Effect of mutation at the interface of Trp-repressor dimeric protein: A steered molecular dynamics simulation

European Biophysics Journal

Volumn 42, Issue 9, 2013, Pages 683-690

  Miño, German ^a   Baez, Mauricio ^a   Gutierrez, Gonzalo ^a  

^a UNIVERSITY OF CHILE   (Chile)

Author keywords

Dimeric proteins; Interface stability; Steered molecular dynamics

Indexed keywords

ASPARAGINE; REPRESSOR PROTEIN; SERINE; TRYPTOPHAN REPRESSOR; UNCLASSIFIED DRUG;

ARTICLE; ATOM; COMPUTER MODEL; ENERGY; GENE MUTATION; MOLECULAR DYNAMICS; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; QUANTUM MECHANICS; WILD TYPE;

BACTERIAL PROTEINS; MOLECULAR DYNAMICS SIMULATION; MUTANT PROTEINS; MUTATION; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, QUATERNARY; REPRESSOR PROTEINS;

EID: 84896689862     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-013-0918-9     Document Type: Article

References (23)

1. Alessandrini A, Facci P (2005) AFM: a versatile tool in biophysics. Meas Sci Technol 16:R65-R92
2. Balsera M, Stepaniants S, Izrailev S, Oono Y, Schulten K (1997) Reconstructing potential energy functions from simulated force-induced unbinding Processes. Biophys J 73:1281-1287
3. Bayas M, Schulten K, Leckband D (2004) Forced dissociation of the strand dimer interface between C-cadherin ectodomains. Mech Chem Biosyst 1:101-111
4. Best R, Paci E, Hummer G, Dudko O (2008) Pulling direction as a reaction coordinate for the mechanical unfolding of single. J Phys Chem B 112:5968-5976
5. Bogan AS, Thorn KS (1998) Anatomy of Hot spots in protein interfaces. J Mol Biol 1:1-9
6. Carra C, Saha J, Cucinotta FA (2012) Theoretical prediction of the binding free energy for mutants of replication protein A. J Mol Model 18:3035-3049
7. Deulfhard P, Hermans J, Leimkuhler B, Mark AE, Reich S, Skeel RD (eds) (1998) computational molecular dynamics: challenges, methods, ideas, vol 4. Lecture Notes in Computational Science and Engineering. Springer, Berlin
8. Gao Y, Wang R, Lai L (2004) Structure-based method for analyzing protein-protein interfaces. J Mol Model 10:44-54
9. Gutierrez G, Menendez-Proupin E, Loyola C, Peralta J, Davis S (2010) Computer simulation study of amorphous compounds: structural and vibrational properties. J Mater Sci 45:5124-5134
10. Humphrey W, Dalke A, Schulten K (1996) VMD - visual molecular dynamics. J Mol Graph 14:33-38
11. Kale L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shinozaki A, Varadarajan K, Schulten K (1999) NAMD2: greater scalability for parallel molecular dynamics. J Comp Phys 151:283-312
12. Kamisetty H, Ramanathan A, Bailey-Kellogg C, Langmead CJ (2011) Accounting for conformational entropy in predicting binding free energies of protein-protein interactions. Proteins 79:444-462
13. Li H, Oberhauser A, Fowler S, Clarke J, Fernandez J (2000) Atomic force microscopy reveals the mechanical design of a modular protein. PNAS 97:6527-6531
14. Lu H, Schulten K (1999) Steered molecular dynamics simulations of force-induced protein domain unfolding. Proteins Struct Funct Genet 35:453-463
15. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck J, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher IWE, Roux B, Schlenkrich M, Smith J, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616
16. Mann C, Matthews CR (1993) Structure and stability of an early folding intermediate of Escherichia coli trp aporepressor measured by far-uv stopped-flow circular-dichroism and 8-anilino-1-naphthalene sulfonate binding. Biochem 32:5282-5290
17. Royer CA, Mann CJ, Matthews CR (1993) Resolution of the fluorescence equilibrium unfolding profile of trp aporepressor using single tryptophan mutants. Protein Sci 2:1844-1852
18. Rumfeldt JAO, Galvagnion C, Vassall KA, Meiering EM (2008) Conformational stability and folding mechanisms of dimeric proteins. Prog Biophys Mol Biol 98:61-84
19. Shank E, Cecconi C, Dill J, Marqusee S, Bustamante C (2010) The folding cooperativity of a protein is controlled by its chain topology. Nature 465:637-640
20. Shao X, Hensley P, Matthews CR (1997) Construction and characterization of monomeric tryptophan repressor: a model for an early intermediate in the folding of a dimeric protein. Biochem 36:9941-9949
21. Shen M, Guan J, Xu L, Yu Y, He J, Jones GW, Song Y (2012) Steered molecular dynamics simulations on the binding of the appendant structure and helix-β2 in domain-swapped human cystation C dimer. J Biomol Struct Dyn 30:652-661
22. Voet D, Voet J (1995) Biochemistry, 2nd edn. Wiley, New York
23. Zhang RG, Joachimiak A, Lawson CL, Schevitz RW, Otwinowski Z, Sigler PB (1987) The crystal structure of trp aporepressor at 1.8 Å shows how binding tryptophan enhances DNA affinity. Nature 327:591-597