Importance of the CMAP correction to the CHARMM22 protein force field: Dynamics of hen lysozyme

Biophysical Journal

Volumn 90, Issue 4, 2006, Pages

  Buck, Matthias ^a   Bouguet Bonnet, Sabine ^a   Pastor, Richard W ^b   MacKerell Jr , Alexander D ^c  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b CENTER FOR BIOLOGICS EVALUATION AND RESEARCH   (United States)

^c UNIVERSITY OF MARYLAND SCHOOL OF PHARMACY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LYSOZYME; PROTEIN; HEN EGG LYSOZYME;

ARTICLE; CHARMM22 PROTEIN FORCE FIELD; CMAP CORRECTION; FORCE; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PARAMETER; PROTEIN STRUCTURE; SIMULATION; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; CHICKEN; COMPUTER SIMULATION; LETTER; PROTEIN CONFORMATION;

ANIMALS; CHICKENS; COMPUTER SIMULATION; MODELS, MOLECULAR; MURAMIDASE; PROTEIN CONFORMATION;

EID: 33645786604     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.078154     Document Type: Article

References (11)

1. MacKerell, A. D. 2004. Empirical force fields for biological macromolecules: overview and issues. J. Comput. Chem. 25:1584-1606.
2. Freedberg, D. I., R. M. Venable, A. Rossi, T. E. Bull, and R. W. Pastor. 2004. Discriminating the helical forms of peptides by NMR and molecular dynamics simulation. J. Am. Chem. Soc. 126:10478-10484.
3. Philippopoulos, M., A. M. Mandel, A. G. Palmer, and C. Lim. 1997. Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics. Proteins: 28:481-493.
4. Buck, M., and M. Karplus. 1999. Internal and overall peptide group motion in proteins. Molecular dynamics simulations for lysozyme compared with results from x-ray and NMR spectroscopy. J. Am. Chem. Soc. 121:9645-9658.
5. Soares, T. A., X. Daura, C. Oostenbrink, L. J. Smith, and W. F. van Gunsteren. 2004. Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme. J. Biomol. NMR. 30:407-422.
6. 15N relaxation measurements for mainchain and sidechain nuclei of hen egg-white lysozyme. Biochemistry. 34:4041-4055.
7. Cole, R., and J. P. Loria. 2003. FAST-ModelFree: a program for rapid automated analysis of solution NMR spin-relaxation data. J. Biomol. NMR. 26:203-213.
8. Case, D. A. 2002. Molecular dynamics and NMR spin relaxation in proteins. Acc. Chem. Res. 35:325-331.
9. Pfeiffer, S., D. Fushman, and D. Cowburn. 2001. Simulated and NMR derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for the βARK1 PH domain. J. Am. Chem. Soc. 123:3021-3036.
10. Chen, J., C. L. Brooks, and P. E. Wright. 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.
11. MacKerell, A. D., M. Feig, and C. L. Brooks. 2004. Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 25:1400-1415.