Keywords: Adhesin, Apoprotein, Collagen, Peptide, Water, Article, Chemistry, Isolation And Purification, Metabolism, Molecular Dynamics, Protein Secondary Structure, Protein Stability, Staphylococcus Aureus, X Ray Crystallography, Bacterial, X-Ray, Molecular Dynamics Simulation, Protein Structure, Bacteria (microorganisms),
Affiliations: *** IBB - CNR ***
Istituto di Biostrutture e Bioimmagini (IBB), Consiglio Nazionale delle Ricerce (CNR), Naples, Italy
Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
References: Ball, P., Water as an active constituent in cell biology (2008) Chemical Reviews, 108 (1), pp. 74-108. , DOI 10.1021/cr068037
Levy, Y., Onuchic, J.N., Water mediation in protein folding and molecular recognition (2006) Annual Review of Biophysics and Biomolecular Structure, 35, pp. 389-415. , DOI 10.1614/WT-05-118R.1
Chandler, D., Interfaces and the driving force of hydrophobic assembly (2005) Nature, 437 (7059), pp. 640-647. , DOI 10.1038/nature04162, PII N04162
Pal, S.K., Peon, J., Zewail, A.H., Biological water at the protein surface: Dynamical solvation probed directly with femtosecond resolution (2002) Proceedings of the National Academy of Sciences of the United States of America, 99 (4), pp. 1763-1768. , DOI 10.1073/pnas.042697899
Zong, C., Papoian, G.A., Wolynes, P.G., Role of topology, nonadditivity, and water-mediated interactions in predicting the structures of a/b proteins (2006) J. Am. Chem. Soc., 128, pp. 5168-5176
Abel, R., Young, T., Farid, R., Berne, B.J., Friesner, R.A., Role of the active-site solvent in the thermodynamics of factor Xa ligand binding (2008) Journal of the American Chemical Society, 130 (9), pp. 2817-2831. , DOI 10.1021/ja0771033
Papoian, G.A., Ulander, J., Wolynes, P.G., Role of water mediated interactions in protein-protein recognition landscapes (2003) Journal of the American Chemical Society, 125 (30), pp. 9170-9178. , DOI 10.1021/ja034729u
Fuxreiter, M., Mezei, M., Simon, I., Osman, R., Interfacial water as a "hydration fingerprint" in the noncognate complex of BamHI (2005) Biophysical Journal, 89 (2), pp. 903-911. , DOI 10.1529/biophysj.105.063263
Fischer, S., Verma, C.S., Binding of buried structural water increases the flexibility of proteins (1999) Proceedings of the National Academy of Sciences of the United States of America, 96 (17), pp. 9613-9615. , DOI 10.1073/pnas.96.17.9613
Hamelberg, D., Shen, T., McCammon, J.A., Insight into the role of hydration on protein dynamics (2006) J. Chem. Phys., 125, p. 094905
De Simone, A., Dodson, G.G., Verma, C.S., Zagari, A., Fraternali, F., Prion and water: Tight and dynamical hydration sites have a key role in structural stability (2005) Proceedings of the National Academy of Sciences of the United States of America, 102 (21), pp. 7535-7540. , DOI 10.1073/pnas.0501748102
Silva, J.L., Foguel, D., Hydration, cavities and volume in protein folding, aggregation and amyloid assembly (2009) Phys. Biol., 6, p. 015002
Choudhury, N., Pettitt, B.M., The dewetting transition and the hydrophobic effect (2007) Journal of the American Chemical Society, 129 (15), pp. 4847-4852. , DOI 10.1021/ja069242a
Cramer, C.J., Truhlar, D.G., A universal approach to solvation modeling (2008) Acc. Chem. Res., 41, pp. 760-768
Despa, F., Fernández, A., Berry, R.S., Dielectric modulation of biological water (2004) Phys. Rev. Lett., 93, p. 228104
Fernández, A., Scott, L.R., Adherence of packing defects in soluble proteins (2003) Phys. Rev. Lett., 91, p. 018102
Myllyharju, J., Kivirikko, K.I., Collagens, modifying enzymes and their mutations in humans, flies and worms (2004) Trends in Genetics, 20 (1), pp. 33-43. , DOI 10.1016/j.tig.2003.11.004
Brodsky, B., Persikov, A.V., Molecular structure of the collagen triple helix (2005) Advances in Protein Chemistry, 70, pp. 301-339. , DOI 10.1016/S0065-3233(05)70009-7, Fibrous Proteins Coiled-Coils, Collagen and Elastomers
Okuyama, K., Revisiting the molecular structure of collagen (2008) Connect. Tissue Res., 49, pp. 299-310
Berisio, R., De Simone, A., Vitagliano, L., Role of side chains in collagen triple helix stabilization and partner recognition (2009) J. Pept. Sci., 15, pp. 131-140
Shoulders, M.D., Raines, R.T., Collagen structure and stability (2009) Annu. Rev. Biochem., 78, pp. 929-958
Leitinger, B., Hohenester, E., Mammalian collagen receptors (2007) Matrix Biology, 26 (3), pp. 146-155. , DOI 10.1016/j.matbio.2006.10.007, PII S0945053X06003945
Emsley, J., Convergent recognition of a triple helical hydrophobic motif in collagen (2010) Structure., 18, pp. 1-2
Zong, Y., Xu, Y., Liang, X., Keene, D.R., Hook, A., Gurusiddappa, S., Hook, M., Narayana, S.V.L., A 'Collagen Hug' Model for Staphylococcus aureus CNA binding to collagen (2005) EMBO Journal, 24 (24), pp. 4224-4236. , DOI 10.1038/sj.emboj.7600888
Emsley, J., Knight, C.G., Liddington, R.C., Structural basis of collagen recognition by integrin a2b1 (2000) Cell., 101, pp. 47-56
Hohenester, E., Sasaki, T., Bächinger, H.P., Structural basis of sequence-specific collagen recognition by SPARC (2008) Proc. Natl. Acad. Sci. USA., 105, pp. 18273-18277
Carafoli, F., Bihan, D., Hohenester, E., Crystallographic insight into collagen recognition by discoidin domain receptor 2 (2009) Structure., 17, pp. 1573-1581
Hae, J.K., Coulibaly, F., Clow, F., Proft, T., Baker, E.N., Stabilizing isopeptide bonds revealed in gram-positive bacterial pilus structure (2007) Science, 318 (5856), pp. 1625-1628. , DOI 10.1126/science.1145806
Inouye, K., Sakakibara, S., Prockop, D.J., Effects of the stereo-configuration of the hydroxyl group in 4-hydroxyproline on the triple-helical structures formed by homogenous peptides resembling collagen (1976) Biochim. Biophys. Acta., 420, pp. 133-141
Berisio, R., Vitagliano, L., Mazzarella, L., Zagari, A., Recent progress on collagen triple helix structure, stability and assembly (2002) Protein and Peptide Letters, 9 (2), pp. 107-116
Doi, M., Nishi, Y., Kobayashi, Y., Collagen-like triple helix formation of synthetic (Pro-Pro-Gly) 10 analogues: (4 (S)-hydroxyprolyl-4 (R)-hydroxyprolyl-Gly) 10, (4 (R)-hydroxyprolyl-4 (R)-hydroxyprolyl-Gly) 10 and (4 (S)-fluoroprolyl-4 (R)-fluoroprolyl-Gly) 10 (2005) J. Pept. Sci., 11, pp. 609-616
Holmgren, S.K., Bretscher, L.E., Taylor, K.M., Raines, R.T., A hyperstable collagen mimic (1999) Chemistry and Biology, 6 (2), pp. 63-70. , DOI 10.1016/S1074-5521(99)80003-9
Hess, B., Kutzner, C., Lindahl, E., GROMACS 4: Algorithms for highly efficient, loadβalanced, and scalable molecular simulation (2008) J. Chem. Theory Comput., 4, pp. 435-447
Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., Simmerling, C., Comparison of multiple amber force fields and development of improved protein backbone parameters (2006) Proteins: Structure, Function and Genetics, 65 (3), pp. 712-725. , DOI 10.1002/prot.21123
Sorin, E.J., Pande, V.S., Exploring the helix-coil transition via all-atom equilibrium ensemble simulations (2005) Biophysical Journal, 88 (4), pp. 2472-2493. , DOI 10.1529/biophysj.104.051938
Horn, H.W., Swope, W.C., Head-Gordon, T., Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew (2004) J. Chem. Phys., 120, pp. 9665-9678
Wickstrom, L., Okur, A., Simmerling, C., Evaluating the performance of the ff99SB force field based on NMR scalar coupling data (2009) Biophys. J., 97, pp. 853-856
Makarov, V.A., Andrews, B.K., Pettitt, B.M., Residence times of water molecules in the hydration sites of myoglobin (2000) Biophys. J., 79, pp. 2966-2974
Colombo, G., Meli, M., De Simone, A., Computational studies of the structure, dynamics and native content of amyloid-like fibrils of ribonuclease A (2008) Proteins: Structure, Function and Genetics, 70 (3), pp. 863-872. , DOI 10.1002/prot.21648
De Simone, A., Corrie, J.E., Fraternali, F., Conformation and dynamics of a rhodamine probe attached at two sites on a protein: Implications for molecular structure determination in situ (2008) J. Am. Chem. Soc., 130, pp. 17120-17128
Hamelberg, D., McCammon, J.A., Standard free energy of releasing a localized water molecule from the binding pockets of proteins: Double-decoupling method (2004) Journal of the American Chemical Society, 126 (24), pp. 7683-7689. , DOI 10.1021/ja0377908
Jenkins, C.L., Raines, R.T., Insights on the conformational stability of collagen (2002) Natural Product Reports, 19 (1), pp. 49-59. , DOI 10.1039/a903001h
Stultz, C.M., Localized unfolding of collagen explains collagenase cleavage near imino-poor sites (2002) Journal of Molecular Biology, 319 (5), pp. 997-1003. , DOI 10.1016/S0022-2836(02)00421-7
Sundar Raman, S., Parthasarathi, R., Subramanian, V., Ramasami, T., Role of aspartic acid in collagen structure and stability: A molecular dynamics investigation (2006) Journal of Physical Chemistry B, 110 (41), pp. 20678-20685. , DOI 10.1021/jp0625715
Ravikumar, K.M., Hwang, W., Region-specific role of water in collagen unwinding and assembly (2008) Proteins., 72, pp. 1320-1332
Bella, J., Brodsky, B., Berman, H.M., Hydration structure of a collagen peptide (1995) Structure., 3, pp. 893-906
Okuyama, K., Hongo, C., Fukushima, R., Wu, G., Narita, H., Noguchi, K., Tanaka, Y., Nishino, N., Crystal structures of collagen model peptides with Pro-Hyp-Gly repeating sequence at 1.26 A resolution: Implications for proline ring puckering (2004) Biopolymers - Peptide Science Section, 76 (5), pp. 367-377. , DOI 10.1002/bip.20107
Melacini, G., Bonvin, A.M., Kaptein, R., Hydration dynamics of the collagen triple helix by NMR (2000) J. Mol. Biol., 300, pp. 1041-1049
Hua, L., Huang, X., Berne, B.J., Dynamics of water confined in the interdomain region of a multidomain protein (2006) J. Phys. Chem. B., 110, pp. 3704-3711
De Simone, A., Spadaccini, R., Fraternali, F., Toward the understanding of MNEI sweetness from hydration map surfaces (2006) Biophys. J., 90, pp. 3052-3061
Despa, F., Berry, R.S., The origin of long-range attraction between hydrophobes in water (2007) Biophysical Journal, 92 (2), pp. 373-378. , http://www.biophysj.org/cgi/reprint/92/2/373.pdf, DOI 10.1529/biophysj.106.087023
Meyer, E.E., Lin, Q., Hassenkam, T., Oroudjev, E., Israelachvili, J.N., Origin of the long-range attraction between surfactant-coated surfaces (2005) Proceedings of the National Academy of Sciences of the United States of America, 102 (19), pp. 6839-6842. , DOI 10.1073/pnas.0502110102
Berisio, R., Granata, V., Vitagliano, L., Zagari, A., Imino acids and collagen triple helix stability: Characterization of collagen-like polypeptides containing Hyp-Hyp-Gly sequence repeats (2004) Journal of the American Chemical Society, 126 (37), pp. 11402-11403. , DOI 10.1021/ja047069h
Murphy IV, F.V., Sweet, R.M., Churchill, M.E., The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequencespecific DNA recognition (1999) EMBO J., 18, pp. 6610-6618
Engel, J., Prockop, D.J., Does bound water contribute to the stability of collagen [1] (1998) Matrix Biology, 17 (8-9), pp. 679-680. , DOI 10.1016/S0945-053X(98)90119-6
Nishi, Y., Uchiyama, S., Doi, M., Nishiuchi, Y., Nakazawa, T., Ohkubo, T., Kobayashi, Y., Different effects of 4-hydroxyproline and 4-fluoroproline on the stability of collagen triple helix (2005) Biochemistry, 44 (16), pp. 6034-6042. , DOI 10.1021/bi047887m
Holmgren, S.K., Taylor, K.M., Raines, R.T., Code for collagen's stability deciphered (1998) Nature., 392, pp. 666-667
Schumacher, M., Mizuno, K., Bachinger, H.P., The crystal structure of the collagen-like polypeptide (Glycyl-4(R)- hydroxyprolyl-4(R)-hydroxyprolyl)9 at 1.55 A resolution shows up-puckering of the proline ring in the Xaa position (2005) Journal of Biological Chemistry, 280 (21), pp. 20397-20403. , DOI 10.1074/jbc.M501453200
Shoulders, M.D., Satyshur, K.A., Raines, R.T., Stereoelectronic and steric effects in side chains preorganize a protein main chain (2010) Proc. Natl. Acad. Sci. USA., 107, pp. 559-564
Tame, J.R.H., Murshudov, G.N., Dodson, E.J., Neil, T.K., Dodson, G.G., Higgins, C.F., Wilkinson, A.J., The structural basis of sequence-independent peptide binding by OppA protein (1994) Science, 264 (5165), pp. 1578-1581
Autenrieth, F., Tajkhorshid, E., Luthey-Schulten, Z., Role of water in transient cytochrome c2 docking (2004) J. Phys. Chem. B., 108, pp. 20376-20378
Keskin, O., Ma, B., Nussinov, R., Hot regions in protein-protein interactions: The organization and contribution of structurally conserved hot spot residues (2005) Journal of Molecular Biology, 345 (5), pp. 1281-1294. , DOI 10.1016/j.jmb.2004.10.077, PII S0022283604013981
Li, X., Keskin, O., Ma, B., Nussinov, R., Liang, J., Protein-protein interactions: Hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: Implications for docking (2004) Journal of Molecular Biology, 344 (3), pp. 781-795. , DOI 10.1016/j.jmb.2004.09.051, PII S0022283604012070
Pal, S. K., Peon, J., Zewail, A. H., Biological water at the protein surface: Dynamical solvation probed directly with femtosecond resolution (2002) Proceedings of the National Academy of Sciences of the United States of America, 99 (4), pp. 1763-1768. , DOI 10. 1073/pnas. 042697899
Papoian, G. A., Ulander, J., Wolynes, P. G., Role of water mediated interactions in protein-protein recognition landscapes (2003) Journal of the American Chemical Society, 125 (30), pp. 9170-9178. , DOI 10. 1021/ja034729u
Silva, J. L., Foguel, D., Hydration, cavities and volume in protein folding, aggregation and amyloid assembly (2009) Phys. Biol., 6, p. 015002
Cramer, C. J., Truhlar, D. G., A universal approach to solvation modeling (2008) Acc. Chem. Res., 41, pp. 760-768
Despa, F., Fern ndez, A., Berry, R. S., Dielectric modulation of biological water (2004) Phys. Rev. Lett., 93, p. 228104
Fern ndez, A., Scott, L. R., Adherence of packing defects in soluble proteins (2003) Phys. Rev. Lett., 91, p. 018102
Shoulders, M. D., Raines, R. T., Collagen structure and stability (2009) Annu. Rev. Biochem., 78, pp. 929-958
Hae, J. K., Coulibaly, F., Clow, F., Proft, T., Baker, E. N., Stabilizing isopeptide bonds revealed in gram-positive bacterial pilus structure (2007) Science, 318 (5856), pp. 1625-1628. , DOI 10. 1126/science. 1145806
Holmgren, S. K., Bretscher, L. E., Taylor, K. M., Raines, R. T., A hyperstable collagen mimic (1999) Chemistry and Biology, 6 (2), pp. 63-70. , DOI 10. 1016/S1074-5521 (99) 80003-9
Sorin, E. J., Pande, V. S., Exploring the helix-coil transition via all-atom equilibrium ensemble simulations (2005) Biophysical Journal, 88 (4), pp. 2472-2493. , DOI 10. 1529/biophysj. 104. 051938
Horn, H. W., Swope, W. C., Head-Gordon, T., Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew (2004) J. Chem. Phys., 120, pp. 9665-9678
Makarov, V. A., Andrews, B. K., Pettitt, B. M., Residence times of water molecules in the hydration sites of myoglobin (2000) Biophys. J., 79, pp. 2966-2974
Jenkins, C. L., Raines, R. T., Insights on the conformational stability of collagen (2002) Natural Product Reports, 19 (1), pp. 49-59. , DOI 10. 1039/a903001h
Stultz, C. M., Localized unfolding of collagen explains collagenase cleavage near imino-poor sites (2002) Journal of Molecular Biology, 319 (5), pp. 997-1003. , DOI 10. 1016/S0022-2836 (02) 00421-7
Ravikumar, K. M., Hwang, W., Region-specific role of water in collagen unwinding and assembly (2008) Proteins., 72, pp. 1320-1332
Meyer, E. E., Lin, Q., Hassenkam, T., Oroudjev, E., Israelachvili, J. N., Origin of the long-range attraction between surfactant-coated surfaces (2005) Proceedings of the National Academy of Sciences of the United States of America, 102 (19), pp. 6839-6842. , DOI 10. 1073/pnas. 0502110102
Murphy IV, F. V., Sweet, R. M., Churchill, M. E., The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequencespecific DNA recognition (1999) EMBO J., 18, pp. 6610-6618
Holmgren, S. K., Taylor, K. M., Raines, R. T., Code for collagen's stability deciphered (1998) Nature., 392, pp. 666-667
Shoulders, M. D., Satyshur, K. A., Raines, R. T., Stereoelectronic and steric effects in side chains preorganize a protein main chain (2010) Proc. Natl. Acad. Sci. USA., 107, pp. 559-564
Tame, J. R. H., Murshudov, G. N., Dodson, E. J., Neil, T. K., Dodson, G. G., Higgins, C. F., Wilkinson, A. J., The structural basis of sequence-independent peptide binding by OppA protein (1994) Science, 264 (5165), pp. 1578-1581
Role of hydration in collagen recognition by bacterial adhesins
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