The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins (original) (raw)
Barfield M (2002) Structural dependencies of interresidue scalar coupling (h3)J(NC), and donor H-1 chemical shifts in the hydrogen bonding regions of proteins. J Am Chem Soc 124:4158–4168 Article Google Scholar
Bax A (2003) Weak alignment offers new NMR opportunities to study protein structure and dynamics. Prot Sci 12:1–16 Article Google Scholar
Beglov D, Roux B (1994) Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations. J Chem Phys 100:9050–9063 ArticleADS Google Scholar
Best RB, Vendruscolo M (2004) Determination of protein structures consistent with NMR order parameters. J Am Chem Soc 126:8090–8091 Article Google Scholar
Bonvin AMJJ, Boelens R, Kaptein R (1994) Time- and ensemble-averaged direct NOE restraints. J Biomol NMR 4:143–149 Article Google Scholar
Bonvin AMJJ, Brunger AT (1995) Conformational variability of solution nuclearmagnetic-resonance structures. J Mol Biol 250:80–93 Article Google Scholar
Bonvin AMJJ, Brünger AT (1996) Do NOE distances contain enough information to assess the relative populations of multi-conformer structures? J Biomol NMR 7:72–76 Article Google Scholar
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: A program for macromolecular energy, minimization and dynamics calculations. J Comp Chem 4:187–217 Article Google Scholar
Brünger A (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355:472–475 ArticleADS Google Scholar
Brünger A, Adams P, Clore G, DeLano W, Gros P, Grosse-Kunstleve R, Jiang J, Kuszewski J, Nilges M, Pannu N, Read R, Rice L, Simonson T, Warren G (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Cryst D 54:905–921 Article Google Scholar
Brünger A, Clore GM, Gronenborn A, Saffrich R, Nilges M (1993) Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation. Science 261:328–331 ArticleADS Google Scholar
Brünger AT, Clore GM, Gronenborn AM, Karplus M (1986) Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: Application to crambin. Proc Natl Acad Sci USA 83:3801–3805 ArticleADS Google Scholar
Bürgi R, Pitera J, van Gunsteren WF (2001) Assessing the effect of conformational averaging on the measured values of observables. J Biomol NMR 19:305–320 Article Google Scholar
Carlson HA (2002) Protein flexibility and drug design: How to hit a moving target. Curr Opin Cell Biol 6:447–452 Google Scholar
Carlson HA, McCammon JA (2000) Accomodating protein flexibility in computational drug design. Mol Pharmacol 57:213–218 Google Scholar
Chang S, Tjandra N (2005) Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR relaxation. J Magn Res 174:43–53 ArticleADS Google Scholar
Chen J, Brooks CL, Wright PE (2004) Model-free analysis of protein dynamics: Assessment of accuracy and model selection protocols based on molecular dynamics simulation. J Biomol NMR 29:243–257 Article Google Scholar
Chou J, Case D, Bax A (2003) Insights into the mobility of methyl-bearing side chains in proteins from 3 J CC and 3JCN couplings. J Am Chem Soc 125:8959–8966 Article Google Scholar
Clore GM, Schwieters CD (2004) How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation? J Am Chem Soc 126:2923–2938 Article Google Scholar
Clore GM, Schwieters CD (2004) Amplitudes of protein backbone dynamics and correlated motions in a small alpha/beta protein: Correspondence of dipolar coupling and heteronuclear relaxation measurements. Biochemistry 43:10678–10691 Article Google Scholar
Clore GM, Schwieters CD (2006) Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small alpha/beta protein: A unified picture of high probability, fast atomic motions in proteins. J Mol Biol 355:879–886 Article Google Scholar
Cordier F, Grzesiek S (1999) Direct observation of hydrogen bonds in proteins by interresidue 3hJNC’ scalar couplings. J Am Chem Soc 117:5179–5197 Google Scholar
Cordier F, Grzesiek S (2002) Temperature-dependence of protein hydrogen bond properties as studied by high-resolution NMR. J Mol Biol 317:739–752 Article Google Scholar
Cornilescu G, Marquardt JL, Ottiger M, Bax A (1998) Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J Am Chem Soc 120:6836–6837 Article Google Scholar
de Alba E, Tjandra N (2002) NMR dipolar couplings for the structure determination of biopolymers in solution. Prog Nucl Mag Res Spec 40:175–197 Article Google Scholar
Fennen J, Torda AE, van Gunsteren WF (1995) Structure refinement with molecular-dynamics and a boltzmann-weighted ensemble. J Biomol NMR 6:163–170 Article Google Scholar
Grunberg R, Leckner J, Nilges M (2004) Complementarity of structure ensembles in protein–protein binding. Science 12:2125–2136 Google Scholar
Grzesiek S, Cordier F, Jaravine V, Barfield M (2004) Insights into biomolecular hydrogen bonds from hydrogen bond scalar couplings. Prog Nucl Mag Res Spec 45:275–300 Article Google Scholar
Henry ER, Szabo A (1985) Influence of vibrational motion on solid state line shapes and NMR relaxation. J Chem Phys 82:4753–4761 ArticleADS Google Scholar
Hess B, Scheek RM (2003) Orientation restraints in molecular dynamics simulations using time and ensemble averaging. J Magn Res 164:19–27 ArticleADS Google Scholar
Ichiye T, Karplus M (1988) Anisotropy and anharmonicity of atomic fluctuations in proteins: Implications for x-ray analysis. Biochemistry 27:3487–3497 Article Google Scholar
Jorgensen WJ, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935 ArticleADS Google Scholar
Karplus M (1963) Vicinal proton coupling in nuclear magnetic resonance. J Am Chem Soc 85:2870–2871 Article Google Scholar
Karplus M, Kuriyan J (2005) Molecular dynamics and protein function. Proc Natl Acad Sci USA 102:6679–6685 ArticleADS Google Scholar
Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Biol 9:646–652 Article Google Scholar
Karplus M, Petsko G (1990) Molecular dynamics simulations in biology. Nature 347:631–639 ArticleADS Google Scholar
Kemmink J, Scheek RM (1995) Dynamic modeling of a helical peptide in solution using NMR data—multiple conformations and multi-spin effects. J Biomol NMR 6:33–40 Article Google Scholar
Kuriyan J, Petsko G, Levy RM, Karplus M (1986) Effect of anisotropy and anharmonicity on protein crystallographic refinement: An evaluation by molecular dynamics. J Mol Biol 190:227–254 Article Google Scholar
Kuszewski J, Gronenborn AM, Clore GM (1999) Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration. J Am Chem Soc 121:2337–2338 Article Google Scholar
Lee AL, Flynn PF, Wand AJ (1999) Comparison of 2 h and 13c NMR: relaxation techniques for the study of protein methyl group dynamics in solution. J Am Chem Soc 121:2891–2902 Article Google Scholar
Lindorff-Larsen K, Best RB, DePristo MA, Dobson CM, Vendruscolo M (2005) Simultaneous determination of protein structure and dynamics. Nature 433:128–132 ArticleADS Google Scholar
Lipari G, Szabo A (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J Am Chem Soc 104:4546–4559 Article Google Scholar
Ma B, Nussinov R (2002) Stabilities and conformations of Alzheimer’s β-amyloid peptide oligomers (Aβ16–22, Aβ16–35, Aβ10–35): Sequence effects. Proc Natl Acad Sci USA 99:14126–14131 ArticleADS Google Scholar
MacKerell Jr AD, Bashford D, Bellot M, Dunbrack RLJ, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Ha S, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich B, Smith JC, Stote RH, Straub J, Wiórkiewicz-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 Article Google Scholar
Mezard M, Parisi G, Virasoro M (1987) Spin glass theory and beyond. Singapore, World Scientific Publishing MATH Google Scholar
Nederveen A, Bonvin AMJJ (2005) NMR relaxation and internal dynamics of ubiquitin from a 0.2 microsecond MD simulation. J Chem Theor Comp 1:363–374 Article Google Scholar
Neuhaus D, Williamson MP (2000) The nuclear Overhauser effect in structural and conformational analysis. New York, Wiley Google Scholar
Paci E, Karplus M (1999) Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations. J Mol Biol 288:441–459 Article Google Scholar
Palmer AG (2004) NMR characterization of the dynamics of biomacromolecules. Chem Rev 104:3623–3640 Article Google Scholar
Perryman AL, Lin J, McCammon JA (2004) HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: Possible contributions to drug resistance and a potential new target site for drugs. Prot Sci 13:1108–1123 Article Google Scholar
Rieping W, Habeck M, Nilges M (2005) Inferential structure determination. Science 309:303–306 ArticleADS Google Scholar
Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion if a system with constraints: molecular dynamics of _n_-alkanes. J Comput Phys 23:327–341 Article Google Scholar
Schneider TR, Brünger AT, Nilges M (1999) Influence of internal dynamics on accuracy of protein NMR structures: Derivation of realistic model distance data from a long molecular dynamics trajectory. J Mol Biol 285:727–740 Article Google Scholar
Schwieters CD, Kuszewski JJ, Clore GM (2005) Using Xplor-NIH for NMR molecular structure determination. Prog Nucl Mag Res Spec 48:47–62 Article Google Scholar
Scott WRP, Hunenberger PH, Tironi IG, Mark AE, Billeter SR, Fennen J, Torda AE, Huber T, Kruger P, van Gunsteren WF (1999) The GROMOS biomolecular simulation program package. J Phys Chem A 103:3596–3607 Article Google Scholar
Scott WRP, Mark AE, van Gunsteren WF (1998) On using time-averaging restraints in molecular dynamics simulation. J Biomol NMR 12:501–508 Article Google Scholar
Spronk CAEM, Nabuurs SB, Krieger E, Vriend G, Vuister GW (2004) Validation of protein structures derived by NMR spectroscopy. Prog Nucl Mag Res Spec 45:315–337 Article Google Scholar
Teague SJ (2003) Implications of protein flexibility for drug discovery. Nat Rev Drug Discov 2:527–541 Article Google Scholar
Tjandra N, Feller SE, Pastor RW, Bax A (1995) Rotational diffusion anisotropy of human ubiquitin from n-15 NMR relaxation. J Am Chem Soc 117:12562–12566 Article Google Scholar
Torda AE, Scheek RM, van Gunsteren WF (1989) Time averaged distance restraints in molecular dynamics simulations. Chem Phys Lett 157:289–294 ArticleADS Google Scholar
Torda AE, Scheek RM, van Gunsteren WF (1990) Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat. J Mol Biol 214:223–235 Article Google Scholar
Vendruscolo M, Dobson CM (2005) Towards complete descriptions of the free-energy landscapes of proteins. Phil Trans R Soc A 363:433–450 ArticleADS Google Scholar
Vendruscolo M, Paci E (2003) Protein folding: Bringing theory and experiment closer together. Curr Opin Struct Biol 13:82–87 Article Google Scholar
Vijay-Kumar S, Bugg CE, Cook WJ (1987) Structure of ubiquitin refined at 1.8 A resolution. J Mol Biol 194:531–544 Article Google Scholar
Wand AJ (2001) Dynamic activation of protein function: A view emerging from NMR spectroscopy. Nat. Struct Biol 8:926–931 Article Google Scholar
Wang T, Cai S, Zuiderweg ERP (2003) Temperature dependence of anisotropic protein backbone dynamics. J Am Chem Soc 125:8639–8643 Article Google Scholar
Wong CF, McCammon JA (2003) Protein flexibility and computer-aided drug design. Annu Rev Pharmacol Toxicol. 43:31–45 Article Google Scholar
Wüthrich K (1986) NMR of proteins and nucleic acids. New York, Wiley Google Scholar
Zagrovic B, van Gunsteren WF (2006) Comparing atomistic simulation data with the NMR experiment: How much can NOEs actually tell us?. Proteins 63:210–218 Article Google Scholar
Zweckstetter M, Bax A (2000) Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR. J Am Chem Soc 122:3791–3792 Article Google Scholar