CO escape from myoglobin with metadynamics simulations

Proteins: Structure, Function and Genetics

Volumn 71, Issue 3, 2008, Pages 1231-1236

  Ceccarelli, Matteo ^a,c   Anedda, Roberto ^a   Casu, Mariano ^a   Ruggerone, Paolo ^a,b  

^a UNIVERSITY OF CAGLIARI   (Italy)

^b DEMOCRITOS NATIONAL SIMULATION CENTER   (Italy)

^c Cittadella Univ di Monserrato   (Italy)

Author keywords

Free energy; Ligand escape; Metadynamics; Molecular dynamics

Indexed keywords

CARBON MONOXIDE; MYOGLOBIN;

ALGORITHM; ARTICLE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS;

ALGORITHMS; ANIMALS; CARBON MONOXIDE; COMPUTER SIMULATION; ELECTROSTATICS; MODELS, MOLECULAR; MYOGLOBIN; PROTEIN STRUCTURE, SECONDARY; WHALES;

EID: 42449132544     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21817     Document Type: Article

References (32)

1. Frauenfelder H, McMahon BH, Austin RH, Chu K, Groves JT. The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin. Proc Natl Acad Sci USA 2001;98:2370-2374.
2. Brunori M, Bourgeois D, Vallone B. The structural dynamics of myoglobin. J Struct Biol 2004;147:223-234.
3. Tilton RF, Kuntz ID, Jr, Petzko GA. Cavities in proteins: structure of a metmyoglobin-xenon complex solved to 1.9 Å. Biochem 1984;23:2849-2857.
4. Schoenborn BP, Watson HC, Kendrew JC. Binding of xenon to sperm whale myoglobin. Nature 1965;207:28-30.
5. Srajer V, Ren Z, Teng T-Y, Schmidt M, Ursby T, Bourgeois D, Pradervand C, Schildkamp W, Wulff M, Moffat K. Protein conformational relaxation and ligand migration in myoglobin: a nanosecond to millisecond molecular movie from time-resolved Laue X-ray diffraction. Biochem 2001;40:13802-13815.
6. Hummer G, Schotte F, Anfinrud PA. Unveiling functional protein motions with picosecond X-ray crystallography and molecular dynamics simulations. Proc Natl Acad Sci USA 2004;101:15330-15334.
7. Brunori M, Vallone B, Cutruzolla F, Travaglino-Allocatelli C, Berendzen J, Chu K, Sweet RM, Schlichting I. The role of cavities in protein dynamics: crystal structure of a photolytic intermediate of a mutant myoglobin. Proc Natl Acad Sci USA 2000;97:2058-2063.
8. Nienhaus K, Lamb DC, Deng P, Nienhaus GU. The effect of ligand dynamics on heme electronic transition band III in myoglobin. Biophys J 2002;82:1059-1067.
9. Scott EE, Gibson QH, Olson JS. Mapping the pathways for O2 entry into and exit from myoglobin. J Biol Chem 2001;276:5177-5188.
10. Nienhaus K, Deng P, Kriegl JM, Nienhaus GU. Structural dynamics of myoglobin: effect of internal cavities on ligand migration and binding. Biochem 2003;42:9647-9658.
11. Tetreau C, Blouquit Y, Novikov E, Quiniou E, Lavalette D. Competition with xenon elicits ligand migration and escape pathways in myoglobin. Biophys J 2004;86:435-447.
12. Perutz MF, Matthews FS. An X-ray study of azide methaemoglobin. J Mol Biol 1966;21:199-202.
13. Case DA, Karplus M. Dynamics of ligand binding to heme proteins. J Mol Biol 1979;132:343-368.
14. Elber R, Karplus M. Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin. J Am Chem Soc 1990;112:9161-9175.
15. Vitkup D, Petsko GA, Karplus M. A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin. Nat Struct Biol 1997;4:202-208.
16. Nutt DR, Meuwly M. CO migration in native and mutant myoglobin: atomistic simulations for the understanding of protein function. Proc Natl Acad Sci USA 2004;101:5998-6002.
17. Bossa C, Anselmi M, Roccatano D, Amadei A, Vallone B, Brunori M, Di Nola A. Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin. Biophys J 2004;86:3855-3862.
18. 2, CO, NO, and Xe inside myoglobin. Biophys J 2006;91:1844-1857.
19. Laio A, Parrinello M. Escaping free energy minima. Proc Natl Acad Sci USA 2002;20:12562-12566.
20. Ceccarelli M, Danelon C, Laio A, Parrinello M. Microscopic mechanism of antibiotics translocation through a porin. Biophys J 2004;87:58-64.
21. Branduardi D, Gervasio FL, Cavalli A, Recanatini M, Parrinello M. The role of the peripheral anionic site and cation-π interactions in the ligand penetration of the human ache gorge. J Am Chem Soc 2005;127:9147-9155.
22. Gervasio FL, Parrinello M, Ceccarelli M, Klein ML. Exploring the gating mechanism in the ClC Chloride Channel via metadynamics. J Mol Biol 2006;361:390-398.
23. Fenimore PW, Frauenfelder H, McMahon BH, Parak FG. Slaving: solvent fluctuations dominate protein dynamics and functions. Proc Natl Acad Sci USA 2002;99:16047-16051.
24. Procacci P, Darden T, Pad E, Marchi M. Orac: a molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions. J Comput Chem 1997;18:1848-1862.
25. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J Am Chem Soc 1995;117:5179-5197.
26. Giammona DA. 1984. Ph.D. Thesis, University of California Davis, California.
27. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
28. Goldbeck RA, Bhaskaran S, Ortega C, Mendoza JL, Olson JS, Soman J, Kliger D, Esquerra RM. Water and ligand entry in myoglobin: assessing the speed and extent of heme pocket hydration after CO photodissociation. Proc Natl Acad Sci USA 2006;103:1254-1259.
29. Marchi M, Procacci P. Coordinates scaling and multiple time step algorithms for simulation of solvated proteins in the NPT ensemble. J Chem Phys 1998;109:5194-5202.
30. Laio A, Rodriguez-Fortea A, Gervasio FL, Ceccarelli M, Parrinello M. Assessing the accuracy of metadynamics. J Phys Chem B 2005;109:6714-6721.
31. Bussi G, Gervasio FL, Laio A, Parrinello M. Free-energy landscape for β-hairpin folding from combined parallel tempering and metadynamics. J Am Chem Soc 2006;128:13435-13441.
32. Babin V, Roland C, Darden TA, Sagui C. The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections. J Chem Phys 2006;125:204909.