Approximate values for force constant and wave number associated with a low-frequency concerted motion in proteins can be evaluated by a comparison of X-ray structures (166 visite)
J Phys Chem B (ISSN: 1520-6106, 1520-5207, 1520-5207electronic), 2007 May 17; 111(19): 5483-5486.
Tipo di articolo: Journal Article,
Impact factor: 4.086, Impact factor a 5 anni: 4.475
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-34249793262&partnerID=40&md5=11d14084b5636097a2b3e5ce203c6cf8
Parole chiave: Crystal Structure, Wave Equations, X Rays, Biological Functions, Force Constant, Wave Number, Proteins,
Affiliazioni:
*** IBB - CNR ***
Dipartimento di Chimica, Università degli Studi di Napoli Federico II, Via Cynthia, 80126 Napoli, Italy
Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 6, 80134 Napoli, Italy
Riferimenti:
Zoete, V., Michielin, O., Karplus, M., (2002) J. Mol. Biol, 315, p. 2
van Aalten, D.M., Conn, D.A., de Groot, B.L., Berendsen, H.J., Findlay, J.B., Amadei, A., (1997) Biophys. J, 73, p. 2891
Zhang, X.J., Wozniak, J.A., Matthews, B.W., (1995) J. Mol. Biol, 250, p. 527
Hayward, S., (1999) Proteins: Struct., Funct., Genet, 36, p. 425
Zaccai, G., (2000) Science, 288, p. 1604
Bicout, D.J., Zaccai, G., (2001) Biophys. J, 80, p. 1115
Brown, K.G., Erfurth, S.C., Small, E.W., Peticolas, W.L., (1972) Proc Natl. Acad Sci. U.S.A, 69, p. 1467
Bartunik, H.D., Jolles, P., Berthou, J., Dianoux, A.J., (1982) Biopolymers, 21, p. 43
Levitt, M., Sander, C., Stern, P.S., (1985) J. Mol. Biol, 181, p. 423
Cao, Z.W., Chen, X., Chen, Y.Z., (2003) J. Mol. Graphics Modell, 21, p. 309
Rasmussen, B.F., Stock, A.M., Ringe, D., Petsko, G.A., (1992) Nature, 357, p. 423
Kartha, G., Bello, J., Harker, D., (1967) Nature, 213, p. 862
Berisio, R., Sica, F., Lamzin, V.S., Wilson, K.S., Zagari, A., Mazzarella, L., (2002) Acta Crystallogr, Sect. D, 58, p. 441
Vitagliano, L., Merlino, A., Zagari, A., Mazzarella, L., (2002) Proteins, 46, p. 97
Merlino, A., Vitagliano, L., Ceruso, M.A., Mazzarella, L., (2003) Proteins, 53, p. 101
Vitagliano, L., Adinolfi, S., Riccio, A., Sica, F., Zagari, A., Mazzarella, (1998) L. Protein Sci, 7, p. 1691
Sica, F., Di Fiore, A., Merlino, A., Mazzarella, L., (2004) J. Biol. Chem, 279, p. 36753
Oleinikova, A., Sasisanker, P., Weingartner, H., (2004) J. Phys. Chem, 108, p. 8467
Herman, H.M., Bhat, T.N., Bourne, P.E., Feng, Z., Gilliland, G., Weissig, H., Westbrook, J., (2000) Nat. Struct. Biol, 7 (SUPPL. 7), p. 957
Wang, M., Borchardt, R.T., Schowen, R.L., Kuczera, K., (2005) Biochemistry, 44, p. 7228
Brooks III, C.L., Karplus, M., Pettitt, B.M., (1988) The Proteins: A theoretical perspective of dynamics, structure and thermodynamics, , Wiley and Sons: New York
Shortle, D., (2003) Protein Sci, 12, p. 1298
Sippl, M.J.J., (1993) Comput.-Aided Mol. Des, 7, p. 473
Bryant, S.H., Lawrence, C.E., (1991) Proteins, 9, p. 108
Chou, P.Y., Fasman, G.D., (1978) Adv. Enzymol. Relat. Areas Mol. Biol, 47, p. 45
Finkelstein, A.V., Badretdinov, A., Gutin, A.M., (1995) Proteins, 23, p. 142
Butterfoss, G.L., Hermans, J., (2003) Protein Sci, 12, p. 2719
MacArthur, M.W., Thornton, J.M., (1991) J. Mol. Biol, 218, p. 397
Burgi, H.B., Dunitz, J.D., (1988) Acta Crystallogr., Sect. B, 44, p. 445
Best, R.B., Lindorff-Larsen, K., DePristo, M.A., Vendruscolo, M., (2006) Proc Natl. Acad. Sci. U.S.A, 103, p. 10901
van Aalten, D. M., Conn, D. A., de Groot, B. L., Berendsen, H. J., Findlay, J. B., Amadei, A., (1997) Biophys. J, 73, p. 2891
Zhang, X. J., Wozniak, J. A., Matthews, B. W., (1995) J. Mol. Biol, 250, p. 527
Bicout, D. J., Zaccai, G., (2001) Biophys. J, 80, p. 1115
Brown, K. G., Erfurth, S. C., Small, E. W., Peticolas, W. L., (1972) Proc Natl. Acad Sci. U. S. A, 69, p. 1467
Bartunik, H. D., Jolles, P., Berthou, J., Dianoux, A. J., (1982) Biopolymers, 21, p. 43
Cao, Z. W., Chen, X., Chen, Y. Z., (2003) J. Mol. Graphics Modell, 21, p. 309
Rasmussen, B. F., Stock, A. M., Ringe, D., Petsko, G. A., (1992) Nature, 357, p. 423
Herman, H. M., Bhat, T. N., Bourne, P. E., Feng, Z., Gilliland, G., Weissig, H., Westbrook, J., (2000) Nat. Struct. Biol, 7 (SUPPL. 7), p. 957
Brooks III, C. L., Karplus, M., Pettitt, B. M., (1988) The Proteins: A theoretical perspective of dynamics, structure and thermodynamics, , Wiley and Sons: New York
Sippl, M. J. J., (1993) Comput. -Aided Mol. Des, 7, p. 473
Bryant, S. H., Lawrence, C. E., (1991) Proteins, 9, p. 108
Chou, P. Y., Fasman, G. D., (1978) Adv. Enzymol. Relat. Areas Mol. Biol, 47, p. 45
Finkelstein, A. V., Badretdinov, A., Gutin, A. M., (1995) Proteins, 23, p. 142
Butterfoss, G. L., Hermans, J., (2003) Protein Sci, 12, p. 2719
MacArthur, M. W., Thornton, J. M., (1991) J. Mol. Biol, 218, p. 397
Burgi, H. B., Dunitz, J. D., (1988) Acta Crystallogr., Sect. B, 44, p. 445
Best, R. B., Lindorff-Larsen, K., DePristo, M. A., Vendruscolo, M., (2006) Proc Natl. Acad. Sci. U. S. A, 103, p. 10901
J Phys Chem B (ISSN: 1520-6106, 1520-5207, 1520-5207electronic), 2007 May 17; 111(19): 5483-5486.
Tipo di articolo: Journal Article,
Impact factor: 4.086, Impact factor a 5 anni: 4.475
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-34249793262&partnerID=40&md5=11d14084b5636097a2b3e5ce203c6cf8
Parole chiave: Crystal Structure, Wave Equations, X Rays, Biological Functions, Force Constant, Wave Number, Proteins,
Affiliazioni:
*** IBB - CNR ***
Dipartimento di Chimica, Università degli Studi di Napoli Federico II, Via Cynthia, 80126 Napoli, Italy
Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 6, 80134 Napoli, Italy
Riferimenti:
Zoete, V., Michielin, O., Karplus, M., (2002) J. Mol. Biol, 315, p. 2
van Aalten, D.M., Conn, D.A., de Groot, B.L., Berendsen, H.J., Findlay, J.B., Amadei, A., (1997) Biophys. J, 73, p. 2891
Zhang, X.J., Wozniak, J.A., Matthews, B.W., (1995) J. Mol. Biol, 250, p. 527
Hayward, S., (1999) Proteins: Struct., Funct., Genet, 36, p. 425
Zaccai, G., (2000) Science, 288, p. 1604
Bicout, D.J., Zaccai, G., (2001) Biophys. J, 80, p. 1115
Brown, K.G., Erfurth, S.C., Small, E.W., Peticolas, W.L., (1972) Proc Natl. Acad Sci. U.S.A, 69, p. 1467
Bartunik, H.D., Jolles, P., Berthou, J., Dianoux, A.J., (1982) Biopolymers, 21, p. 43
Levitt, M., Sander, C., Stern, P.S., (1985) J. Mol. Biol, 181, p. 423
Cao, Z.W., Chen, X., Chen, Y.Z., (2003) J. Mol. Graphics Modell, 21, p. 309
Rasmussen, B.F., Stock, A.M., Ringe, D., Petsko, G.A., (1992) Nature, 357, p. 423
Kartha, G., Bello, J., Harker, D., (1967) Nature, 213, p. 862
Berisio, R., Sica, F., Lamzin, V.S., Wilson, K.S., Zagari, A., Mazzarella, L., (2002) Acta Crystallogr, Sect. D, 58, p. 441
Vitagliano, L., Merlino, A., Zagari, A., Mazzarella, L., (2002) Proteins, 46, p. 97
Merlino, A., Vitagliano, L., Ceruso, M.A., Mazzarella, L., (2003) Proteins, 53, p. 101
Vitagliano, L., Adinolfi, S., Riccio, A., Sica, F., Zagari, A., Mazzarella, (1998) L. Protein Sci, 7, p. 1691
Sica, F., Di Fiore, A., Merlino, A., Mazzarella, L., (2004) J. Biol. Chem, 279, p. 36753
Oleinikova, A., Sasisanker, P., Weingartner, H., (2004) J. Phys. Chem, 108, p. 8467
Herman, H.M., Bhat, T.N., Bourne, P.E., Feng, Z., Gilliland, G., Weissig, H., Westbrook, J., (2000) Nat. Struct. Biol, 7 (SUPPL. 7), p. 957
Wang, M., Borchardt, R.T., Schowen, R.L., Kuczera, K., (2005) Biochemistry, 44, p. 7228
Brooks III, C.L., Karplus, M., Pettitt, B.M., (1988) The Proteins: A theoretical perspective of dynamics, structure and thermodynamics, , Wiley and Sons: New York
Shortle, D., (2003) Protein Sci, 12, p. 1298
Sippl, M.J.J., (1993) Comput.-Aided Mol. Des, 7, p. 473
Bryant, S.H., Lawrence, C.E., (1991) Proteins, 9, p. 108
Chou, P.Y., Fasman, G.D., (1978) Adv. Enzymol. Relat. Areas Mol. Biol, 47, p. 45
Finkelstein, A.V., Badretdinov, A., Gutin, A.M., (1995) Proteins, 23, p. 142
Butterfoss, G.L., Hermans, J., (2003) Protein Sci, 12, p. 2719
MacArthur, M.W., Thornton, J.M., (1991) J. Mol. Biol, 218, p. 397
Burgi, H.B., Dunitz, J.D., (1988) Acta Crystallogr., Sect. B, 44, p. 445
Best, R.B., Lindorff-Larsen, K., DePristo, M.A., Vendruscolo, M., (2006) Proc Natl. Acad. Sci. U.S.A, 103, p. 10901
van Aalten, D. M., Conn, D. A., de Groot, B. L., Berendsen, H. J., Findlay, J. B., Amadei, A., (1997) Biophys. J, 73, p. 2891
Zhang, X. J., Wozniak, J. A., Matthews, B. W., (1995) J. Mol. Biol, 250, p. 527
Bicout, D. J., Zaccai, G., (2001) Biophys. J, 80, p. 1115
Brown, K. G., Erfurth, S. C., Small, E. W., Peticolas, W. L., (1972) Proc Natl. Acad Sci. U. S. A, 69, p. 1467
Bartunik, H. D., Jolles, P., Berthou, J., Dianoux, A. J., (1982) Biopolymers, 21, p. 43
Cao, Z. W., Chen, X., Chen, Y. Z., (2003) J. Mol. Graphics Modell, 21, p. 309
Rasmussen, B. F., Stock, A. M., Ringe, D., Petsko, G. A., (1992) Nature, 357, p. 423
Herman, H. M., Bhat, T. N., Bourne, P. E., Feng, Z., Gilliland, G., Weissig, H., Westbrook, J., (2000) Nat. Struct. Biol, 7 (SUPPL. 7), p. 957
Brooks III, C. L., Karplus, M., Pettitt, B. M., (1988) The Proteins: A theoretical perspective of dynamics, structure and thermodynamics, , Wiley and Sons: New York
Sippl, M. J. J., (1993) Comput. -Aided Mol. Des, 7, p. 473
Bryant, S. H., Lawrence, C. E., (1991) Proteins, 9, p. 108
Chou, P. Y., Fasman, G. D., (1978) Adv. Enzymol. Relat. Areas Mol. Biol, 47, p. 45
Finkelstein, A. V., Badretdinov, A., Gutin, A. M., (1995) Proteins, 23, p. 142
Butterfoss, G. L., Hermans, J., (2003) Protein Sci, 12, p. 2719
MacArthur, M. W., Thornton, J. M., (1991) J. Mol. Biol, 218, p. 397
Burgi, H. B., Dunitz, J. D., (1988) Acta Crystallogr., Sect. B, 44, p. 445
Best, R. B., Lindorff-Larsen, K., DePristo, M. A., Vendruscolo, M., (2006) Proc Natl. Acad. Sci. U. S. A, 103, p. 10901
Low-frequency internal motions in protein molecules play a key role in biological functions. A direct relationship between low-frequency motions and enzymatic activity has been suggested for bovine pancreatic ribonuclease (RNase A). The flexibility-function relationship in this enzyme has been attributed to a subtle and concerted breathing motion of the beta-sheet regions occurring upon substrate binding and release. Here, we calculate an approximate value for the force constant and the wave number of the low-frequency beta-sheet breathing motion of RNase A, by using the Boltzmann hypothesis on a set of data derived from a simple conventional structural superimposition of an unusual large number of X-ray structures available for the protein. The results agree with previous observations and with theoretical predictions on the basis of normal-mode analysis. To the best of our knowledge, this is the first example in which the wave number and the force constant of a low-frequency concerted motion in a protein are directly derived from X-ray structures.
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