Comparison of Generalised Born/Surface Area with Periodic Boundary Simulations to Study Protein Unfolding

References

• Booth , DR , Sunde , M , Bellotti , V , Robinson , CV , Hutchinson , WL , Fraser , PE , Hawkins , PN , Dobson , CM , Radford , SE , Blake , CC and Pepys , MB . 1997 . Instability, unfolding and aggregation of human lysozyme variants underlying amyloid fibrillogenesis . Nature , 385 : 787
   PubMed Web of Science ®Google Scholar
• Dobson , CM . 2003 . Protein folding and disease: a view from the first Horizon Symposium . Nat. Rev. Drug Discov. , 2 : 154
   PubMed Web of Science ®Google Scholar
• Dumoulin , M , Last , AM , Desmyter , A , Decanniere , K , Canet , D , Larsson , G , Spencer , A , Archer , DB , Sasse , J , Muyldermans , S , Wyns , L , Redfield , C , Matagne , A , Robinson , CV and Dobson , CM . 2003 . A camelid antibody fragment inhibits the formation of amyloid fibrils by human lysozyme . Nature , 424 : 783
   PubMed Web of Science ®Google Scholar
• Hammarstrom , P , Wiseman , RL , Powers , ET and Kelly , JW . 2003 . Prevention of transthyretin amyloid disease by changing protein misfolding energetics . Science , 299 : 713
   PubMed Web of Science ®Google Scholar
• Dobson , C . 2002 . Protein misfolding and human disease . Sci. World J. , 2 : 132
   Google Scholar
• Neira , JL and Fersht , AR . 1999 . Exploring the folding funnel of a polypeptide chain by biophysical studies on protein fragments . J. Mol. Biol. , 285 : 1309
   PubMedGoogle Scholar
• Neira , JL , Itzhaki , LS , Ladurner , AG , Davis , B , de Prat Gay , G and Fersht , AR . 1997 . Following co-operative formation of secondary and tertiary structure in a single protein module . J. Mol. Biol. , 268 : 185
   PubMed Web of Science ®Google Scholar
• Fersht , AR and Daggett , V . 2002 . Protein folding and unfolding at atomic resolution . Cell , 108 : 573
   PubMed Web of Science ®Google Scholar
• Torshin , IY and Harrison , RW . 2003 . Protein folding: search for basic physical models . Sci. World J. , 3 : 623
   Google Scholar
• Ivankov , DN , Garbuzynskiy , SO , Alm , E , Plaxco , KW , Baker , D and Finkelstein , AV . 2003 . Contact order revisited: influence of protein size on the folding rate . Protein Sci. , 12 : 2057
   PubMed Web of Science ®Google Scholar
• Makarov , DE and Plaxco , KW . 2003 . The topomer search model: a simple, quantitative theory of two-state protein folding kinetics . Protein Sci. , 12 : 17
   PubMedGoogle Scholar
• Chen , YR and Clark , AC . 2003 . Equilibrium and kinetic folding of an alpha-helical Greek key protein domain: caspase recruitment domain (CARD) of RICK . Biochemistry , 42 : 6310
   PubMedGoogle Scholar
• Chiti , F , Stefani , M , Taddei , N , Ramponi , G and Dobson , CM . 2003 . Rationalization of the effects of mutations on peptide and protein aggregation rates . Nature , 424 : 805
   PubMed Web of Science ®Google Scholar
• Klein-Seetharaman , J , Oikawa , M , Grimshaw , SB , Wirmer , J , Duchardt , E , Ueda , T , Imoto , T , Smith , LJ , Dobson , CM and Schwalbe , H . 2002 . Long-range interactions within a nonnative protein . Science , 295 : 1719
   PubMed Web of Science ®Google Scholar
• Jaenicke , R and Slingsby , C . 2001 . Lens crystallins and their microbial homologs: structure, stability, and function . Crit. Rev. Biochem. Mol. Biol. , 36 : 435
   PubMed Web of Science ®Google Scholar
• Benedek , GB . 1997 . Cataract as a protein condensation disease: the Proctor Lecture . Investig. Ophthalmol. Vis. Sci. , 38 : 1911
   PubMed Web of Science ®Google Scholar
• Doyle , SM , Anderson , E , Zhu , D , Braswell , EH and Teschke , CM . 2003 . Rapid unfolding of a domain populates an aggregation-prone intermediate that can be recognized by GroEL . J. Mol. Biol. , 332 : 937
   PubMedGoogle Scholar
• Doruker , P , Atilgan , AR and Bahar , I . 2000 . Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor . Proteins , 40 : 512
   PubMed Web of Science ®Google Scholar
• Zhou , R . 2003 . Free energy landscape of protein folding in water: explicit vs. implicit solvent . Proteins , 53 : 148
   PubMed Web of Science ®Google Scholar
• Ferrara , P , Apostolakis , J and Caflisch , A . 2002 . Evaluation of a fast implicit solvent model for molecular dynamics simulations . Proteins , 46 : 24
   PubMed Web of Science ®Google Scholar
• Paci , E , Smith , LJ , Dobson , CM and Karplus , M . 2001 . Exploration of partially unfolded states of human alpha-lactalbumin by molecular dynamics simulation . J. Mol. Biol. , 306 : 329
   PubMedGoogle Scholar
• Li , A and Daggett , V . 1998 . Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate . J. Mol. Biol. , 275 : 677
   PubMed Web of Science ®Google Scholar
• Takei , J , Chu , RA and Bai , Y . 2000 . Absence of stable  intermediates on the folding pathway of barnase . Proc. Natl Acad. Sci. USA , 97 : 10796
   PubMed Web of Science ®Google Scholar
• Fersht , AR . 2000 . A kinetically significant intermediate in the folding of barnase . Proc. Natl Acad. Sci. USA , 97 : 14121
   PubMed Web of Science ®Google Scholar
• Arcus , VL , Vuilleumier , S , Freund , SM , Bycroft , M and Fersht , AR . 1995 . A comparison of the pH, urea, and temperature-denatured states of barnase by heteronuclear NMR: implications for the initiation of protein folding . J. Mol. Biol. , 254 : 305
   PubMed Web of Science ®Google Scholar
• Dalby , PA , Clarke , J , Johnson , CM and Fersht , AR . 1998 . Folding intermediates of wild-type and mutants of barnase. II. Correlation of changes in equilibrium amide exchange kinetics with the population of the folding intermediate . J. Mol. Biol. , 276 : 647
   PubMedGoogle Scholar
• Killick , TR , Freund , SM and Fersht , AR . 1998 . Real-time NMR studies on folding of mutants of barnase and chymotrypsin inhibitor 2 . FEBS Lett. , 423 : 110
   PubMedGoogle Scholar
• Fersht , AR , Matouschek , A and Serrano , L . 1992 . The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding . J. Mol. Biol. , 224 : 771
   PubMed Web of Science ®Google Scholar
• Matouschek , A , Serrano , L and Fersht , AR . 1992 . The folding of an enzyme. IV. Structure of an intermediate in the refolding of barnase analysed by a protein engineering procedure . J. Mol. Biol. , 224 : 819
   PubMedGoogle Scholar
• Bond , CJ , Wong , KB , Clarke , J , Fersht , AR and Daggett , V . 1997 . Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway . Proc. Natl Acad. Sci. USA , 94 : 13409
   PubMed Web of Science ®Google Scholar
• Wang , T and Wade , RC . 2003 . Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation . Proteins , 50 : 158
   PubMed Web of Science ®Google Scholar
• Perlman , DA , Case , DA , Caldwell , JW , Ross , WS , Cheatham , TE III , DeBolt , S , Ferguson , D , Seibel , G and Kollman , PA . 1995 . amber . Comp. Phys. Commun. , 91 : 1
   Google Scholar
• Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham, T.E., III, Wang, J., Ross, W.S., Simmerling, C.L., Darden, T.A., Merz, K.M., Stanton, R.V., Cheng, A.L., Vincent, J.J., Crowley, M., Tsui, V., Gohlke, H., Radmer, R.J., Duan, Y., Pitera, J., Massova, I., Seibel, G.L., Singh, U.C., Weiner, P.K. and Kollman, P.A. (2002) “amber
   Google Scholar
• Tsui , V and Case , DA . 2000 . Theory and applications of the generalized Born solvation model in macromolecular simulations . Biopolymers , 56 : 275
   PubMed Web of Science ®Google Scholar
• Bashford , D and Case , DA . 2000 . Generalized born models of macromolecular solvation effects . Annu. Rev. Phys. Chem. , 51 : 129
   PubMed Web of Science ®Google Scholar
• Moraitakis , G , Purkiss , AG and Goodfellow , JM . 2003 . Simulated dynamics and biological macromolecules . Rep. Prog. Phys. , 66 : 383
   Google Scholar
• Frishman , D and Argos , P . 1995 . Knowledge-based protein secondary structure assignment . Proteins , 23 : 566
   PubMed Web of Science ®Google Scholar
• Hubbard, S.J. and Thornton, J.M. (1993) “naccesswww.http://wolf.bms.umist.ac.uk/naccess/].
   Google Scholar
• Purkiss, A.G. (2003) “contaxwww http://people.cryst.bbk.ac.uk/(bpurk01/contax/index.html].
   Google Scholar
• Koradi , R , Billeter , M and Wuthrich , K . 1996 . molmol . J. Mol. Graph. , 14 : 51
   PubMedGoogle Scholar
• Purkiss , A , Slingsby , C and Goodfellow , JM . 2000 . Simulation of the highly stable  protein: bovine gammaB-crystallin at room and high temperature . Protein Pept. Lett. , 7 : 211
   Google Scholar