Abstract
Molecular recognition processes depend on the complementarity in shape and physical chemical properties of the surface of the molecules or macromolecules which interact. While generally accepted, this general statement has little heuristic value, for it does not quantify the role of hydrophobicity, H-bond forming capacity, electric charge distribution and other relevant properties. We present here an analysis of specific protein-protein complexes for which detailed atomic structures are available, and we show that shape complementarity is a valid criterion for a first selection of interacting surfaces on macromolecules.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Amit AG, Mariuzza RA, Phillips SEV, Poljak RJ (1986) Three-dimensional structure of an antigen-antibody complex at 2.8 Å resolution. Science 233:747–753
Bode W, Schwager P, Huber R (1978) The transition of bovine trypsinogen to a trypsin-like state upon strong ligand binding. J Mol Biol 118: 99–112
Bode W, Walter J, Huber R, Wenzel HJ, Tschesche H (1984) The refined 2.2-Å (0.22-nm) X-ray crystal structure of the ternary complex formed by bovine trypsinogen, valine-valine and the Arg15 analogue of bovine pancreatic trypsin inhibitor. Eur J Biochem 144: 185–190
Bode W, Papamokos E, Musil D, Seemueller U, Fritz H (1986) Refined 1.2 Å crystal structure of the complex formed between subtilisin Carlsberg and the inhibitor eglin c.Molecular structure of eglin and its detailed interaction with subtilisin. EMBO J 5: 813–818
Bode W, Wei AZ, Huber R, Meyer R, Travis J, Neumann S (1986) X-ray crystal structure of the complex of human leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor. EMBO J 5: 2453–2458
Bolognesi M, Gatti G, Menegatti E, Guarneri M, Marquait M, Papamokos E, Huber R (1982) Three-dimensional structure of the complex between pancreatic secretory trypsin inhibitor (kazal type) and trypsinogen at 1.8 Å resolution. J Mol Biol 162: 839–868
Chen Z, Bode W (1983) Refined 2.5 Å X-ray crystal structure of the complex formed by porcine kallikrein A and the ovine pancreatic trypsin inhibitor. J Mol Biol 164: 283–311
Chothia C (1975) Structural invariants in protein folding. Nature 254: 304–308
Chothia C, Janin J (1975) Principles in protein-protein recognition. Nature 256: 705–708
Colman PM, Laver WG, Varghese JN, Baker AT, Tulloch PA, Air GM, Webster RG (1987) Three-dimensional structure of a complex of antibody with influenza virus neuraminidase. Nature 326: 358–363
Finkelstein AV, Janin J (1989) The price of lost freedom: entropy of biomolecular complex formation. Protein Engineering 3:1–3
Fujinaga M, Sielecki AR, Read RJ, Ardelt W, Laskowski M, James MNG (1987) Crystal and molecular structures of the complex of α-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 Å resolution. J Mol Biol 195: 397–418
Huber R, Kukla D, Bode W, Schwager P, Bartels K, Deisenhofer J, Steigemann W (1974) Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. J Mol Biol 89: 73–101
Janin J, Wodak SJ (1985) Reaction pathway for the quaternay structure change in hemoglobin. Biopolymers 24: 509–526
Janin J, Miller S, Chothia C (1988) Surface, subunit interfaces and interior of oligomeric proteins. J Mol Biol 204: 155–164
Lee BK, Richards FM (1971) Interpretation of protein structures: Estimation of static accessibility. J Mol Biol 55:379–400
Levinthal C, Wodak SJ, Kahn P, Dadivanian A (1975) Hemoglobin interaction in sickle cell fibes I: Theoretical approaches to the molecular contacts. Proc Natl Acad Sci USA 72: 1330–1334
Levitt M (1976) A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol 104: 59–107
McPhalen CA, James MNG (1988) Structure comparison of two serine proteinase-protein inhibitor complexes: Eglin-C-Subtilisin Carlsberg and CI-2—Subtilisin Novo. Biochemistry 27: 6582–6598
Mariuzza RA, Phillips SEV, Poljak RJ (1987) The structural basis of antigen-antibody recognition. Ann Rev Biophys Biophys Chem 16: 139–159
Padlan EA, Silverton EW, Sheriffs, Cohen GH, Smith-Gill SJ, Davies D (1989) Structure of an antibody—antigen complex: Crystal structure of the HyHEL-10 Fab—lysozyme complex. Proc Nad Acad Sci USA 86: 5938–5942
Read RJ, Fujinaga M, Sielecki AR, James MNG (1983) Structure of the complex of Streptomyces griseus protease B and the third domain of the turkey ovomucoid inhibitor at 1.8-Å resolution. Biochemistry 22: 4420–4433
Rees DC, Lipscomb WN(1982) Refined crystal structure of the potato inhibitor complex of carboxypeptidase A at 2.5 Å resolution. J Mol Biol 160: 475–498
Sheriff S, Silverton EW, Padlan EA, Cohen GH, Smith-Gill SJ, Finzel BC, Davies D (1987) Three-dimensional structure of an antibidy-antigen complex. Proc Natl Acad Sci USA 84: 8075–8079
Varghese JN, Webster RG, Laver WG, Colman PM (1988) Structure of an escape mutant of glycoprotein N2 neuraminidase of influenza virus A/Tokyo/3/67 at 3 Å. J Mol Biol 200: 201–203
Wodak S J, Janin J (1978) Computer analysis of protein—protein interaction. J Mol Biol 124: 323–342
Wodak SJ, Janin J (1980) Analytical approximation to the accessible surface area of proteins. Proc Nad Acad Sci USA 77: 1736–1740
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1993 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Janin, J., Cherfils, J., Duquerroy, S. (1993). Principles of Protein — Protein Recognition in Protease-Inhibitor and Antigen-Antibody Complexes. In: Soumpasis, D.M., Jovin, T.M. (eds) Computation of Biomolecular Structures. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-77798-1_9
Download citation
DOI: https://doi.org/10.1007/978-3-642-77798-1_9
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-77800-1
Online ISBN: 978-3-642-77798-1
eBook Packages: Springer Book Archive