Free energy calculations of glycosaminoglycan - Protein interactions

Glycobiology

Volumn 19, Issue 10, 2009, Pages 1103-1115

  Gandhi, Neha S ^a,b   Mancera, Ricardo L ^a,b  

^a CURTIN UNIVERSITY   (Australia)

^b CURTIN UNIVERSITY   (Australia)

Author keywords

AMBER; Annexin; GLYCAM; Heparin; PECAM 1

Indexed keywords

CALCIUM ION; CD31 ANTIGEN; GAG PROTEIN; GLYCOSAMINOGLYCAN; HEPARIN; LIPOCORTIN 2;

ARTICLE; BINDING AFFINITY; BIOENERGY; CONTROLLED STUDY; HYDROGEN BOND; MATHEMATICAL COMPUTING; MOLECULAR MECHANICS POISSON BOLTZMANN SURFACE AREA; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

ANNEXIN A1; ANTIGENS, CD31; CARBOHYDRATE SEQUENCE; HEPARIN; HUMANS; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; STATIC ELECTRICITY;

EID: 70249092883     PISSN: 09596658     EISSN: 14602423     Source Type: Journal    
DOI: 10.1093/glycob/cwp101     Document Type: Article

References (67)

1. Angulo J, Nieto PM, Martín-Lomas M. 2003. A molecular dynamics description of the conformational flexibility of the L-iduronate ring in glycosaminoglycans. Chem Commun. 1512-1513.
2. Basma M, Sundara S, Çalgan D, Vernali T, Woods RJ. 2001. Solvated ensemble averaging in the calculation of partial atomic charges. J Comput Chem. 22:1125-1137.
3. Bayly CI, Cieplak P, Cornell W, Kollman PA. 1993. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model. J Phys Chem. 97:10269-10280.
4. Becker CF, Guimarães JA, Verli H. 2005. Molecular dynamics and atomic charge calculations in the study of heparin conformation in aqueous solution. Carbohydr Res. 340:1499-1507.
5. Berendsen HJC, Postma JPM, Gunsteren WFv, DiNola A, Haak JR. 1984. Molecular dynamics with coupling to an external bath. J Chem Phys. 81:3684-3690.
6. Canales A, Lozano R, Lopez-Mendez B, Angulo J, Ojeda R, Nieto PM, Martin-Lomas M, Gimenez-Gallego G, Jimenez-Barbero J. 2006. Solution NMR structure of a human FGF-1 monomer, activated by a hexasaccharide heparin-analogue. FEBS J. 273:4716.
7. Cao G, O'Brien CD, Zhou Z, Sanders SM, Greenbaum JN, Makrigiannakis A, DeLisser HM. 2002. Involvement of human PECAM-1 in angiogenesis and in vitro endothelial cell migration. Am J Physiol Cell Physiol. 282:1181-1190.
8. Capila I, Hernaiz MJ, Mo YD, Mealy TR, Campos B, Dedman JR, Linhardt RJ, Seaton BA. 2001. Annexin V-heparin oligosaccharide complex suggests heparan sulfate-mediated assembly on cell surfaces. Structure. 9: 57-64.
9. Case DA. 1994. Normal mode analysis of protein dynamics. Curr Opin Struct Biol. 4:285-290.
10. Case DA, Cheatham Iii TE, Darden T, Gohlke H, Luo R, Merz KMJr, Onufriev A, Simmerling C, Wang B, Woods RJ. 2005. The Amber biomolecular simulation programs. J Comput Chem. 26:1668-1688.
11. Cheatham III TE, Young MA. 2001. Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise. Biopolymers. 56:232-256.
12. Chen ME, Cang HX, Nymeyer H. http://noch.sourceforge.net/.
13. 2+ binding site. Eur J Org Chem. 2367: 2376.
14. Chevalier F, Lucas R, Angulo J, Martin-Lomas M, Nieto PM. 2004. The heparin-Ca (2+) interaction: The influence of the O-sulfation pattern on binding. Carbohydr Res. 339:975-983.
15. Cochran S, Li CP, Bytheway I. 2005. An experimental and molecular-modeling study of the binding of linked sulfated tetracyclitols to FGF-1 and FGF-2. ChemBioChem. 6:1882-1890.
16. Coombe DR, Stevenson SM, Kinnear BF, Gandhi NS, Mancera RL, Osmond RIW, Kett WC. 2008. Platelet endothelial cell adhesion molecule 1 (PECAM-1) and its interactions with glycosaminoglycans: 2. Biochemical analyses. Biochemistry. 47:4863-4875.
17. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc. 117:5179-5197.
18. Cornell WD, Cieplak P, Bayly CI, Kollmann PA. 1993. Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation. J Am Chem Soc. 115:9620-9631.
19. Deaglio S, Morra M, Mallone R, Ausiello CM, Prager E, Garbarino G, Dianzani U, Stockinger H, Malavasi F. 1998. Human CD38 (ADP-Ribosyl Cyclase) is a counter-receptor of CD31, an Ig superfamily member 1. J Immunol. 160:395-402.
20. DeLisser HM, Yan HC, Newman PJ, Muller WA, Buck CA, Albelda SM. 1993. Platelet/endothelial cell adhesion molecule-1 (CD31)-mediated cellular aggregation involves cell surface glycosaminoglycans. J Biol Chem. 268:16037-16046.
21. Fogolari F, Brigo A, Molinari H. 2003. Protocol for MM/PBSA molecular dynamics simulations of proteins. Biophys J. 85:159-166.
22. Ford MG, Weimar T, Köhli T, Woods RJ. 2003. Molecular dynamics simulations of galectin-1-oligosaccharide complexes reveal the molecular basis for ligand diversity. Proteins. 53:229-240.
23. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA Jr, Stratmann RE, Burant JC. 1998. Gaussian 98, Revision A. 7. Pittsburgh (PA): Gaussian Inc.
24. Gandhi NS, Coombe DR, Mancera RL. 2008. Platelet endothelial cell adhesion molecule 1 (PECAM-1) and its Interactions with glycosaminoglycans: 1. Molecular modeling studies. Biochemistry. 47:4851-4862.
25. 2+ signalling to membrane dynamics. Nat Rev Mol Cell Biol. 6:449-461.
26. Gilson MK, Honig B. 1988. Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis. Proteins. 4:7-18.
27. Holger G, David AC. 2004. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J Comput Chem. 25:238-250.
28. Honig B, Nicholls A. 1995. Classical electrostatics in biology and chemistry. Science. 268:1144.
29. Hsu S-TD, Peter C, van Gunsteren WF, Bonvin AMJJ. 2005. Entropy calculation of HIV-1 Env gp120, its receptor CD4, and their complex: An analysis of configurational entropy changes upon complexation. Biophys J. 88:15-24.
30. Huige CJM, Altona C. 1995. Force field parameters for sulfates and sulfamates based on Ab initio calculations: Extensions of AMBER and CHARMm fields. J Comput Chem. 16:56-79.
31. Jin L, Barran PE, Deakin JA, Lyon M, an Uhrín D, Matter S. 2005. Conformation of glycosaminoglycans by ion mobility mass spectrometry and molecular modelling. Phys Chem Chem Phys. 7:3464-3471.
32. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. 1983. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 79:926.
33. Kassam G, Manro A, Braat CE, Louie P, Fitzpatrick SL, Waisman DM. 1997. Characterization of the heparin binding properties of annexin II tetramer. J Biol Chem. 272:15093-15100.
34. Keserü GM, Kolossváry I. 1999. Molecular Mechanics and Conformational Analysis in Drug Design. Oxford: Blackwell Publishing.
35. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W. 2000. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Acc Chem Res. 33:889-897.
36. Krieger E, Geretti E, Brandner B, Goger B, Wells TN, Kungl AJ. 2004. A structural and dynamic model for the interaction of interleukin-8 and glycosaminoglycans: Support from isothermal fluorescence titrations. Proteins. 54:768-775.
37. Massova I, Kollman PA. 1999. Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies. J Am Chem Soc. 121:8133-8143.
38. McDowell SE, Spackova N, Sponer J, Walter NG. 2007. Molecular dynamics simulations of RNA: An in silico single molecule approach. Biopolymers. 85:169-184.
39. Mikhailov D, Linhardt RJ, Mayo KH. 1997. NMR solution conformation of heparin-derived hexasaccharide. Biochem J. 328:51-61.
40. Mikhailov D, Mayo KH, Vlahov IR, Toida T, Pervin A, Linhardt RJ. 1996. NMR solution conformation of heparin-derived tetrasaccharide. Biochem J. 318:93-102.
41. Muller WA. 1993. PECAM-1 is required for transendothelial migration of leukocytes. J Exp Med. 178:449-460.
42. Mulloy B, Forster MJ. 2000. Conformation and dynamics of heparin and heparan sulfate. Glycobiology. 10:1147-1156.
43. Mulloy B, Forster MJ, Jones C, Davies DB. 1993. Nmr and molecular-modelling studies of the solution conformation of heparin. Biochem J. 293:849-858.
44. Murphy KJ, McLay N, Pye DA. 2008. Structural studies of heparan sulfate hexasaccharides: New insights into iduronate conformational behavior. J Am Chem Soc. 130:12435-12444.
45. Newman PJ. 1997. The biology of PECAM-1. J Clin Invest. 99:3-8.
46. Nguyen DT, Case DA. 1985. On finding stationary states on large-molecule potential energy surfaces. J Phys Chem. 89:4020-4026.
47. Penkett CJ, Redfield C, Dodd I, Hubbard J, McBay DL, Mossakowska DE, Smith RAG, Dobson CM, Smith LJ. 1997. NMR analysis of main-chain conformational preferences in an unfolded fibronectin-binding protein. J Mol Biol. 274:152-159.
48. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. 2004. UCSF Chimera - A visualization system for exploratory research and analysis. J Comput Chem. 25:1605-1612.
49. Piali L. 1995. CD31/PECAM-1 is a ligand for alpha v beta 3 integrin involved in adhesion of leukocytes to endothelium. J Cell Biol. 130:451-460.
50. Prager E. 1996. Interaction of CD31 with a heterophilic counterreceptor involved in downregulation of human T cell responses. J Exp Med. 184:41-50.
51. Ryckaert J-P, Ciccotti G, Berendsen HJC. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J Comput Phys. 23:327-341.
52. Sanner MF, Olson AJ, Spehner J-C. 1996. Reduced surface: An efficient way to compute molecular surfaces. Biopolymers. 38:305-320.
53. Schlitter J. 1993. Estimation of absolute and relative entropies of macromolecules using the covariance matrix. Chem Phys Lett. 215:617-621.
54. Shao C, Zhang F, Kemp MM, Linhardt RJ, Waisman DM, Head JF, Seaton BA. 2006. Crystallographic analysis of calcium-dependent heparin binding to annexin A2. J Biol Chem. 281:31689.
55. Sitkoff D, Sharp KA, Honig B. 1994. Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem. 98:1978-1988.
56. Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA. 1998. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J Am Chem Soc. 120:9401-9409.
57. Still WC, Tempczyk A, Hawley RC, Hendrickson T. 1990. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc. 112:6127-6129.
58. Swanson JM, Henchman RH, McCammon JA. 2004. Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys J. 86:67-74.
59. Teeter MM, Case DA. 1990. Harmonic and quasiharmonic descriptions of crambin. J Phys Chem. 94:8091-8097.
60. Tidor B, Karplus M. 1994. The contribution of vibrational entropy to molecular association: The dimerization of insulin. J Mol Biol. 238:405-414.
61. Tom D, Darrin Y, Lee P. 1993. Particle mesh Ewald: An N [center-dot] log(N) method for Ewald sums in large systems. J Chem Phys. 98:10089-10092.
62. Tsui V, Case DA. 2001. Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers. 56:257-291.
63. Verli H, Guimarães JA. 2004. Molecular dynamics simulation of a decasaccharide fragment of heparin in aqueous solution. Carbohydr Res 339:281-290.
64. Woods RJ, Dwek RA, Edge CJ, Fraser-Reid B. 1995. Molecular mechanical and molecular dynamic simulations of glycoproteins and oligosaccharides: 1. GLYCAM 93 parameter development. J Phys Chem. 99:3832-3846.
65. Zehnder JL, Shatsky M, Leung LL, Butcher EC, McGregor JL, Levitt LJ. 1995. Involvement of CD31 in lymphocyte-mediated immune responses: Importance of the membrane-proximal immunoglobulin domain and identification of an inhibiting CD31 peptide. Blood. 85:1282.
66. Zhang Z, McCallum SA, Xie J, Nieto L, Corzana F, Jiménez-Barbero J, Chen M, Liu J, Linhardt RJ. 2008. Solution structures of chemoenzymatically synthesized heparin and its precursors. J Am Chem Soc. 130:12998-13007.
67. 2+ coordination position 5 of parvalbumin on the calciumbinding affinity: A computational study. J Inorg Biochem. 100:1879-1887.