc.7b00185. Epub 2017 Apr 12
Article CAS PubMed Google Scholar
Adam C, Peters AD, Lizio MG, Whitehead GFS, Diemer V, Cooper JA, Cockroft SL, Clayden J, Webb SJ (2018) The Role of terminal functionality in the membrane and antibacterial activity of peptaibol-mimetic aib foldamers. Chemistry 24(9):2249–2256. https://doi.org/10.1002/chem.201705299. Epub 2018 Jan 17. PubMed PMID: 29210477
Article CAS PubMed Google Scholar
Aggeli A, Nyrkova IA, Bell M, Harding R, Carrick L, McLeish TCB, Semenov AN, Boden N (2001) Hierarchical self-assembly of chiral rod-like molecules as a model for peptide beta -sheet tapes, ribbons, fibrils, and fibers. Proc Natl Acad Sci USA 98:11857–11862
Article CAS PubMed PubMed Central Google Scholar
Ago H, Kanaoka AH, Irikura D et al (2007) Crystal structure of a human membrane protein involved in cysteinyl leukotriene biosynthesis. Nature 448:609–612
Article CAS PubMed Google Scholar
De Alba E (2009) Structure and interdomain dynamics of apoptosis-associated speck-like protein containing a CARD (ASC). J Biol Chem 284:32932–32941
Article PubMed PubMed Central CAS Google Scholar
Al Khamici H, Hossain KR, Cornell BA, Valenzuela SM (2016) Investigating sterol and redox regulation of the ion channel activity of CLIC1 using tethered bilayer membranes. Membranes (Basel). 6(4). pii: E51. PubMed PMID: 27941637; PubMed Central PMCID: PMC5192407
Article PubMed Central CAS Google Scholar
Alushin GM, Ramey VH, Pasqualato S, Ball DA, Grigorieff N, Musacchio A, Nogales E (2010) The Ndc80 kinetochore complex forms oligomeric arrays along microtubules. Nature 467:805–810
Article CAS PubMed PubMed Central Google Scholar
Alvarez BH, Gruber M, Ursinus A, Dunin-Horkawicz S, Lupas AN, Zeth K (2010) A transition from strong right-handed to canonical left-handed supercoiling in a conserved coiled-coil segment of trimeric autotransporter adhesins. J Struct Biol 170(2):236–245. https://doi.org/10.1016/j.jsb.2010.02.009. Epub 2010 Feb 21. PubMed PMID: 20178846
Article CAS PubMed Google Scholar
Andrade MA, Perez-Iratxeta C, Ponting CP (2001) Protein repeats: structures, functions, and evolutions. J Struct Biol 134:117–131
Article CAS PubMed Google Scholar
Andrews SC, Smith JM, Guest JR, Harrison PM (1989) Amino acid sequence of the bacterioferritin (cytochrome b1) of Escherichia coli-K12. Biochem Biophys Res Commun 158(2):489–496. PubMed PMID: 2644932
Article CAS PubMed Google Scholar
Aravinda S, Shamala N, Balaram P (2008) Aib residues in peptaibiotics and synthetic sequences: analysis of nonhelical conformations. Chem Biodivers 5(7):1238–1262. https://doi.org/10.1002/cbdv.200890112
Article CAS PubMed Google Scholar
Arcy SD, Davies OR, Blundell TL, Bolanos-Garcia VM (2010) Defining the molecular basis of BubR1 kinetochore interactions and APC/C-CDC20 inhibition. J Biol Chem 285:14764–14776
Article PubMed PubMed Central CAS Google Scholar
Balasco N, Smaldone G, Ruggiero A, De Simone A, Vitagliano L (2018) Local structural motifs in proteins: Detection and characterization of fragments inserted in helices. Int J Biol Macromol. pii: S0141-8130(18)32822–32828. https://doi.org/10.1016/j.ijbiomac.2018.07.047. [Epub ahead of print] PubMed PMID: 30017977
Article CAS PubMed Google Scholar
Balashova TA, Shenkarev ZO, Tagaev AA, Ovchinnikova TV, Raap J, Arseniev AS (2000) NMR structure of the channel-former zervamicin IIB in isotropic solvents. FEBS Lett 466(2-3):333–336. PubMed PMID: 10682854
Article CAS PubMed Google Scholar
Banci L, Bertini I, Cefaro C, Ciofi-Baffoni S, Gallo A (2011) Functional role of two interhelical disulfide bonds in human Cox17 protein from a structural perspective. J Biol Chem 286(39):34382–34390. https://doi.org/10.1074/jbc.M111.246223. Epub 2011 Aug 4. PubMed PMID: 21816817; PubMed Central PMCID: PMC3190761
Article CAS PubMed PubMed Central Google Scholar
Banner DW, Kokkinidis M, Tsernoglou D (1987) Structure of the ColE1 rop protein at 1.7 A resolution. J Mol Biol 196(3):657–675. PubMed PMID: 3681971
Article CAS PubMed Google Scholar
Barua B (2013) Periodicities designed in the tropomyosin sequence and structure define its functions. Bioarchitecture 3(3):51–56. https://doi.org/10.4161/bioa.2561
Article PubMed PubMed Central Google Scholar
Berisio R, Vitagliano L (2012) Polyproline and triple helix motifs in host-pathogen recognition. Curr Protein Pept Sci 13(8):855–865. https://doi.org/10.2174/138920312804871157
Article CAS PubMed PubMed Central Google Scholar
Bhyravbhatla B, Watowich SJ, Caspar DL (1998) Refined atomic model of the four-layer aggregate of the tobacco mosaic virus coat protein at 2.4-Å resolution. Biophys J 74:604–615
Article CAS PubMed PubMed Central Google Scholar
Blatch GL, Lassle M (1999) The tetratricopeptide repeat: a structural motif mediating protein-protein interactions. Bioassays 21:932–939
Article CAS Google Scholar
Boscutti G, Nardon C, Marchiò L, Crisma M, Biondi B, Dalzoppo D, Dalla Via L, Formaggio F, Casini A, Fregona D (2018) Anticancer gold(III) peptidomimetics: from synthesis to in vitro and ex vivo biological evaluation. ChemMedChem. https://doi.org/10.1002/cmdc.201800098. [Epub ahead of print] PubMed PMID: 29570944
Article CAS PubMed Google Scholar
Boudko SP, Bächinger HP (2016) Structural insight for chain selection and stagger control in collagen. Sci Rep 6:37831. https://doi.org/10.1038/srep37831
Article CAS PubMed PubMed Central Google Scholar
Branden, C., Tooze, J (1991) Introduction to protein structure.
Google Scholar
Brennan SO (2015) Variation of fibrinogen oligosaccharide structure in the acute phase response: possible haemorrhagic implications. BBA Clinical 3:221–226. https://doi.org/10.1016/j.bbacli.2015.02.007
Article PubMed PubMed Central Google Scholar
Brinkmann U, Di Carlo A, Vasmatzis G, Kurochkina N, Beers R, Lee B, Pastan I (1997) Stabilization of a recombinant Fv fragment by base loop interconnection and VH-VL permutation. J Mol Biol 268:107–117
Article CAS PubMed Google Scholar
Brunner JD, Lim NK, Schenck S, Duerst A, Dutzler R (2014) X-ray structure of a calcium-activated TMEM16 lipid scramblase. Nature 516(7530):207–212. https://doi.org/10.1038/nature13984. Epub 2014 Nov 12. PubMed PMID: 25383531
Article CAS PubMed Google Scholar
Bunick CG, Milstone LM (2017) The X-ray crystal structure of the keratin 1-keratin 10 helix 2B heterodimer reveals molecular surface properties and biochemical insights into human skin disease. J Invest Dermatol;137(1):142–150.: https://doi.org/10.1016/j.jid.2016.08.018. Epub 2016 Sep 3.
Article CAS Google Scholar
Burgess AW, Leach SJ (1973) An obligatory alpha-helical amino acid residue. Biopolymers 12(11):2599–2605. PubMed PMID: 4780721
Article CAS PubMed Google Scholar
Cabrele C, Langer M, Bader R, Wieland HA, Doods HN, Zerbe O, Beck-Sickinger AG (2000) The first selective agonist for the neuropeptide YY5 receptor increases food intake in rats. J Biol Chem 275(46):36043–36048
Article CAS PubMed Google Scholar
Caffrey M, Cai M, Kaufman J, Stahl SJ, Wingfield PT, Covell DG, Gronenborn AM, Clore GM (1998) Three-dimensional solution structure of the 44 kDa ectodomain of SIV gp41. Embo J 17:4572–4584
Article CAS PubMed PubMed Central Google Scholar
Cervantes-Madrid D, Dominguez-Gomez G, Gonzalez-Fierro A, Perez-Cardenas E, Taja-Chayeb L, Trejo-Becerril C, Duenas-Gonzalez A (2017) Feasibility and antitumor efficacy in vivo, of simultaneously targeting glycolysis, glutaminolysis and fatty acid synthesis using lonidamine, 6-diazo-5-oxo-L-norleucine and orlistat in colon cancer. Oncology Letters 13(3):1905–1910. https://doi.org/10.3892/ol.2017.5615
Article CAS PubMed PubMed Central Google Scholar
Chen Q, Wells MM, Arjunan P, Tillman TS, Cohen AE, Xu Y, Tang P (2018) Structural basis of neurosteroid anesthetic action on GABA(A) receptors. Nat Commun 9(1):3972. https://doi.org/10.1038/s41467-018-06361-4. PubMed PMID: 30266951; PubMed Central PMCID: PMC6162318
Article CAS PubMed PubMed Central Google Scholar
Chingle R, Proulx C, Lubell WD (2017) Azapeptide synthesis methods for expanding side-chain diversity for biomedical applications. Acc Chem Res 50(7):1541–1556. https://doi.org/10.1021/acs.accounts.7b00114. Epub 2017 Jun 9
Article CAS PubMed Google Scholar
Chothia C (1973) Conformation of twisted beta-pleated sheets in proteins. J Mol Biol 75:295–302
Article CAS PubMed Google Scholar
Chothia C (1975) Structural invariants in protein folding. Nature 254:304–308
Article CAS PubMed Google Scholar
Chothia C, Levitt M, Richardson D (1981) Helix to helix packing in proteins. J Mol Biol 145:215–250
Article CAS PubMed Google Scholar
Chothia C, Janin J (1982) Orthogonal packing of beta-pleated sheets in proteins. Biochemistry 21(17):3955–3965. PubMed PMID: 6751382
Article CAS PubMed Google Scholar
Chou KC (1988) Review: Low-frequency collective motion in biomacromolecules and its biological functions. Biophysical Chemistry 30:3–48
Article CAS PubMed Google Scholar
Chou KC (1992) Energy-optimized structure of antifreeze protein and its binding mechanism. J Mol Biol 223:509–517
Article CAS PubMed Google Scholar
Chou KC, Nemethy G, Scheraga HA (1990) Review: Energetics of interactions of regular structural elements in proteins. Acc Chem Res 23:134–141
Article CAS Google Scholar
Chou KC, Maggiora GM, Nemethy G, Scheraga HA (1988) Energetics of the structure of the four-alpha-helix bundle in proteins. Proc Natl Acad Sci USA 85:4295–4299
Article CAS PubMed PubMed Central Google Scholar
Chou KC, Maggiora GM, Scheraga HA (1992) The role of loop-helix interactions in stabilizing four-helix bundle proteins. Proc Natl Acad Sci USA 89:7315–7319
Article CAS PubMed PubMed Central Google Scholar
Cook JD, Soto-Montoya H, Korpela MK, Lee JE (2015) Electrostatic architecture of the Infectious Salmon Anemia Virus (ISAV) Core fusion protein illustrates a Carboxyl-Carboxylate pH Sensor. J Biol Chem 290(30):18495–18504. https://doi.org/10.1074/jbc.M115.644781. Epub 2015 Jun 16. PubMed PMID: 26082488; PubMed Central PMCID: PMC4513110
Article CAS PubMed PubMed Central Google Scholar
Cordopatis P, Manessi-Zoupa E, Theodoropoulos D, Bossé R, Bouley R, Gagnon S, Escher E (1994) Methylation in positions 1 and 7 of angiotensin II. A structure-activity relationship study. Int J Pept Protein Res 44(4):320–324. PubMed PMID: 7875933
Article CAS PubMed Google Scholar
Costil R, Fernández-Nieto F, Atkinson RC, Clayden J (2018) α-Methyl phenylglycines by asymmetric α-arylation of alanine and their effect on the conformational preference of helical Aib foldamers. Org Biomol Chem doi: 10.1039/c8ob00551f. [Epub ahead of print] PubMed PMID: 29595846
Article CAS Google Scholar
Crick F (1953) Acta Crystallogr 6:689
Article CAS Google Scholar
Dadheech T, Shah R, Pandit R, Hinsu A, Chauhan PS, Jakhesara S, Kunjadiya A, Rank D, Joshi C (2018) Cloning, molecular modeling and characterization of acidic cellulase from buffalo rumen and its applicability in saccharification of lignocellulosic biomass. Int J Biol Macromol 113:73–81. https://doi.org/10.1016/j.ijbiomac.2018.02.100. Epub 2018 Feb 15. PubMed PMID: 29454942
Article CAS PubMed Google Scholar
Das T, Häring M, Haldar D, Díaz DD (2017) Phenylalanine and derivatives as versatile low-molecular-weight gelators: design, structure and tailored function. Biomater Sci 6(1):38–59. https://doi.org/10.1039/c7bm00882a. Review. PubMed PMID: 29164186
Article CAS PubMed Google Scholar
Davies TG, Hubbard RE, Tame JR (1999) Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes. Protein Sci 8(7):1432–1444
Article CAS PubMed PubMed Central Google Scholar
Dowling DP, Croft AK, Drennan CL (2012) Radical use of Rossmann and TIM barrel architectures for controlling coenzyme B12 chemistry. Annu Rev Biophys 41:403–427. https://doi.org/10.1146/annurev-biophys-050511-102225. Review. PubMed PMID: 22577824
Article CAS PubMed Google Scholar
Dulhunty A, Gage P, Curtis S et al (2001) The glutathione transferase structural family includes a nuclear chloride channel and a ryanodine receptor calcium release channel modulator. J Biol Chem 276:3319–3323
Article CAS PubMed Google Scholar
Efimov AV (1979) Packing of alpha-helices in globular proteins. Layer-structure of globin hydrophobic cores. J Mol Biol 134(1):23–40
Article CAS PubMed Google Scholar
Elkin I, Maris T, Melkoumov A, Hildgen P, Banquy X, Leclair G, Barrett C (2018) Crystal structure of 2-oxopyrrolidin-3-yl 4-(2-phenyl-diazen-1-yl)benzoate. Acta Crystallogr E Crystallogr Commun 6;74(Pt 4):458–460. doi: 10.1107/S205698901800333X. eCollection 2018 Apr 1. PubMed PMID: 29765745; PubMed Central PMCID: PMC5946967
Article CAS PubMed Central Google Scholar
Eriksson M, Hassan S, Larsson R, Linder S, Ramqvist T, Lövborg H, Vikinge T, Figgemeier E, Müller J, Stetefeld J, Dalianis T, Ozbek S (2009) Utilization of a right-handed coiled-coil protein from archaebacterium Staphylothermus marinus as a carrier for cisplatin. Anticancer Res 29(1):11–18. PubMed PMID: 19331128
CAS PubMed Google Scholar
Ferguson AD, Mckeever BM, Wisniewski D et al (2007) Crystal structure of inhibitor-bound human 5-lipoxygenase-activating protein. Science 317:510–512
Article CAS PubMed Google Scholar
Ferner J, Suhartono M, Breitung S, Jonker HR, Hennig M, Wöhnert J, Göbel M, Schwalbe H (2009) Structures of HIV TAR RNA-ligand complexes reveal higher binding stoichiometries. Chembiochem 10(9):1490–1494. https://doi.org/10.1002/cbic.200900220
Article CAS PubMed Google Scholar
Ferrone FA (2016) Sickle cell disease: Its molecular mechanism and the one drug that treats it. Int J Biol Macromol 93(Pt A):1168–1173. https://doi.org/10.1016/j.ijbiomac.2016.09.073. Epub 2016 Sep 22
Article CAS PubMed Google Scholar
Ferofontov A, Strulovich R, Marom M, Giladi M, Haitin Y (2018) Inherent flexibility of CLIC6 revealed by crystallographic and solution studies. Sci Rep 8(1):6882. https://doi.org/10.1038/s41598-018-25231-z. PubMed PMID: 29720717; PubMed Central PMCID: PMC5931990
Article CAS PubMed PubMed Central Google Scholar
Fisher E (1901) Z Physiol Chem 33:151
Article Google Scholar
Fisher E (1902) Chem Ber 35:2660
Article Google Scholar
Formaggio F, Crisma M, Bonora GM, Pantano M, Valle G, Toniolo C, Aubry A, Bayeul D, Kamphuis J (1995) (R)-isovaline homo-peptides adopt the left-handed 3(10)-helical structure. Pept Res 8(1):6–15. PubMed PMID: 7756755
CAS PubMed Google Scholar
Fung T, Asiri YI, Wall R, Schwarz SKW, Puil E, MacLeod BA (2017) Variations of isovaline structure related to activity in the formalin foot assay in mice. Amino Acids 49(7):1203–1213. https://doi.org/10.1007/s00726-017-2421-6. Epub 2017 Apr 21. PubMed PMID: 28432424
Article CAS PubMed Google Scholar
Gamlin CR, Yu WQ, Wong ROL, Hoon M (2018) Assembly and maintenance of GABAergic and Glycinergic circuits in the mammalian nervous system. Neural Dev 13(1):12. https://doi.org/10.1186/s13064-018-0109-6. Review. PubMed PMID: 29875009; PubMed Central PMCID: PMC5991458
Article CAS PubMed PubMed Central Google Scholar
Gernert KM, Surles MC, Labean TH, Richardson JS, Richardson DC (1995) Alacoil: a very tight, antiparallel coiled-coil of helices. Protein Science 4:2252–2260
Article CAS PubMed PubMed Central Google Scholar
Goh KL, Holmes DF (2017) Collagenous extracellular matrix biomaterials for tissue engineering: lessons from the common sea urchin tissue. Int J Mol Sci 18(5):901. https://doi.org/10.3390/ijms18050901
Article CAS PubMed Central Google Scholar
Görbitz CH, Karen P, Dušek M, Petrícek V (2016) An exceptional series of phase transitions in hydrophobic amino acids with linear side chains. IUCrJ 3(Pt 5):341–353. https://doi.org/10.1107/S2052252516010472
Article CAS PubMed PubMed Central Google Scholar
Gord JR, Hewett DM, Hernandez-Castillo AO, Blodgett KN, Rotondaro MC, Varuolo A, Kubasik MA, Zwier TS (2016) Conformation-specific spectroscopy of capped, gas-phase Aib oligomers: tests of the Aib residue as a 310-helix former. Phys Chem Chem Phys 18(36):25512–25527
Article CAS PubMed Google Scholar
Grauer AA, Cabrele C, Zabel M, König B (2009) Stable right- and left-handed peptide helices containing C(alpha)-tetrasubstituted alpha-amino acids. J Org Chem 74(10):3718–3726. doi: https://doi.org/10.1021/jo900222g. PubMed PMID: 19354242
Article CAS PubMed Google Scholar
Guerra ME, Fadel V, Maltarollo VG, Baldissera G, Honorio KM, Ruggiero JR, Dos Santos Cabrera MP (2017) MD simulations and multivariate studies for modeling the antileishmanial activity of peptides. Chem Biol Drug Des 2017 Mar 7. https://doi.org/10.1111/cbdd.12970. [Epub ahead of print]
Article CAS Google Scholar
Gunning PW, Hardeman EC, Lappalainen P, Mulvihill DP (2015) Tropomyosin - master regulator of actin filament function in the cytoskeleton. J Cell Sci 128(16):2965–2974. https://doi.org/10.1242/jcs.172502. Epub 2015 Aug 3
Article CAS PubMed Google Scholar
Harbury PB, Zhang T, Kim PS, Alber T (1993) A switch between two-, three-. and four-stranded coiled coils in GCN4 leucine zipper mutants. Science 262(5138):1401–1407
Article CAS PubMed Google Scholar
Harbury PB, Plecs JJ, Tidor B, Alber T, Kim PS (1998) High-resolution protein design with backbone freedom. Science 282(5393):1462–1467. PubMed PMID: 9822371
Article CAS PubMed Google Scholar
Harris NL, Presnell SR, Cohen FE (1994) Four helix bundle diversity in proteins. J Mol Biol 236:1356–1368
Article CAS PubMed Google Scholar
Harrop SJ, DeMaere MZ, Fairlie WD et al (2001) Crystal structure of a soluble form of the intracellular chloride ion channel CLIC1 (NCC27) at 1.4-A resolution. J Biol Chem 276:44993–45000
Article CAS PubMed Google Scholar
Harsini FM, Chebrolu S, Fuson KL, White MA, Rice AM, Sutton RB (2018) FerA is a membrane-associating four-helix bundle domain in the Ferlin family of membrane-fusion proteins. Sci Rep;8(1):10949. https://doi.org/10.1038/s41598-018-29184-1. PubMed PMID: 30026467; PubMed Central PMCID: PMC6053371.
Hodges RS, Sodek J, Smillie LB et al (1972) Amino-acid sequence of rabbit skeletal tropomyosin and its coiled-coil structure. Proc Natl Acad Sci 69:3800–3804
Article PubMed PubMed Central Google Scholar
Hollman AL, Tchounwou PB, Huang HC (2016) The Association between gene-environment interactions and diseases involving the human GST superfamily with SNP variants. Int J Environ Res Public Health 13(4):379. https://doi.org/10.3390/ijerph13040379. Review. PubMed PMID: 27043589; PubMed Central PMCID: PMC4847041
Article CAS PubMed PubMed Central Google Scholar
Holm PJ, Bhakat P, Jegerschold C, Gyobu N, Mitsuoka K, Fujiyoshi Y, Morgenstern R, Hebert H (2006) Structural basis for detoxification and oxidative stress protection in membranes. J Mol Biol 360:934–945
Article CAS PubMed Google Scholar
Holmes TC (2002) Novel peptide-based biomaterial scaffolds for tissue engineering. Trends Biotechnol 20(1):16–21. Review. PubMed PMID: 11742673
Article CAS PubMed Google Scholar
Holton A, Alber J (2004) Automated protein crystal structure determination using elves. Proc Natl Acad Sci 101:1537–1542
Article CAS PubMed PubMed Central Google Scholar
Hou Q, Bourgeas R, Pucci F, Rooman M (2018) Computational analysis of the amino acid interactions that promote or decrease protein solubility. Sci Rep 8(1):14661. https://doi.org/10.1038/s41598-018-32988-w. PubMed PMID: 30279585; PubMed Central PMCID: PMC6168528
Article CAS PubMed PubMed Central Google Scholar
Huber R, Romish J, Paques EP (1990) The crystal and molecular structure of human annexin V, an anticoagulant protein that binds to calcium and membranes. Embo J 9:3867–3874
Article CAS PubMed PubMed Central Google Scholar
Ida M, Sato A, Matsumoto I et al (2004) Human annexin V binds to sulfatide: contribution to regulation of blood coagulation. J Mol Biol 135:583–588
CAS Google Scholar
Ishitsuka R, Kojima K, Utsumi H et al (1998) Glycosaminoglycan Binding Properties of Annexin IV, V, and VI. J Biol Chem 273:9935–9941
Article CAS PubMed Google Scholar
Jaffe EK (2017) New protein structures provide an updated understanding of phenylketonuria. Mol Genet Metab 121(4):289–296. https://doi.org/10.1016/j.ymgme.2017.06.005. Epub 2017 Jun 15. Review. PubMed PMID: 28645531; PubMed Central PMCID: PMC5549558
Article CAS PubMed PubMed Central Google Scholar
Jeppesen MG, Ortiz P, Shepard W et al (2003) The Crystal Structure of the Glutathione S-Transferase-like Domain of Elongation Factor 1B from Saccharomyces cerevisiae. J Biol Chem 278:47190–47198
Article CAS PubMed Google Scholar
Jiang Q, Li K, Lu WJ, Li S, Chen X, Liu XJ, Yuan J, Ding Q, Lan F, Cai SQ (2018) Identification of small-molecule ion channel modulators in C. elegans channelopathy models. Nat Commun 9(1):3941. https://doi.org/10.1038/s41467-018-06514-5. PubMed PMID: 30258187; PubMed Central PMCID: PMC6158242
Article CAS PubMed PubMed Central Google Scholar
Juncosa JI, Takaya K, Le HV, Moschitto MJ, Weerawarna PM, Mascarenhas R, Liu D, Dewey SL, Silverman RB (2018) Design and Mechanism of (S)-3-Amino-4-(difluoromethylenyl)cyclopent-1-ene-1-carboxylic Acid, a Highly Potent ?-Aminobutyric Acid Aminotransferase Inactivator for the Treatment of Addiction. J Am Chem Soc 140(6):2151–2164. https://doi.org/10.1021/jacs.7b10965. Epub 2018 Jan 30. PubMed PMID: 29381352; PubMed Central PMCID: PMC5812813
Article CAS PubMed PubMed Central Google Scholar
Kadir M, Wang X, Zhu B, Liu J, Harland D, Popescu C (2017) The structure of the “amorphous” matrix of keratins. J Struct Biol 198(2):116–123. doi: 10.1016/j.jsb.2017.04.001. Epub 2017 Apr 5
Article CAS PubMed Google Scholar
Kantharaju RS, Aravinda S, Shamala N, Balaram P (2010) Helical conformations of hexapeptides containing N-terminus diproline segments. Biopolymers 94(3):360–370. https://doi.org/10.1002/bip.21395
Article CAS Google Scholar
Kapinos LE, Burkhard P, Herrmann H, Aebi U, Strelkov SV (2011) Simultaneous formation of right- and left-handed anti-parallel coiled-coil interfaces by a coil2 fragment of human lamin A. J Mol Biol 408(1):135–146. https://doi.org/10.1016/j.jmb.2011.02.037. Epub 2011 Feb 24. PubMed PMID: 21354179
Article CAS PubMed Google Scholar
Kasznel AJ, Zhang Y, Hai Y, Chenoweth DM (2017) Structural basis for aza-glycine stabilization of collagen. J Am Chem Soc 2017 Jul 19;139(28):9427–9430. https://doi.org/10.1021/jacs.7b03398. Epub 2017 Jul 6.
Article CAS PubMed Google Scholar
Kendrew JC (1959) Structure and function in myoglobin and other proteins. Fed Proc 18(2, Part 1):740–751. PubMed PMID: 136722
CAS PubMed Google Scholar
Khanapur M, Alvala M, Prabhakar M, Shiva Kumar K, Edwin RK, Sri Saranya PS, Patel RK, Bulusu G, Misra P, Pal M (2017) Mycobacterium tuberculosis chorismate mutase: A potential target for TB. Bioorg Med Chem 25(6):1725–1736. https://doi.org/10.1016/j.bmc.2017.02.001. Epub 2017 Feb 4. Review. PubMed PMID: 28202315
Article CAS PubMed Google Scholar
Kikuchi N, Fujiwara K, Ikeguchi M (2018) ß-strand twisting/bending in soluble and transmembrane ß-barrel structures. Proteins. https://doi.org/10.1002/prot.25576. [Epub ahead of print] PubMed PMID: 30019770
Article CAS Google Scholar
Kitaigorodsky AI (1973) Molecular crystals and molecules. Academic Press, New York
Google Scholar
Kohn WD, Mant CT, Hodges RS (1977) Helical protein assembly motifs. J Biol Chem 272:2583–2586
Article Google Scholar
Kollman JM, Pandi L, Sawaya MR, Riley M, Doolittle RF (2009) Crystal structure of human fibrinogen. Biochemistry 48(18):3877–3886. https://doi.org/10.1021/bi802205g
Article CAS PubMed Google Scholar
Konno K, Rangel M, Oliveira JS, Dos Santos Cabrera MP, Fontana R, Hirata IY, Hide I, Nakata Y, Mori K, Kawano M, Fuchino H, Sekita S, Neto JR (2017) Decoralin, a novel linear cationic alpha-helical peptide from the venom of the solitary eumenine wasp Oreumenes decoratus. Peptides 28(12):2320–2327. Epub 2007 Sep 29
Article CAS Google Scholar
Krzywda S, Brzozowski AM, Higashitsuji H, Fujita J, Welchman R, Dawson S, Mayer RJ, Wilkinson AJ (2004) The Crystal Structure of Gankyrin, an Oncoprotein Found in Complexes with Cyclin-dependent Kinase 4, a 19 S Proteasomal ATPase Regulator, and the Tumor Suppressors Rb and p53. J Biol Chem 279:1541–1545
Article CAS PubMed Google Scholar
Kuang Q, Purhonen P, Ålander J, Svensson R, Hoogland V, Winerdal J, Spahiu L, Ottosson-Wadlund A, Jegerschöld C, Morgenstern R, Hebert H (2017) Dead-end complex, lipid interactions and catalytic mechanism of microsomal glutathione transferase 1, an electron crystallography and mutagenesis investigation. Sci Rep 7(1):7897. https://doi.org/10.1038/s41598-017-07912-3. PubMed PMID: 28801553; PubMed Central PMCID: PMC5554250
Article CAS PubMed PubMed Central Google Scholar
Kurochkina N (2007) J Theor Biol 247:110–121
Article CAS PubMed Google Scholar
Kurochkina N (2008) J Theor Biol 255:188–198
Article CAS PubMed Google Scholar
Kurochkina N (2011) Common structural characteristics of fibrous and globular proteins. In: Haggerty LM (ed) Protein Structure. Nova Science Publishers, Inc, Hauppauge. https://www.springer.com/us/book/9783319200972
Kurochkina N, Choekyi T (2011) Helix-helix interfaces and ligand binding. J Theor Biol 283:92–102
Article CAS PubMed Google Scholar
Ladner JE, Parsons JF, Rife CL, Gilliland GL, Armstrong RN (2004) Parallel evolutionary pathways for glutathione transferases: structure and mechanism of the mitochondrial class kappa enzyme rGSTK1-1. Biochemistry 43(2):352–361. PubMed PMID: 14717589
Article CAS PubMed Google Scholar
Lance E, Arnich N, Maignien T, Biré R (2018) Occurrence of β-N-methylamino-l-alanine (BMAA) and Isomers in Aquatic Environments and Aquatic Food Sources for Humans. Toxins (Basel) 10(2):pii: E83. https://doi.org/10.3390/toxins10020083. Review.PubMed PMID: 29443939; PubMed Central PMCID: PMC5848184
Article CAS Google Scholar
Lasker MV, Gajjar MM, Nair SK (2005) Molecular Structure of the IL-1R-Associated Kinase-4 Death Domain and Its Implications for TLR signaling. J Immun 175:4175–4179
Article CAS PubMed Google Scholar
Lee C-H, Kim M-S, Chung BM, Leahy DJ, Coulombe PA (2012) Structural basis for heteromeric assembly and perinuclear organization of keratin filaments. Nat Struct Mol Biol 19(7). https://doi.org/10.1038/nsmb.2330
Article CAS Google Scholar
Lee B, Richards FM (1971) The interpretation of protein structures: estimation of static accessibility. J Mol Biol 55:379–400
Article CAS PubMed Google Scholar
Lee H, Song C, Hong YS, Kim MS, Cho HR, Kang T, Shin K, Choi SH, Hyeon T, Kim DH (2017) Wearable/disposable sweat-based glucose monitoring device with multistage transdermal drug delivery module. Sci Adv 3(3):e1601314. doi:10.1126/sciadv.1601314. eCollection 2017 Mar. PubMed PMID: 28345030; PubMed Central PMCID: PMC5342654
Article PubMed PubMed Central CAS Google Scholar
Lee LK, Stewart AG, Donohoe M, Bernal RA, Stock D (2010) The structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase. Nat Struct Mol Biol. 17(3):373–378. https://doi.org/10.1038/nsmb.1761. Epub 2010 Feb 21. PubMed PMID: 20173764; PubMed Central PMCID: PMC2912985
Article CAS PubMed PubMed Central Google Scholar
Leung K. (2010) (R)-3-[(18)F]Fluoro-2-methyl-2-N-(methylamino)propanoic acid. [updated 2010 Jul 29]. Molecular Imaging and Contrast Agent Database (MICAD) [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2004-2013. Available from http://www.ncbi.nlm.nih.gov/books/NBK45198/ PubMed PMID: 20662134.
Li Y, Zhou M, Hu Q, Bai XC, Huang W, Scheres SH, Shi Y (2017) Mechanistic insights into caspase-9 activation by the structure of the apoptosome holoenzyme. Proc Natl Acad Sci U S A 114(7):1542–1547. https://doi.org/10.1073/pnas.1620626114. Epub 2017 Jan 31. PubMed PMID: 28143931; PubMed Central PMCID: PMC5320974
Article CAS PubMed PubMed Central Google Scholar
Lin S-C, Lo Y-C, Wu H (2010) Helical assembly in the MyD88–IRAK4–IRAK2 complex in TLR/IL-1R signaling. Nature 465:885–890
Article CAS PubMed PubMed Central Google Scholar
Littler DR, Harrop SJ, Brown LJ et al (2008) Comparison of vertebrate and invertebrate CLIC proteins: the crystal structures of Caenorhabditis elegans EXC-4 and Drosophila melanogaster DmCLIC. Proteins 71:364–378
Article CAS PubMed Google Scholar
Liu J, Deng Y, Dey AK, Moore JP, Lu M (2009) Structure of the HIV-1 gp41membrane-proximal ectodomain region in a putative prefusion conformation. Biochemistry 48(13):2915–2923. https://doi.org/10.1021/bi802303b. PubMed PMID: 19226163; PubMed Central PMCID: PMC2765501
Article CAS PubMed Google Scholar
Liu J, Taylor DW, Krementsova EB, Trybus KM, Taylor KA (2006a) Three-dimensional structure of the myosin V inhibited state by cryoelectron tomography. Nature 442(7099):208–211. Epub 2006 Apr 16.
Article CAS PubMed Google Scholar
Liu J, Deng Y, Zheng Q, Cheng CS, Kallenbach NR, Lu M (2006b) A parallel coiled-coil tetramer with offset helices. Biochemistry 45(51):15224–15231. Epub 2006b Nov 29. PubMed PMID: 17176044
Article CAS PubMed Google Scholar
Lovejoy B, Choe S, Cascio D, McRorie DK, DeGrado WF, Eisenberg D (1993) Crystal structure of a synthetic triple-stranded alpha-helical bundle. Science 259:1288–1293
Article CAS PubMed Google Scholar
Lovejoy B, Le TC, Luthy R, Cascio D, O’Neil KT, DeGrado WF, Eisenberg D (1992) X-ray grade crystals of a designed a-helical coiled coil. Protein Sci 1:956–957
Article CAS PubMed PubMed Central Google Scholar
Malashkevich VN, Schneider BJ, McNally ML, Milhollen MA, Pang JX, Kim PS (1999) Core structure of the envelope glycoprotein GP2 from Ebola virus at 1.9-A resolution. Proc Natl Acad Sci U S A. 96(6):2662–2667. PubMed PMID: 10077567; PubMed Central PMCID: PMC15825
Article CAS PubMed PubMed Central Google Scholar
Martins DB, Vieira MR, Fadel V, Santana VAC, Guerra MER, Lima ML, Tempone AG, Dos Santos Cabrera MP (2017) Membrane targeting peptides toward antileishmanial activity: design, structural determination and mechanism of interaction. Biochim Biophys Acta pii: S0304-4165(17):30248–30249. https://doi.org/10.1016/j.bbagen.2017.08.003. [Epub ahead of print]
Article CAS Google Scholar
Masood R, Ullah K, Ali H, Ali I, Betzel C, Ullah A (2018) Spider’s venom phospholipases D: A structural review. Int J Biol Macromol 107(Pt A):1054–1065. https://doi.org/10.1016/j.ijbiomac.2017.09.081. Epub 2017 Sep 23. Review. PubMed PMID: 28951301
Article CAS PubMed Google Scholar
Medved L, Nieuwenhuizen W (2003) Molecular mechanisms of initiation of fibrinolysis by fibrin. Thromb Haemost. 2003 Mar;89(3):409–419.
Article PubMed Google Scholar
Moitra J, Szilak L, Krylov D, Vinson C (1997) Leucine is the most stabilizing aliphatic amino acid in the d position of a dimeric leucine zipper coiled coil. Biochemistry 36:12567–12573
Article CAS PubMed Google Scholar
Moll JR, Ruvinov SB, Pastan I, Vinson C (2001) Designed heterodimerizing leucine zippers with a ranger of pI’s and stabilities up to 10–15 M. Protein Sci 10:649–655
Article CAS PubMed PubMed Central Google Scholar
Mykhailiuk PK, Kubyshkin V, Bach T, Budisa N (2017) Peptidyl-prolyl model study: how does the electronic effect influence the amide bond Conformation? J Org Chem. https://doi.org/10.1021/acs.joc.7b00803. [Epub ahead of print]
Article CAS PubMed Google Scholar
Namba K, Stubbs G (1986) Structure of tobacco mosaic virus at 3.6 Angstroms resolution. Implications for assembly. Science 231:1401–1406
Article CAS PubMed Google Scholar
Namba K, Pattanayek R, Stubbs G (1989) Visualization of protein-nucleic acid interactions in a virus. Structure of intact tobacco mosaic virus at 2.9 Angstrom resolution by X-ray fiber diffraction. J Mol Biol 208:307–325
Article CAS PubMed Google Scholar
Navarro E, Fenude E, Celda B (2002) Solution structure of a D, L-alternating oligonorleucine as a model of double-stranded antiparallel beta-helix. Biopolymers 64(4):198–209
Article CAS PubMed Google Scholar
Navarro E, Fenude E, Celda (2004) Conformational and structural analysis of the equilibrium between single- and double-strand beta-helix of a D,L-alternating oligonorleucine. Biopolymers 73(2):229–241
Article CAS PubMed Google Scholar
Navarro E, Tejero R, Fenude E, Celda B (2001) Solution NMR structure of a D,L-alternating oligonorleucine as a model of beta-helix. Biopolymers 59(2):110–119
Article CAS PubMed Google Scholar
Newberry RW, Raines RT (2017) 4-Fluoroprolines: conformational analysis and effects on the stability and folding of peptides and proteins. Top Heterocycl Chem 48:1–25. https://doi.org/10.1007/7081_2015_196
Article CAS PubMed Google Scholar
Oshaben KM, Horne WS (2014) Tuning assembly size in Peptide-based supramolecular polymers by modulation of subunit association affinity. Biomacromolecules 15(4):1436–1442. https://doi.org/10.1021/bm5000423. Epub 2014 Mar 17
Article CAS PubMed Google Scholar
O’Shea EK, Klemm JD, Kim PS, Alber T (1991) Crystal structure of GCN4 leucine zipper, a two-stranded parallel coiled coil. Science 254:539
Article PubMed Google Scholar
Paliakasis CD, Kokkinidis M (1991) The stability of the four-α-helix bundle motif in proteins. Protein Eng 4:849
Article CAS PubMed Google Scholar
Park HH, Logette E, Raunser S, Cuenin S, Walz T, Tschopp J, Wu H (2007) Death domain assembly mechanism revealed by crystal structure of the oligomeric PIDDosome core complex. Cell 128:533–546
Article CAS PubMed PubMed Central Google Scholar
Parry DAD, Fraser RD, Squire JM (2008) Fifty years of coiled-coils and α-helical bundles: a close relationship between sequence and structure. J Struct Biol 163:258–269
Article CAS PubMed Google Scholar
Passon DM, Lee M, Rackham O, Stanley WA, Sadowska A, Filipovska A, Fox AH, Bond CS (2012) Structure of the heterodimer of human NONO and paraspeckle protein component 1 and analysis of its role in subnuclear body formation. Proc Natl Acad Sci USA 109(13):4846–4850. https://doi.org/10.1073/pnas.1120792109. Epub 2012 Mar 13. PubMed PMID: 22416126; PubMed Central PMCID: PMC3324020
Article CAS Google Scholar
Pauling L, Corey RB, Branson HR (1951) The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 37:205
Article CAS PubMed PubMed Central Google Scholar
Pechik I, Madrazo J, Mosesson MW, Hernandez I, Gilliland GL, Medved L (2004) Crystal structure of the complex between thrombin and the central “E” region of fibrin. Proc Natl Acad Sci USA 101(9):2718–2723. https://doi.org/10.1073/pnas.0303440101
Article CAS PubMed PubMed Central Google Scholar
Pielak RM, Schnell JR, Chou JJ (2009) Mechanism of drug inhibition and drug resistance of influenza A M2 channel. Proc Natl Acad Sci USA 106:7379–7384
Article CAS PubMed PubMed Central Google Scholar
Pitman KA, Borgland SL, MacLeod B, Puil E (2015) Isovaline does not activate GABA(B) receptor-coupled potassium currents in GABA(B) expressing AtT-20 cells and cultured rat hippocampal neurons. PLoS One 10(2):e0118497. https://doi.org/10.1371/journal.pone.0118497. eCollection 2015. PubMed PMID: 25706125; PubMed Central PMCID: PMC4337901
Article PubMed PubMed Central CAS Google Scholar
Plecs JJ, Harbury PB, Kim PS, Alber T (2004) Structural test of the parameterized-backbone method for protein design. J Mol Biol 342(1):289–297. PubMed PMID: 15313624.
Article CAS PubMed Google Scholar
Ponder JW, Richards FM (1987) Tertiary templates for proteins. J Mol Biol 193:775
Article CAS PubMed Google Scholar
Raghavender US, Kantharaju Aravinda S, Shamala N, Balaram P (2010) Hydrophobic peptide channels and encapsulated water wires. J Am Chem Soc 132(3):1075–1086. https://doi.org/10.1021/ja9083978
Article CAS PubMed Google Scholar
Ramachandran GN, Ramakrishnan C, Sasisekharan V (1963) Stereochemistry of polypeptide chain configurations. J Mol Biol 7:95–99
Article CAS PubMed Google Scholar
Reinert ZE, Lengyel GA, Horne WS (2013) Protein-like tertiary folding behavior from heterogeneous backbones.J Am Chem Soc 135(34):12528–12531. https://doi.org/10.1021/ja405422v. Epub 2013 Aug 15
Article CAS PubMed PubMed Central Google Scholar
Richards FM (1977) Areas, volumes, packing, and protein structure. Ann Rev Biophys Bioeng 6:151–176
Article CAS Google Scholar
Ruba A, Yang W (2016) O-GlcNAc-ylation in the nuclear pore complex. Cell Mol Bioeng 9(2):227–233. https://doi.org/10.1007/s12195-016-0440-0. Epub 2016 Apr 26. PubMed PMID: 28638491; PubMed Central PMCID: PMC5475274
Article CAS PubMed Google Scholar
Rubinson EH, Gowda AS, Spratt TE, Gold B, Eichman BF (2010) An unprecedented nucleic acid capture mechanism for excision of DNA damage. Nature 468:406–411
Article CAS PubMed PubMed Central Google Scholar
Le Rumeur E, Hubert JF, Winder SJ (2012) A new twist to coiled coil. FEBS Lett 586(17):2717–2722. https://doi.org/10.1016/j.febslet.2012.05.004. Epub 2012 May 11. Review. PubMed PMID: 22584055
Article CAS PubMed Google Scholar
Sakai H (2017) Overview of potential clinical applications of Hemoglobin Vesicles (HbV) as artificial red cells, evidenced by preclinical studies of the academic research consortium. J Funct Biomater 8(1):10. https://doi.org/10.3390/jfb8010010
Article CAS PubMed Central Google Scholar
Salnikov ES, Anantharamaiah GM, Bechinger B (2018) Supramolecular organization of apolipoprotein-A-I-derived peptides within disc-like arrangements. Biophys J 115(3):467–477. https://doi.org/10.1016/j.bpj.2018.06.026. Epub 2018 Jul 11. PubMed PMID: 30054032; PubMed Central PMCID: PMC6085177
Article CAS PubMed PubMed Central Google Scholar
Samatey FA, Imada K, Nagashima S, Vonderviszt F, Kumasaka T, Yamamoto M, Namba K (2001) Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling. Nature 410:331–337
Article CAS PubMed Google Scholar
Schrauber H, Eisenhaber F, Argos P (1993) Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins. J Mol Biol 230(2):592–612
Article CAS PubMed Google Scholar
Scott FL, Stec B, Pop C, Dobaczewska MK, Lee JJ, Monosov E, Robinson H, Salvesen GS, Schwarzenbacher R, Riedl SJ (2009) The Fas/FADD death domain complex structure unravels signaling by receptor clustering. Nature 457:1019–1022
Article CAS PubMed Google Scholar
Shao C, Zhang F, Kemp MM, Linhardt RJ, Waisman DM, Head JF, Seaton BA (2006) Crystallographic analysis of calcium-dependent heparin binding to Annexin A2. J Biol Chem 281:31689–31695
Article CAS PubMed Google Scholar
Sharma K, Dhillon A, Goyal A (2018) Insights into structure and reaction mechanism of β-mannanases. Curr Protein Pept Sci 19(1):34–47. https://doi.org/10.2174/1389203717666161013115724. Review. PubMed PMID: 27739373
Sheehan D, Meade G, Foley VM, Dowd CA (2001) Structure, function and evolution of glutathione transferases: implications for classification of non-mammalian members of an ancient enzyme superfamily. Biochem J 360:1–16
Article CAS PubMed PubMed Central Google Scholar
Sheriff S, Hendrickson WA, Smith JL (1987) Structure of myohemerythrin in the azidomet state at 1.7/1.3 angstroms resolution. J Mol Biol 197:273–296
Article CAS PubMed Google Scholar
Shoulders MD, Raines RT (2009) Collagen structure and stability. Annu Rev Biochem 78:929–958. https://doi.org/10.1146/annurev.biochem.77.032207.120833
Article CAS PubMed PubMed Central Google Scholar
Smith AI, Lew RA, Shrimpton CN, Evans RG, Abbenante G (2000) A novel stable inhibitor of endopeptidases EC 3.4.24.15 and 3.4.24.16 potentiates bradykinin-induced hypotension. Hypertension 35(2):626–630. PubMed PMID: 10679508
Article CAS PubMed Google Scholar
Song X, Zhang Y, Wang Y (2011) Antimicrobial peptides peptaibols from trichoderma—a review. Wei Sheng Wu Xue Bao 51(4):438–444. Review. Chinese. PubMed PMID: 21796977
Google Scholar
Spyroulias GA, Papazacharias S, Pairas G, Cordopatis P (2002) Monitoring the structural consequences of Phe12—>D-Phe and Leu15—>Aib substitution in human/rat corticotropin releasing hormone. Implications for design of CRH antagonists. Eur J Biochem 269(24):6009–6019. PubMed PMID: 12473096
Google Scholar
Squire JM, Paul DM, Morris EP (2017) Myosin and actin filaments in muscle: structures and interactions. Subcell Biochem 82:319–371. https://doi.org/10.1007/978-3-319-49674-0_11
Article CAS PubMed Google Scholar
Stanfield R, Cabezas E, Satterthwait A, Stura E, Profy A, Wilson I (1999) Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs. Structure 7(2):131–142. PubMed PMID: 10368281
Article CAS PubMed Google Scholar
Stetefeld J, Jenny M, Schulthess T, Landwehr R, Engel J, Kammerer RA (2000) Crystal structure of a naturally occurring parallel right-handed coiled coil tetramer. Nat Str Biol 7:772–776
Article CAS Google Scholar
Stevens J, Corper AL, Basler CF, Taubenberger JK, Palese P, Wilson IA (2004) Structure of the uncleaved human H1 hemagglutinin from the extinct 1918 influenza virus. Science 303:1866–1870
Article CAS PubMed Google Scholar
Strelkov SV, Herrmann H, Geisler N, Wedig T, Zimbelmann R, Aebi U, Burkhard P (2002) Conserved segments 1A and 2B of the intermediate filament dimer: their atomic structures and role in filament assembly. EMBO J 21(6):1255–1266. PubMed PMID: 11889032; PubMed Central PMCID: PMC125921
Article CAS PubMed PubMed Central Google Scholar
Subbalakshmi C, Basak P, Nagaraj R (2017) Self-assembly of t-Butyloxycarbonyl protected dipeptide methyl esters composed of leucine, isoleucine and valine into highly organized structures from alcohol and aqueous alcohol mixtures. Biopolymers https://doi.org/10.1002/bip.23033. [Epub ahead of print]
Article CAS Google Scholar
Sudha G, Singh P, Swapna LS, Srinivasan N (2015) Weak conservation of structural features in the interfaces of homologous transient protein–protein complexes. Protein Sci A Publ Protein Soc 24(11):1856–1873. https://doi.org/10.1002/pro.2792
Article CAS Google Scholar
Sutton RB, Fasshauer F, Jahn R, Brunger AT (1998) Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 Å resolution. Nature 395:347–353
Article CAS PubMed Google Scholar
Taylor KC, Buvoli M, Korkmaz EN, Buvoli A, Zheng Y, Heinze NT, Cui Q, Leinwand LA, Rayment I (2015) Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly. Proc Natl Acad Sci USA 112(29):E3806–E3815. https://doi.org/10.1073/pnas.1505813112. Epub 2015 Jul 6. PubMed PMID: 26150528; PubMed Central PMCID: PMC4517226
Article CAS Google Scholar
Touw DS, Nordman CE, Stuckey JA, Pecorano VL (2007) Identifying important structural characteristics of arsenic resistance proteins by using designed three-stranded coiled-coils. Proc Natl Acad Sci 104:11969–11974
Article CAS PubMed PubMed Central Google Scholar
Tseng T-S, Wang S-H, Chang T-W, Wei H-M, Wang Y-J, Tsai K-C et al (2016) Sarkosyl-induced helical structure of an antimicrobial peptide GW-Q6 plays an essential role in the binding of surface receptor OprI in Pseudomonas aeruginosa. PLoS ONE 11(10):e0164597. https://doi.org/10.1371/journal.pone.0164597
Article CAS PubMed PubMed Central Google Scholar
Vasudev PG, Ananda K, Chatterjee S, Aravinda S, Shamala N, Balaram P (2007) Hybrid peptide design. Hydrogen bonded conformations in peptides containing the stereochemically constrained gamma-amino acid residue, gabapentin. J Am Chem Soc 129(13):4039–4048. Epub 2007 Mar 10
Article CAS PubMed Google Scholar
Vasudev PG, Chatterjee S, Shamala N, Balaram P (2009) Gabapentin: a stereochemically constrained gamma amino acid residue in hybrid peptide design. Acc Chem Res 42(10):1628–1639. https://doi.org/10.1021/ar9001153. Review. PubMed PMID: 19572698
Article CAS PubMed Google Scholar
Venanzi M, Gatto E, Formaggio F, Toniolo C (2017) The importance of being Aib. Aggregation and self-assembly studies on conformationally constrained oligopeptides. J Pept Sci 23(2):104-116. https://doi.org/10.1002/psc.2956. Epub 2017 Jan 5. Review. PubMed PMID: 28054413
Article CAS PubMed Google Scholar
Very N, Vercoutter-Edouart AS, Lefebvre T, Hardivillé S, El Yazidi-Belkoura I (2018 Oct 9) Cross-Dysregulation of O-GlcNAcylation and PI3K/AKT/mTOR Axis in Human Chronic Diseases. Front Endocrinol (Lausanne). 9:602. doi: 10.3389/fendo.2018.00602. eCollection 2018. Review. PubMed PMID: 30356686; PubMed Central PMCID: PMC6189293
Google Scholar
Vitagliano L, Berisio R, Mazzarella L, Zagari A (2001) Structural bases of collagen stabilization induced by proline hydroxylation. Biopolymers 58(5):459–464
Article CAS PubMed Google Scholar
Vollmar M, Schlieper D, Winn M, Büchner C, Groth G (2009) Structure of the c14 rotor ring of the proton translocating chloroplast ATP synthase. J Biol Chem 284(27):18228–18235. https://doi.org/10.1074/jbc.M109.006916. Epub 2009 May 7. PubMed PMID: 19423706; PubMed Central PMCID: PMC2709358
Article CAS Google Scholar
Yadav MK, Redman JE, Leman LJ, Alvarez-Gutiérrez JM, Zhang Y, Stout CD, Ghadiri MR (2005) Structure-based engineering of internal cavities in coiled-coil peptides. Biochemistry 44(28):9723–9732. PubMed PMID: 16008357; PubMed Central PMCID: PMC1779508
Article CAS PubMed Google Scholar
Yang J, Ma YQ, Page RC, Misra S, Plow EF, Qin J (2009) Structure of an integrin alphaIIb beta3 transmembrane-cytoplasmic heterocomplex provides insight into integrin activation. Proc Natl Acad Sci USA 106(42):17729–17734. https://doi.org/10.1073/pnas.0909589106. Epub 2009 Oct 1. PubMed PMID: 19805198; PubMed Central PMCID: PMC2764936
Article CAS Google Scholar
Young SC (2018) A systematic review of antiamyloidogenic and metal-chelating peptoids: two structural motifs for the treatment of Alzheimer’s disease. Molecules 23(2). pii: E296. https://doi.org/10.3390/molecules23020296. Review. PubMed PMID: 29385058
Article PubMed Central CAS Google Scholar
Wada SI, Takesada A, Nagamura Y, Sogabe E, Ohki R, Hayashi J, Urata H (2017) Structure-activity relationship study of Aib-containing amphipathic helical peptide-cyclic RGD conjugates as carriers for siRNA delivery. Bioorg Med Chem Lett;27(24):5378–5381. https://doi.org/10.1016/j.bmcl.2017.11.018. Epub 2017 Nov 10. PubMed PMID: 29157863
Article CAS Google Scholar
Wagschal K, Lavigna P, Mant C, Hodges RS (1999) The role of position a in determining the stability and oligomerization state of a-helical coiled coils: 20 amino acid stability coefficients in the hydrophobic core of proteins. Protein Sci 8:2312–2329
Article CAS PubMed PubMed Central Google Scholar
Weber CH, Vincenz C (2001) The death domain superfamily: a tale of two interfaces? TIBS 26:475–481
CAS PubMed Google Scholar
Wells WW, Yang Y, Deits TL, Gan ZR (1993) Thioltransferases. Adv Enzymol Relat Areas Mol Biol;66:149–201. Review. PubMed PMID: 8430514
Woolfson DN (2010) Building fibrous biomaterials from -helical and collagen-like coiled-coil peptides. Biopolymers 94:118–127
Article CAS PubMed Google Scholar
Xie L, Yang S (2016) Brain globins in physiology and pathology. Med Gas Res 6(3):154–163. https://doi.org/10.4103/2045-9912.191361
Article CAS PubMed PubMed Central Google Scholar
Yeo HJ, Yokoyama T, Walkiewicz K, Kim Y, Grass S, Geme JW (2007) The structure of the Haemophilus influenzae HMW1 pro-piece reveals a structural domain essential for bacterial two-partner secretion. J Biol Chem 282(42):31076–31084. Epub 2007 Aug 14. PubMed PMID: 17699157
Article CAS Google Scholar
Yin Z, Shi K, Banerjee S, Pandey KK, Bera S, Grandgenett DP, Aihara H (2016) Crystal structure of the Rous sarcoma virus intasome. Nature 530(7590):362–366. https://doi.org/10.1038/nature16950. PubMed PMID: 26887497; PubMed Central PMCID: PMC4881392
Article CAS PubMed PubMed Central Google Scholar
Zhang Y (2017) Energetics, kinetics, and pathway of SNARE folding and assembly revealed by optical tweezers. Protein Sci;26(7):1252–1265. https://doi.org/10.1002/pro.3116. Epub 2017 Mar 8. Review. PubMed PMID: 28097727; PubMed Central PMCID: PMC5477538.
Article CAS PubMed PubMed Central Google Scholar
Zhao H, Qin X, Yang D, Jiang Y, Zheng W, Wang D, Tian Y, Liu Q, Xu N, Li Z (2017) The development of activatable lytic peptides for targeting triple negative breast cancer. Cell Death Discov 3:17037. https://doi.org/10.1038/cddiscovery.2017.37. eCollection 2017. PubMed PMID: 29263848; PubMed Central PMCID: PMC5629628
Zhou GP (2011) The structural determinations of the leucine zipper coiled-coil domains of the cGMP-dependent protein kinase I alpha and its interaction with the myosin binding subunit of the myosin light chains phosphase. Proteins Pept Lett 18:966–978
Article CAS Google Scholar

Download references

Author information

Authors and Affiliations

Department of Biophysics, School of Theoretical Modeling, Washington, DC, USA
Natalya Kurochkina

Authors

Natalya Kurochkina
View author publications
You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

Copyright information

About this chapter

Cite this chapter

Kurochkina, N. (2019). Proteins and Protein Structure. In: Protein Structure and Modeling. Springer, Singapore. https://doi.org/10.1007/978-981-13-6601-7_1

Download citation

DOI: https://doi.org/10.1007/978-981-13-6601-7_1
Published: 05 June 2019
Publisher Name: Springer, Singapore
Print ISBN: 978-981-13-6600-0
Online ISBN: 978-981-13-6601-7
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)

Publish with us

Policies and ethics