Karplus analyses

Karplus analyses of the NH-a-CH coupling constants which correlate with the characteristic torsion angle d, offer valuable information about the conformation of the peptide [17]. We compared the iJ values of the free peptides with those in the complex with their optimized binders. Usually signals became much sharper and the coupling constants markedly increased, approaching the calculated values (MacroModel). 

In a subsequent paper [4], partially motivated by some criticism on the limitation of the theory, Karplus analysed the effect of the substituent s electronegativity and the dependence upon the bond angle and lengths (the latter turned out to be of minor relevance). On the basis of valence-bond arguments [5], Karplus introduced is most celebrated general equation for the dependence of the vicinal J-couplings on the dihedral angle, in the form of a series of (real) Fourier coefficients truncated after the third term ... 

A. Dejaegere and M. Karplus, Analysis of coupUng schemes in free energy simulations A unified description of nonbonded contributions to solvation free energies. J. Phys. Chem. 100, 11148-11164 (1996). 

Boresch, S., Archontis, G., Karplus, M. Free energy simulations The meaning of the individual contributions from component analysis. Proteins Str. Funct. Genet., 20 (1994) 25-33... 

J. Gao, K. Kuczera, B. Tldor, and M. Karplus. Hidden thermodynamics of mutant proteins A molecular dynamics analysis. Science, 244 1069-1072, 1989. 

Bashford, D., Karplus, M. Multiple-site titration curves of proteins an analysis of exact and approximate methods for their calculation. J. Phys. Chem. 95 (1991) 9556-9561. 

Brooks, B. R., Janezic, D., Karplus, M. Harmonic Analysis of Large Systems I. Methodology. J. Comput. Chem. 16 (1995) 1522-1542 Janezic, D., Brooks, B. R. Harmonic Analysis of Large Systems II. Comparison of Different Protein Models. J. Comput. Chem. 16 (1995) 1543-1553 Janezic, D., Venable, R. M., Brooks, B. R. Harmonic Analysis of Large Systems. HI. Comparison with Molecular Dynamics. J. Comput. Chem. 16 (1995) 1554-1566... 

Chatfield C and A J Collins 1980. Introduction to Multivariate Analysis. London, Chapman Hall. Dobson C M, A Sali and M Karplus 1998. Protein Folding A Perspective from Theory and Experiment. 

Tiers N L, W D Carlson and M Karplus 1987 Analysis of Side-Chain Orientations in Homologous Proteins. Journal of Molecular Biology 196 175-198. 

Boresch S, G Archontis and M Karplus 1994. Free Energy Simulations The Meaning of the Indi-. id Contributions from a Component. Analysis. Proteins Structure, Function and Gau tics 20 25-33. 

Boresch S and M Karplus 1995. The Meaning of Component Analysis Decomposition of the Free Energy in Terms of Specific Interactions. Journal of Molecular Biology 254 801-807. 

Ha S, J Gao, B Tidor, J W Brady and M Karplus 1991. Solvent Effect on the Anomeric Equilibrium in d Glucose A Free Eneigy Simulation Analysis. Journal of the American Chemical Sod. ty 113 1553-1557... 

Yu H-A and M Karplus 1988. A Thermodynamic Analysis of Solvation. ]ouniul of Chemical Physics 89 2366-2379. 

Fiber, R. Karplus, M. Multiple conformational states of proteins a molecular dynamics analysis of myoglobin. Science 235 318-321, 1987. 

K Kuezera, JK Wiorkiewicz, M Karplus. MOLVIB Program for the Analysis of Molecular Vibrations, CHARMM, Harvard University, 1993. 

T Ichiye, M Karplus. Collective motions m proteins A covariance analysis of atomic fluctuations m molecular dynamics and normal mode simulations. Proteins Stiaict Eunct Genet 11 205-217, 1991. 

J Novotny, R Bruccoleri, M Karplus. An analysis of incorrectly folded protein models Implications for structural predictions. J Mol Biol 177 787-818, 1984. 

Analysis and prediction of side-chain conformation have long been predicated on statistical analysis of data from protein structures. Early rotamer libraries [91-93] ignored backbone conformation and instead gave the proportions of side-chain rotamers for each of the 18 amino acids with side-chain dihedral degrees of freedom. In recent years, it has become possible to take account of the effect of the backbone conformation on the distribution of side-chain rotamers [28,94-96]. McGregor et al. [94] and Schrauber et al. [97] produced rotamer libraries based on secondary structure. Dunbrack and Karplus [95] instead examined the variation in rotamer distributions as a function of the backbone dihedrals ( ) and V /, later providing conformational analysis to justify this choice [96]. Dunbrack and Cohen [28] extended the analysis of protein side-chain conformation by using Bayesian statistics to derive the full backbone-dependent rotamer libraries at all... 

MJ McGregor, SA Islam, MJE Sternberg. Analysis of the relationship between sidecham conformation and secondary stiaicture m globular proteins. J Mol Biol 198 295-310, 1987. RL Dunbrack Jr, M Karplus. Backbone-dependent rotamer library for proteins Application to sidecham prediction. J Mol Biol 230 543-571, 1993. 

RL Dunbrack Jr, M Karplus. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechams. Nature Struct Biol 1 334-340, 1994. 

Haasnoot, C. A. G., De Leeuw, F. A. A. M., De Leeuw, H. P. M., Altona, C. Relationship between proton-proton NMR coupling constants and substituent electronegativities. III. Conformational analysis of proline rings in solution using a generalized Karplus equation. Biopolymers 1981, 20,1211-1245. 

Garcia-Viloca M, Gao J, Karplus M, Truhlar DG (2004) How enzymes work Analysis by modem rate theory and computer simulations. Science (Washington, DC) 303(5655) 186-195... 

Boresch, S. Karplus, M., The role of bonded terms in free energy simulations I. Theoretical analysis, J. Phys. Chem. A 1999,103, 103-118... 

Paci, E. Karplus, M., Forced unfolding of fibronectin type 3 modules. An analysis by biased molecular dynamics simulations, J. Mol. Biol. 1999, 288, 441 —459... 

Brooks, B.R. lanezic, D. Karplus, M., Harmonic-analysis of large systems. 1. Methodology, 7. Comput. Chem. 1995,16, 1522-1542... 

Ma, J.P. Karplus, M., Ligand-induced conformational changes in ras p21 a normal mode and energy minimization analysis, 7. Mol. Biol. 1997, 274,114—131... 

Boresch, S. Karplus, M., The meaning of component analysis decomposition of the free energy in terms of specific interactions, J. Mol. Biol. 1995, 254, 801-807. 

Prevost, M. Wodak, S. J. Tidor, B. Karplus, M., Contribution of the hydrophobic effect to protein stability — analysis based on simulations of the Ile-96- Ala mutation in barnase, Proc. Natl Acad. Sci. USA 1991, 88,10880-10884. 

Garcia-Viloca, M. Gao, J. Karplus, M. Truhlar, D.G., How enzymes work analysis by modern reaction rate theory and computer simulations, Science 2004, 303, 186-195. 

Moulin E, Zoete V, Barluenga S, Karplus M, Winssinger N, Design, synthesis, and biological evaluation of HSP90 inhibitors based on conformational analysis of radicicol and its analogues, / Am Chem Soc 127 6999—7004, 2005. 

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