Conformational changes and allosteric communications in human serum albumin due to ligand binding

References

• Ahmed, A. , Villinger, S. , & Gohlke, H. (2010). Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses. Proteins: Structure , Function, and Bioinformatics , 78 , 3341–3352.
   PubMed Web of Science ®Google Scholar
• Altschul, S. F. , Madden, T. L. , Schaffer, A. A. , Zhang, J. , Zhang, Z. , Miller, W. , & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research , 25 , 3389–3402.10.1093/nar/25.17.3389
   PubMed Web of Science ®Google Scholar
• Ascenzi, P. , Bocedi, A. , Notari, S. , Menegatti, E. , & Fasano, M. (2005). Heme impairs allosterically drug binding to human serum albumin sudlow’s site I. Biochemical and Biophysical Research Communications , 334 , 481–486.10.1016/j.bbrc.2005.06.127
   PubMed Web of Science ®Google Scholar
• Ascenzi, P. , & Fasano, M. (2010). Allostery in a monomeric protein: The case of human serum albumin. Biophysical Chemistry , 148 , 16–22.10.1016/j.bpc.2010.03.001
   PubMed Web of Science ®Google Scholar
• Atilgan, A. R. , Durell, S. R. , Jernigan, R. L. , Demirel, M. C. , Keskin, O. , & Bahar, I. (2001). Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophysical Journal , 80 , 505–515.10.1016/S0006-3495(01)76033-X
   PubMed Web of Science ®Google Scholar
• Bahar, I. , Atilgan, A. R. , Demirel, M. C. , & Erman, B. (1998). Vibrational dynamics of folded proteins: Significance of slow and fast motions in relation to function and stability. Physical Review Letters , 80 , 2733–2736.10.1103/PhysRevLett.80.2733
   Web of Science ®Google Scholar
• Bahar, I. , Lezon, T. R. , Bakan, A. , & Shrivastava, I. H. (2010). Normal mode analysis of biomolecular structures: Functional mechanisms of membrane proteins. Chemical Reviews , 110 , 1463–1497.
   PubMed Web of Science ®Google Scholar
• Bahar, I. , Lezon, T. R. , Yang, L. W. , & Eyal, E. (2010). Global dynamics of proteins: Bridging between structure and function. Annual Review of Biophysics , 39 , 23–42.
   PubMed Web of Science ®Google Scholar
• Bakan, A. , & Bahar, I. (2009). The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proceedings of the National Academy of Sciences , 106 , 14349–14354.10.1073/pnas.0904214106
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C. , Postma, J. P. M. , Vangunsteren, W. F. , Dinola, A. , & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics , 81 , 3684–3690.10.1063/1.448118
   Web of Science ®Google Scholar
• Berman, H. M. , Westbrook, J. , Feng, Z. , Gilliland, G. , Bhat, T. N. , Weissig, H. , … Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research , 28 , 235–242.10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Best, R. B. , Lindorff-Larsen, K. , DePristo, M. A. , & Vendruscolo, M. (2006). Relation between native ensembles and experimental structures of proteins. Proceedings of the National Academy of Sciences , 103 , 10901–10906.10.1073/pnas.0511156103
   PubMed Web of Science ®Google Scholar
• Bhattacharya, A. A. , Grune, T. , & Curry, S. (2000). Crystallographic analysis reveals common modes of binding of medium and long-chain fatty acids to human serum albumin. Journal of Molecular Biology , 303 , 721–732.10.1006/jmbi.2000.4158
   PubMed Web of Science ®Google Scholar
• Boehr, D. D. , Nussinov, R. , & Wright, P. E. (2009). The role of dynamic conformational ensembles in biomolecular recognition. Nature Chemical Biology , 5 , 789–796.10.1038/nchembio.232
   PubMed Web of Science ®Google Scholar
• Bussi, G. , Donadio, D. , & Parrinello, M. (2007). Canonical sampling through velocity rescaling. Journal of Chemical Physics , 126 , 014101.
   PubMed Web of Science ®Google Scholar
• Curry, S. (2009). Lessons from the crystallographic analysis of small molecule binding to human serum albumin. Drug Metabolism and Pharmacokinetics , 24 , 342–357.10.2133/dmpk.24.342
   PubMed Web of Science ®Google Scholar
• Curry, S. , Mandelkow, H. , Brick, P. , & Franks, N. (1998). Crystal structure of human serum albumin complexed with fatty acid reveals an asymmetric distribution of binding sites. Nature Structural Biology , 5 , 827–835.10.1038/1869
   PubMed Web of Science ®Google Scholar
• Darden, T. , York, D. , & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics , 98 , 10089–10092.10.1063/1.464397
   Web of Science ®Google Scholar
• Eargle, J. , & Luthey-Schulten, Z. (2012). NetworkView: 3D display and analysis of protein. RNA interaction networks. Bioinformatics , 28 , 3000–3001.10.1093/bioinformatics/bts546
   PubMed Web of Science ®Google Scholar
• Edgar, R. C. (2004). Muscle: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research , 32 , 1792–1797.10.1093/nar/gkh340
   PubMed Web of Science ®Google Scholar
• Emekli, U. , Schneidman-Duhovny, D. , Wolfson, H. J. , Nussinov, R. , & Haliloglu, T. (2008). HingeProt: Automated prediction of hinges in protein structures. Proteins-Structure Function and Bioinformatics , 70 , 1219–1227.
   PubMed Web of Science ®Google Scholar
• Fanali, G. , di Masi, A. , Trezza, V. , Marino, M. , Fasano, M. , & Ascenzi, P. (2012). Human serum albumin: From bench to bedside. Molecular Aspects of Medicine , 33 , 209–290.10.1016/j.mam.2011.12.002
   PubMed Web of Science ®Google Scholar
• Fanali, G. , Pariani, G. , Ascenzi, P. , & Fasano, M. (2009). Allosteric and binding properties of Asp1-Glu382 truncated recombinant human serum albumin – An optical and NMR spectroscopic investigation. FEBS Journal , 276 , 2241–2250.10.1111/ejb.2009.276.issue-8
   PubMed Web of Science ®Google Scholar
• Frauenfelder, H. , Sligar, S. G. , & Wolynes, P. G. (1991). The energy landscapes and motions of proteins. Science , 254 , 1598–1603.
   PubMed Web of Science ®Google Scholar
• Fujiwara, S. , & Amisaki, T. (2008). Identification of high affinity fatty acid binding sites on human serum albumin by MM-PBSA method. Biophysical Journal , 94 , 95–103.10.1529/biophysj.107.111377
   PubMed Web of Science ®Google Scholar
• Ghuman, J. , Zunszain, P. A. , Petitpas, I. , Bhattacharya, A. A. , Otagiri, M. , & Curry, S. (2005). Structural basis of the drug-binding specificity of human serum albumin. Journal of Molecular Biology , 353 , 38–52.10.1016/j.jmb.2005.07.075
   PubMed Web of Science ®Google Scholar
• Haliloglu, T. , Keskin, O. , Ma, B. Y. , & Nussinov, R. (2005). How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. Biophysical Journal , 88 , 1552–1559.10.1529/biophysj.104.051342
   PubMed Web of Science ®Google Scholar
• Hess, B. , Bekker, H. , Berendsen, H. J. C. , & Fraaije, J. G. E. M. (1997). Lincs: A linear constraint solver for molecular simulations. Journal of Computational Chemistry , 18 , 1463–1472.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Henzler-Wildman, K. , & Kern, D. (2007). Dynamic personalities of proteins. Nature , 450 , 964–972.
   PubMed Web of Science ®Google Scholar
• Hinsen, K. (1998). Analysis of domain motions by approximate normal mode calculations. Proteins: Structure, Function, and Genetics , 33 , 417–429.10.1002/(ISSN)1097-0134
   PubMed Web of Science ®Google Scholar
• Horn, H. W. , Swope, W. C. , Pitera, J. W. , Madura, J. D. , Dick, T. J. , Hura, G. L. , & Head-Gordon, T. (2004). Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. The Journal of Chemical Physics , 120 , 9665–9678.10.1063/1.1683075
   PubMed Web of Science ®Google Scholar
• Humphrey, W. , Dalke, A. , & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics , 14 , 27–38.
   Google Scholar
• Jana, B. , Adkar, B. V. , Biswas, R. , & Bagchi, B. (2011). Dynamic coupling between the LID and NMP domain motions in the catalytic conversion of ATP and AMP to ADP by adenylate kinase. The Journal of Chemical Physics , 134 , 035101.
   PubMed Web of Science ®Google Scholar
• Koshland, D. E. (1958). Application of a theory of enzyme specificity to protein synthesis. Proceedings of the National Academy of Sciences , 44 , 98–104.10.1073/pnas.44.2.98
   PubMed Web of Science ®Google Scholar
• Krenzel, E. S. , Chen, Z. , & Hamilton J. A. (2013). Correspondence of fatty acid and drug binding sites on human serum albumin: A two-dimensional nuclear magnetic resonance study. Biochemistry , 52 , 1559–1567.10.1021/bi301458b
   PubMed Web of Science ®Google Scholar
• Kundu, S. , Sorensen, D. C. , & Phillips, G. N. (2004). Automatic domain decomposition of proteins by a Gaussian network model. Proteins-Structure Function and Bioinformatics , 57 , 725–733.10.1002/(ISSN)1097-0134
   PubMed Web of Science ®Google Scholar
• Lange, O. F. , & Grubmuller, H. (2006). Generalized correlation for biomolecular dynamics. Proteins , 62 , 1053–1061.
   PubMed Web of Science ®Google Scholar
• Lange, O. F. , Lakomek, N. A. , Fares, C. , Schroder, G. F. , Walter, K. F. , Becker, S. , ... de Groot, B. L. (2008). Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science , 320 , 1471–1475.
   PubMed Web of Science ®Google Scholar
• Lockless, S. W. , & Ranganathan, R. (1999). Evolutionarily conserved pathways of energetic connectivity in protein families. Science , 286 , 295–299.10.1126/science.286.5438.295
   PubMed Web of Science ®Google Scholar
• Ma, B. , Kumar, S. , Tsai, C. J. , & Nussinov, R. (1999). Folding funnels and binding mechanisms. Protein Engineering Design and Selection , 12 , 713–720.10.1093/protein/12.9.713
   Web of Science ®Google Scholar
• Miyamoto, S. , & Kollman, P. A. (1992). Settle: An analytical version of the shake and rattle algorithm for rigid water models. Journal of Computational Chemistry , 13 , 952–962.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Monod, J. , Wyman, J. , & Changeux, J. P. (1965). On the nature of allosteric transitions: A plausible model. Journal of Molecular Biology , 12 , 88–118.10.1016/S0022-2836(65)80285-6
   PubMed Web of Science ®Google Scholar
• Orellana, L. , Rueda, M. , Ferrer-Costa, C. , Lopez-Blanco, J. R. , Chacon, P. , & Orozco, M. (2010). Approaching elastic network models to molecular dynamics flexibility. Journal of Chemical Theory and Computation , 6 , 2910–2923.10.1021/ct100208e
   PubMed Web of Science ®Google Scholar
• Parrinello, M. , & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics , 52 , 7182–7190.10.1063/1.328693
   Web of Science ®Google Scholar
• Peng, C. , & Head-Gordon, T. (2011). The dynamical mechanism of auto-inhibition of AMP-activated protein kinase. Plos Computational Biology , 7 , e1004009.
   Web of Science ®Google Scholar
• Peng, C. , Zhang, L. Q. , & Head-Gordon, T. (2010). Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions. Biophysical Journal , 98 , 2356–2364.
   PubMed Web of Science ®Google Scholar
• Petitpas, I. , Grune, T. , Bhattacharya, A. A. , & Curry, S. (2001). Crystal structures of human serum albumin complexed with monounsaturated and polyunsaturated fatty acids. Journal of Molecular Biology , 314 , 955–960.10.1006/jmbi.2000.5208
   PubMed Web of Science ®Google Scholar
• Romo, T. D. , & Grossfield, A. (2011). Validating and improving elastic network models with molecular dynamics simulations. Proteins: Structure, Function and Bioinformatics , 79 , 23–34.
   PubMed Web of Science ®Google Scholar
• Rueda, M. , Chacon, P. , & Orozco, M. (2007). Thorough validation of protein normal mode analysis: A comparative study with essential dynamics. Structure , 15 , 565–575.
   PubMed Web of Science ®Google Scholar
• Sanejouand, Y. H. (2013). Elastic network models: Theoretical and empirical foundations. Methods in Molecular Biology , 924 , 601–616.
   PubMedGoogle Scholar
• Sethi, A. , Eargle, J. , Black, A. A. , & Luthey-Schulten, Z. (2009). Dynamical networks in tRNA:protein complexes. Proceedings of the National Academy of Sciences , 106 , 6620–6625.10.1073/pnas.0810961106
   PubMed Web of Science ®Google Scholar
• Simard, J. R. , Zunszain, P. A. , Ha, C. E. , Yang, J. S. , Bhagavan, N. V. , Petitpas, I. , … Hamilton, J. A. (2005). Locating high-affinity fatty acid-binding sites on albumin by X-ray crystallography and NMR spectroscopy. Proceedings of the National Academy of Sciences , 102 , 17958–17963.10.1073/pnas.0506440102
   PubMed Web of Science ®Google Scholar
• Simard, J. R. , Zunszain, P. A. , Hamilton, J. A. , & Curry, S. (2006). Location of high and low affinity fatty acid binding sites on human serum albumin revealed by NMR drug-competition analysis. Journal of Molecular Biology , 361 , 336–351.10.1016/j.jmb.2006.06.028
   PubMed Web of Science ®Google Scholar
• Skjaerven, L. , Martinez, A. , & Reuter, N. (2011). Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit. Proteins: Structure, Function and Bioinformatics , 79 , 232–243.
   PubMed Web of Science ®Google Scholar
• Smock, R. G. , & Gierasch, L. M. (2009). Sending signals dynamically. Science , 324 , 198–203.
   PubMed Web of Science ®Google Scholar
• Smock, R. G. , Rivoire, O. , Russ, W. P. , Swain, J. F. , Leibler, S. , Ranganathan, R. , & Gierasch, L. M. (2010). An interdomain sector mediating allostery in Hsp70 molecular chaperones. Molecular Systems Biology , 6 , 414.
   PubMed Web of Science ®Google Scholar
• Sudhamalla, B. , Gokara, M. , Ahalawat, N. , Amooru, D. G. , & Subramanyam, R. (2010). Molecular dynamics simulation and binding studies of β-sitosterol with human serum albumin and its biological relevance. The Journal of Physical Chemistry B , 114 , 9054–9062.10.1021/jp102730p
   PubMed Web of Science ®Google Scholar
• Suel, G. M. , Lockless, S. W. , Wall, M. A. , & Ranganathan, R. (2003). Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nature Structural Biology , 10 , 59–69.10.1038/nsb881
   PubMedGoogle Scholar
• Sugio, S. , Kashima, A. , Mochizuki, S. , Noda, M. , & Kobayashi, K. (1999). Crystal structure of human serum albumin at 2.5 A resolution. Protein Engineering Design and Selection , 12 , 439–446.10.1093/protein/12.6.439
   Web of Science ®Google Scholar
• Tama, F. , & Brooks, C. L. (2006). Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annual Review of Biophysics and Biomolecular Structure , 35 , 115–133.
   PubMedGoogle Scholar
• Tama, F. , Gadea, F. X. , Marques, O. , & Sanejouand, Y. H. (2000). Building-block approach for determining low-frequency normal modes of macromolecules. Proteins-Structure Function and Genetics , 41 , 1–7.10.1002/(ISSN)1097-0134
   PubMed Web of Science ®Google Scholar
• Tokuriki, N. , & Tawfik, D. S. (2009). Protein dynamism and evolvability. Science , 324 , 203–207.
   PubMed Web of Science ®Google Scholar
• Van Der Spoel, D. , Lindahl, E. , Hess, B. , Groenhof, G. , Mark, A. E. , & Berendsen, H. J. (2005). Gromacs: Fast, flexible, and free. Journal of Computational Chemistry , 26 , 1701–1718.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Vanwart, A. T. , Eargle, J. , Luthey-Schulten, Z. , & Amaro, R. E. (2012). Exploring residue component contributions to dynamical network models of allostery. Journal of Chemical Theory and Computation , 8 , 2949–2961.10.1021/ct300377a
   PubMed Web of Science ®Google Scholar
• Wang, J. , Wang, W. , Kollman, P. A. , & Case, D. A. (2006). Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling , 25 , 247–260.10.1016/j.jmgm.2005.12.005
   PubMed Web of Science ®Google Scholar
• Wang, J. , Wolf, R. M. , Caldwell, J. W. , Kollman, P. A. , & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry , 25 , 1157–1174.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Yang, L. , Song, G. , Carriquiry, A. , & Jernigan, R. L. (2008). Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes. Structure , 16 , 321–330.10.1016/j.str.2007.12.011
   PubMed Web of Science ®Google Scholar
• Yang, L. , Song, G. , & Jernigan, R. L. (2007). How well can we understand large-scale protein motions using normal modes of elastic network models? Biophysical Journal , 93 , 920–929.
   PubMed Web of Science ®Google Scholar
• Yang, L. , Song, G. , & Jernigan, R. L. (2009). Protein elastic network models and the ranges of cooperativity. Proceedings of the National Academy of Sciences , 106 , 12347–12352.10.1073/pnas.0902159106
   PubMed Web of Science ®Google Scholar
• Zheng, W. (2008). A unification of the elastic network model and the Gaussian network model for optimal description of protein conformational motions and fluctuations. Biophysical Journal , 94 , 3853–3857.10.1529/biophysj.107.125831
   PubMed Web of Science ®Google Scholar
• Zheng, W. J. , Brooks, B. R. , & Thirumalai, D. (2006). Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proceedings of the National Academy of Sciences , 103 , 7664–7669.
   PubMed Web of Science ®Google Scholar
• Zunszain, P. A. , Ghuman, J. , Komatsu, T. , Tsuchida, E. , & Curry, S. (2003). Crystal structural analysis of human serum albumin complexed with hemin and fatty acid. BMC Structural Biology , 3 , 1–9.
   PubMed Web of Science ®Google Scholar
• Zunszain, P. A. , Ghuman, J. , McDonagh, A. F. , & Curry, S. (2008). Crystallographic analysis of human serum albumin complexed with 4Z,15E-bilirubin-IXα. Journal of Molecular Biology , 381 , 394–406.10.1016/j.jmb.2008.06.016
   PubMed Web of Science ®Google Scholar