Kinematic mobility analysis of peptide based nano-linkages

Mechanism and Machine Theory

Volumn 42, Issue 8, 2007, Pages 903-918

  Subramanian, Raghavendran ^a   Kazerounian, Kazem ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEGREES OF FREEDOM (MECHANICS); HYDROGEN BONDS; IDENTIFICATION (CONTROL SYSTEMS); MICROFABRICATION; POLYPEPTIDES; PROTEINS;

ARTIFICIAL NANO DEVICES; CONNECTIVITY MATRIX; KINEMATIC MOBILITY ANALYSIS; PROTEIN MOLECULES;

NANOSYSTEMS;

EID: 34248587520     PISSN: 0094114X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mechmachtheory.2006.09.010     Document Type: Article

References (29)

1. Merkle R.C. Design considerations for an assembler. Nanotechnology 7 (1996) 210-215
2. Kim M.K., Jernigan R.L., and Chirikjian G.S. Rigid-cluster models of conformational transitions in macromolecular machines and assemblies. Biophys. J. 89 July (2005) 43-55
3. Kazerounian K. From mechanisms and robotics to protein conformation and drug design. ASME J. Mech. Des. 126 (2004) 1-6
4. Burkert U., and Allinger N. Molecular Mechanics (1982), Oxford University Press
5. Nichols W.L., Rose G.D., Ten Eyck L.F., and Zimm B.H. Rigid domains in proteins: an algorithmic approach to their identification. Proteins 23 (1995) 38-48
6. Wriggers W., and Schulten K. Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins 29 (1997) 1-14
7. Levitt M., Sander C., and Stern P.S. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol. 181 (1985) 423-447
8. Doruker P., Bahar I., Baysal C., and Erman B. Collective deformations in proteins determined by a mode analysis molecular dynamics trajectories. Polymer 43 (2002) 431-439
9. Jacobs D.J., Rader A.J., Kuhn L.A., and Thorpe M.F. Protein flexibility predictions using graph theory. Proteins 44 (2001) 150-165
10. Lesk A.M. Protein Architecture (1991), Oxford University Press, New York
11. Zheng W., and Brooks B.R. Normal modes based prediction of protein conformational changes guided by distance constraints. Biophys. J. (2005)
12. Schuyler A.D., and Chirikjian G.S. Normal mode analysis of proteins: a comparison of rigid cluster modes and C (Alpha) coarse graining. J. Mol. Graphics Model. 22 January (2004) 183-193
13. Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins 33 (1998) 417-429
14. Jacobs D.J. Generic rigidity in three-dimensional bond bending networks. J. Phys. A: Math. Gen. 31 (1998) 6653-6668
15. Crossley F.R.E. The permutations of kinematic chains of eight members or less from graph theoretic viewpoint. Develop. Theoret. Appl. Mech. 2 (1965) 467-487
16. Woo L.S. Type synthesis of plane linkages. ASME J. Eng. Ind. Feb. (1967) 159-172
17. Manolescu N.I. A method based on Barnov Trusses, and using graph theory to find the set of planar jointed kinematic chains and mechanisms. Mech. Machine Theory 8 (1973) 3-22
18. Mruthyunjaya T.S., and Raghavan M.R. Structural analysis of kinematic chains and mechanisms based on matrix representation. ASME J. Mech. Des. 101 (1979) 488-494
19. Mruthyunjaya T.S. Structural synthesis by transformation of binary chains. Mech. Machine Theory 14 (1979) 221-231
20. K. Kazerounian, Is design of new drugs a challenge for kinematics? in: Presented at Proceedings of the 8th Int. Conf. on Advance Robot Kinematics (ARK), Caldes de Malavalla, 2002.
21. K. Kazerounian, K. Rodriguez, K. Latif, C. Alvarado, ProtoFold I: Nano-kinematics for analysis of protein molecules, in: Presented at ASME Journal of Mechanical Design, Salt lake city, Utah, 2004.
22. Kazerounian K., Alvarado C., and Latif K. ProtoFold: a successive kineto-static compliance method for protein conformation prediction. ASME J. Mech. Des. (2004)
23. S. Raghavendran, K. Kazerounian, Residue level inverse kinematics of peptide chains in the presence of observation inaccuracies and bond length changes, in: presented at IDETC/CIE 2005, Long Beach, California, 2005.
24. Baker E., and Hubbard R. Hydrogen bonding in globular proteins. Prog. Biophys. Mol. Biol. 44 (1984) 97-179
25. Eswar N., and Ramakrishnan C. Deterministic features of side chain-main chain hydrogen bonds in globular proteins. Protein Eng. 13 (2000) 227-238
26. Berman H., Westbrook J., Feng Z., Gilliland G., Bhat T., Weissig H., Shindyaloy I., and Bourne P. The protein data bank. Nucl. Acids Res. 28 (2000) 235-242
27. Sowdhamini R., Srinivasan N., Shoichet B., Santi D., Ramakrishnan C., and Balaram P. Stereo chemical modeling of disulfide bridges: criteria for introduction into proteins by site-directed mutagenesis. Protein Eng. 3 (1989)
28. S. Raghavendran, Calibration of the structural variables and mobility analysis, of the proteins, Department of Mechanical Engineering, M.S. thesis, Storrs, University of Connecticut, 2005.
29. Echols N., Milburn D., and Gerstein M. MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucl. Acids Res. 31 (2003) 478-482