Hydrogen bonds and kinematic mobility of protein molecules

Journal of Mechanisms and Robotics

Volumn 2, Issue 2, 2010, Pages 1-9

  Shahbazi, Zahra ^a   Ilieş, Horea T ^a   Kazerounian, Kazem ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PRINCIPLES; FLEXIBLE SEGMENTS; FOLDING PROCESS; INTERNAL MOBILITY; KINEMATIC CHAIN; KINEMATIC MOBILITY; KINEMATIC MODEL; MOBILITY ANALYSIS; NUMBER OF DEGREES OF FREEDOM; PROTEIN FOLDING SIMULATION; PROTEIN MODELS; PROTEIN MOLECULES;

BIOLOGY; HYDROGEN; KINEMATICS; MOLECULES; PROTEIN FOLDING;

HYDROGEN BONDS;

EID: 78651543110     PISSN: 19424302     EISSN: 19424310     Source Type: Journal    
DOI: 10.1115/1.4001088     Document Type: Article

References (58)

1. Langer, R., 1998, Drug Delivery and Targeting, Nature (London), 392, pp. 5-10.
2. Kiser, P. F., Wilson, G., and Needham, D., 1998, A Synthetic Mimic of the Secretory Granule for Drug Delivery, Nature (London), 394(6692), pp. 459-62.
3. Ong, S., Liu, H., Qiu, X., Bhat, G., and Pidgeon, C., 1995, Membrane Partition Coefficients Chromatographically Measured Using Immobilized Artificial Membrane Surfaces, Anal. Chem., 67(4), pp. 755-62.
4. Kuhn, L. A., and Thorpe, M. F., 2001, Introduction and Foreword to the Special Issue on Protein Flexibility and Folding, J. Mol. Graphics Modell., 19(1), pp. 1-2.
5. Kuhn, L. A., and Thorpe, M. F. 2009, Protein Folding and Misfolding: Neurodegenerative Diseases (Focus on Structural Biology), J. Ovadi and F. Orosz, eds., Springer, New York, Vol. 7.
6. Kern, D., and Zuiderweg, E. R., 2003, The Role of Dynamics in Allosteric Regulation, Curr. Opin. Struct. Biol., 13(6), pp. 748-757.
7. Geeves, M. A., and Holmes, K. C., 1999, Structural Mechanism of Muscle Contraction, Annu. Rev. Biochem., 68, pp. 687-728.
8. Liu, J., Zhang, J., Yang, Y., Huang, H., Shen, W., Hu, Q., Wang, X., Wu, J., and Shi, Y., 2008, Conformational Change Upon Ligand Binding and Dynamics of the PDZ Domain From Leukemia-Associated Rho Guanine Nucleotide Exchange Factor, Protein Sci., 17, pp. 1003-1014.
9. Zheng, W., Brooks, B. R., and Hummer, G., 2007, Protein Conformational Transitions Explored by Mixed Elastic Network Models, Proteins: Struct., Funct., Bioinf., 69(1), pp. 43-57.
10. Chirikjian, G. S., Kazerounian, K., and Mavroidis, C., 2005, Analysis and Design of Protein Based Nanodevices: Challenges and Opportunities in Mechanical Design, ASME J. Mech. Des., 127(4), pp. 695-698.
11. Madden, C., Bohnenkamp, P., Kazerounian, K., and Ilieş H. T., 2008, Interdisciplinary Applications of Kinematics, A. Kecskemethy, ed., Elsevier, New York.
12. Branden, C., and Tooze, J., 1999, Introduction to Protein Structure, 2nd ed., Garland, New York, NY.
13. Wales, T. E., and Fitzgerald, M. C., 2001, The Energetic Contribution of Backbone-Backbone Hydrogen Bonds to the Thermodynamic Stability of a Hyperstable p22 Arc Repressor Mutant, J. Am. Chem. Soc., 123(31), pp. 7709-10.
14. Perutz, M. F., and Raidt, H., 1975, Stereochemical Basis of Heat Stability in Bacterial Ferredoxins and in Haemoglobin, Nature (London), 255, pp. 256-259.
15. Grutter, M. G., Hawkes, R. B., and Mattews, B. W., 1979, Molecular Basis of Thermostability in the Lysozyme From Bacteriophage t4, Nature (London), 277, pp. 667-669.
16. Chatake, T., Higuchi, Y., Mizuno, N., Tanaka, I., Niimura, N., and Morimoto, Y., 2008, Hydrogen Bonds of dsrd Protein Revealed by Neutron Crystallography, J. Synchrotron Radiat., 15, pp. 277-280.
17. Hinsen, K., 2007, Structural Flexibility in Proteins: Impact of the Crystal Environment, Bioinformatics, 24(4), pp. 521-528.
18. Kumar, S., Wolfson, H. J., and Nussinov, R., 2001, Protein Flexibility and Electrostatic Interactions, IBM J. Res. Dev., 45(3-4), pp. 499-512.
19. Najmanovich, R., Kuttner, J., Sobolev, V., and Edelman, M., 2000, Side-Chain Flexibility in Proteins Upon Ligand Binding, Proteins: Struct., Funct., Genet., 39(3), pp. 261-268.
20. Carlson, H. A., and McCammon, J. A., 2000, Accommodating Protein Flexibility in Computational Drug Design, Mol. Pharmacol., 57(2), pp. 213-218.
21. Nichols, W. L., Rose, G. D., Ten Eyck, L. F., and Zimm, B. H., 1995, Rigid Domains in Proteins: An Algorithmic Approach to Their Identification, Proteins, 23(1), pp. 38-48.
22. Wriggers, W., and Schulten, K., 1997, Protein Domain Movements: Detection of Rigid Domains and Visualization of Hinges in Comparisons of Atomic Coordinates, Proteins, 29(1), pp. 1-14.
23. Doruker, P., Bahara, I., Baysalb, C., and Erman, B., 2002, Collective Deformations in Proteins Determined by a Mode Analysis Molecular Dynamics Trajectories, Polymer, 43, pp. 431-439.
24. Jacobs, D. J., Rader, A. J., Kuhn, L. A., and Thorpe, M. F., 2001, Protein Flexibility Predictions Using Graph Theory, Proteins, 44(2), pp. 150-65.
25. Ceccarelli, C., Jeffrey, G. A., and Taylor, R., 1981, A Survey of O-H O Hydrogen Bond Geometries Determined by Neutron Diffraction, J. Mol. Struct., 70, pp. 255-271.
26. Grabowski, S. J., 2004, Hydrogen Bonding Strength-Measures Based on Geometric and Topological Parameters, J. Phys. Org. Chem., 17(1), pp. 18-31.
27. Mitra, J., and Ramakrishnan, C., 1977, Analysis of O-H O Hydrogen Bonds, Int. J. Pept. Protein Res., 9, pp. 27-48.
28. Mitra, J., and Ramakrishnan, C., 1981, Studies of Hydrogen Bonds, Int. J. Pept. Protein Res., 17, pp. 401-411.
29. Murray-Rust, P., and Glusker, J., 1984, Directional Hydrogen Bonding to sp2- and sp3-Hybridized Oxygen Atoms and Its Relevance to Ligand-Macromolecule Interactions, J. Am. Chem. Soc., 106(4), pp. 1018-1025.
30. Taylor, R., Kennard, O., and Versichel, W., 1983, Geometry of the N-H O=C Hydrogen Bond. 1. Lone-Pair Directionality, J. Am. Chem. Soc., 105(18), pp. 5761-5766.
31. Taylor, R., and Kennard, O., 1984, Hydrogen-Bond Geometry in Organic Crystals, Acc. Chem. Res., 17, pp. 320-326.
32. Lutz, H. D., 2003, Structure and Strength of Hydrogen Bonds in Inorganic Solids, J. Mol. Struct., 646(1-3), pp. 227-236.
33. Baker, E. N., and Hubbard, R. E., 1984, Hydrogen Bonding in Globular Proteins, Prog. Biophys. Mol. Biol., 44(2), pp. 97-179.
34. Eswar, N., and Ramakrishnan, C., 2000, Deterministic Features of Side-Chain Main-Chain Hydrogen Bonds in Globular Protein Structures, Protein Eng., 13(4), pp. 227-238.
35. Kortemme, T., Morozov, A. V., and Baker, D., 2003, An Orientation-Dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes, J. Mol. Biol., 326(4), pp. 1239-1259.
36. Panasik, N., Fleming, P. J., and Rose, G. D., 2005, Hydrogen-Bonded Turns in Proteins: The Case for a Recount, Protein Sci., 14(11), pp. 2910-2914.
37. Alexandrescu, A. T., Snyder, D. R., and Abildgaard, F., 2001, NMR of Hydrogen Bonding in Cold-Shock Protein A and an Analysis of the Influence of Crystallographic Resolution on Comparisons of Hydrogen Bond Lengths, Protein Sci., 10(9), pp. 1856-1868.
38. Flores, M., Isaacson, R., Abresch, E., Calvo, R., Lubitz, W., and Feher, G., 2007, Protein-Cofactor Interactions in Bacterial Reaction Centers From Rhodobacter Sphaeroides R-26: II. Geometry of the Hydrogen Bonds to the Primary Quinone Q(A)(-) by H-1 and H-2 ENDOR Spectroscopy, Biophys. J., 92(2), pp. 671-682.
39. Langkilde, A., Kristensen, S. M., Lo Leggio, L., Molgaard, A., Jensen, J. H., Houk, A. R., Poulsen, J. C. N., Kauppinen, S., and Larsen, S., 2008, Short Strong Hydrogen Bonds in Proteins: A Case Study of Rhamnogalacturonan Acetylesterase, Acta Crystallogr., Sect. D: Biol. Crystallogr., 64, pp. 851-863.
40. Artymiuk, P. J., and Blake, C. C., 1981, Refinement of Human Lysozyme at 1.5 a Resolution Analysis of Non-Bonded and Hydrogenbond Interactions, J. Mol. Biol., 152(4), pp. 737-762.
41. Singh, J., Thornton, J. M., Snarey, M., and Campbell, S. F., 1987, The Geometries of Interacting Arginine-Carboxyls in Proteins, FEBS Lett., 224(1), pp. 161-71.
42. Fernandez, A., and Berry, R. S., 2002, Extent of Hydrogen-Bond Protection in Folded Proteins: A Constraint on Packing Architectures, Biophys. J., 83(5), pp. 2475-2481.
43. Fleming, P. J., and Rose, G. D., 2005, Do All Backbone Polar Groups in Proteins Form Hydrogen Bonds?, Protein Sci., 14(7), pp. 1911-1917.
44. Jeffrey, G., and Maluszynska, H., 1982, A Survey of Hydrogen Bond Geometries in the Crystal Structure of Amino Acids, Int. J. Biol. Macromol., 4, pp. 173-185.
45. McDonald, I. K., and Thornton, J. M., 1994, Satisfying Hydrogen-Bonding Potential in Proteins, J. Mol. Biol., 238(5), pp. 777-793.
46. Sticke, D. F., Presta, L. G., Dill, K. A., and Rose, G. D., 1992, Hydrogen Bonding in Globular Proteins, J. Mol. Biol., 226(4), pp. 1143-59.
47. Torshin, I. Y., Weber, I. T., and Harrison, R. W., 2002, Geometric Criteria of Hydrogen Bonds in Proteins and Identification of 'Bifurcated' Hydrogen Bonds, Protein Eng., 15(5), pp. 359-363.
48. Xu, D., Tsai, C. J., and Nussinov, R., 1997, Hydrogen Bonds and Salt Bridges Across Protein-Protein Interfaces, Protein Eng., 10(9), pp. 999-1012.
49. Ackbarow, T., Chen, X., Keten, S., and Buehler, M. J., 2007, Hierarchies, Multiple Energy Barriers, and Robustness Govern the Fracture Mechanics of Alpha-Helical and Beta-Sheet Protein Domains, Proc. Natl. Acad. Sci. U.S.A., 104(42), pp. 16410-16415.
50. Jang, S., Kim, E., and Pak, Y., 2007, Direct Folding Simulation of Alpha-Helices and Beta-Hairpins Based on a Single All-Atom Force Field With an Implicit Solvation Model, Proteins, 66(1), pp. 53-60.
51. Pauling, L., Corey, R. B., and Branson, H. R., 1951, The Structure of Proteins: Two Hydrogen Bonded Helical Configurations of the Polypeptide Chain, Proc. Natl. Acad. Sci. U.S.A., 37, pp. 205-211.
52. Pauling, L., and Corey, R. B., 1951, Configurations of Polypeptide Chains With Favored Orientations Around Single Bonds: Two New Pleated Sheets, Proc. Natl. Acad. Sci. U.S.A., 37, pp. 729-740.
53. Kazerounian, K., Latif, K., and Alvarado, C., 2005, Protofold: A Successive Kinetostatic Compliance Method for Protein Conformation Prediction, ASME J. Mech. Des., 127(4), pp. 712-717.
54. Subramanian, R., and Kazerounian, K., 2007, Kinematic Mobility Analysis of Peptide Based Nano-Linkages, Mech. Mach. Theory, 42(8), pp. 903-918.
55. Floyd, R. W., 1967, Nondeterministic Algorithms, J. ACM, 14(4), pp. 636-644.
56. Brent, R. P., 1980, An Improved Monte Carlo Factorization Algorithm, BIT, 20(2), pp. 176-184.
57. Allender, E. W., and Klawe, M. M., 1985, Improved Lower Bounds for the Cycle Detection Problem, Theor. Comput. Sci., 36(2-3), pp. 231-237.
58. Gogu, G., 2005, Chebychev-Grbler-Kutzbach's Criterion for Mobility Calculation of Multi-Loop Mechanisms Revisited Via Theory of Linear Transformations, Eur. J. Mech. A/Solids, 24(3), pp. 427-441.