Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 2, 2011, Pages 603-608

  Johnson, Margaret E ^a   Hummer, Gerhard ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

Contact potentials; Hamming bound; Interactome; Protein protein binding; Proteome size

Indexed keywords

FUNGAL PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING COMPETITION; CALCULATION; CELL COMPARTMENTALIZATION; CELL SHAPE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION;

ANIMALS; CAENORHABDITIS ELEGANS; FUNGAL PROTEINS; GENOME; HUMANS; KINETICS; MODELS, STATISTICAL; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEOME; PROTEOMICS; TEMPERATURE; THERMODYNAMICS;

CAENORHABDITIS ELEGANS;

EID: 79551667508     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1010954108     Document Type: Article

References (34)

1. Clamp M, et al. (2007) Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci USA 104:19428-19433.
2. Claverie J-M (2001) What if there are only 30,000 human genes? Science 291:1255-1257.
3. Huang LL, Guan RJ, Pardee AB (1999) Evolution of transcriptional control from prokaryotic beginnings to eukaryotic complexities. Crit Rev Eukaryotic Gene Expression 9:175-182.
4. Bird AP (1995) Gene number, noise reduction and biological complexity. Trends Genet 11:94-100.
5. Nilsen TW, Graveley BR (2010) Expansion of the eukaryotic proteome by alternative splicing. Nature 463:457-463.
6. Rual JF, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437:1173-1178.
7. Yu H, et al. (2008) High-Quality binary protein interaction map of the yeast interactome network. Science 322:104-110.
8. Gavin A-C, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440:631-636.
9. Krogan NJ, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440:637-643.
10. Yook SH, Oltvai ZN, Barabasi A-L (2004) Functional and topological characterization of protein interaction networks. Proteomics 4:928-942. (Pubitemid 38445953)
11. Kim PM, Korbel JO, Gerstein MB (2007) Positive selection at the protein network periphery: Evaluation in terms of structural constrains and cellular context. Proc Natl Acad Sci USA 104:20274-20279.
12. Maslov S, Sneppen K (2002) Specificity and stability in topology of proteins networks. Science 296:910-913.
13. Gursoy A, Keskin O, Nussinov R (2008) Topological properties of protein interaction networks from a structural perspective. Biochem Soc Trans 36:1398-1403.
14. Kim PM, Lu LJ, Xia Y, Gerstein MB (2006) Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314:1938-1941.
15. Han JDJ, et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430:88-93.
16. Jeong H, Mason SP, Barabasi A-L, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411:41-42.
17. Chakrabarti O, Hegde RS (2009) Functional depletion of mahogunin by cytosolically exposed prion protein contributes to neurodegeneration. Cell 137:1136-1147.
18. Dobson CM (2003) Protein folding and misfolding. Nature 426:884-890.
19. Kosmrlj A, et al. (2010) Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection. Nature 465:350-354.
20. Zhang J, Maslov S, Shakhnovich EI (2008) Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size. Mol Syst Biol 4:210.
21. Deeds EJ, Ashenberg O, Gerardin J, Shakhnovich EI (2007) Robust protein-protein interactions in crowded cellular environments. Proc Natl Acad Sci USA 104:14952-14957.
22. Bussemaker HJ, Thirumalai D, Bhattacharjee JK (1997) Thermodynamic stability of folded proteins against mutations. Phys Rev Lett 79:3530-3533.
23. Jones S, Thornton JM (1996) Principles of protein-protein interactions. Proc Natl Acad Sci USA 93:13-20.
24. Kim YC, Tang C, Clore GM, Hummer G (2008) Replica exchange simulations of transient encounter complexes in protein-protein association. Proc Natl Acad Sci USA 105:12855-12860.
25. Kim YC, Hummer G (2008) Coarse-grained models for simulations of multiprotein complexes: Application to ubiquitin binding. J Mol Biol 375:1416-1433.
26. Miyazawa S, Jernigan RL (1996) Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 256:623-644.
27. Kosmrlj A, Jha AK, Huseby ES, Kardar M, Chakraborty AK (2008) How the thymus designs antigen-specific and self-tolerant T cell receptor sequences. Proc Natl Acad Sci USA 105:16671-16676.
28. Glaser F, Steinberg DM, Vakser IA, Ben-Tal N (2001) Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 43:89-102.
29. Skolnick J, Jaroszewski L, Kolinski A, Godzik A (1997) Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci 6:676-688.
30. Betancourt MR, Thirumalai D (1999) Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci 8:361-369.
31. Li H, Tang C, Wingreen NS (1997) Nature of driving force for proteins folding: A result from analyzing the statistical potential. Phys Rev Lett 79:765-768.
32. Jansen R, Gerstein M (2004) Analyzing protein function on a genomic scale: The importance of gold-standard positives and negatives for network prediction. Curr Opin Microbiol 7:535-545.
33. Frenkel D, Smit B (2002) Understanding Molecular Simulation (Academic, San Diego).
34. MacWilliams FJ, Sloane NJA (1977) The Theory of Error-Correcting Codes (Elsevier, Amsterdam).