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Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pKα calculations and molecular dynamics simulations (90 views)

Langella E, Improta R, Crescenzi O, Barone V

Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2006 Jul 1; 64(1): 167-177.

Abstract
A thorough study of the acid-base behavior of the four histidines and the other titratable residues of the structured domain of human prion protein (125-228) is presented. By using multitautomer electrostatic calculations, average titration curves have been built for all titratable residues, using the whole bundles of NMR structures determined at pH 4.5 and 7.0. According to our results, (1) only histidine residues are likely to be involved in the first steps of the pH-driven conformational transition of prion protein; (2) the pKα's of His140 and His177 are ≈7.0, whereas those of His155 and His187 are < 5.5.10-ns long molecular dynamics simulations have been performed on five different models, corresponding to the most significant combinations of histidine protonation states. A critical comparison between the available NMDR structures and our computational results (1) confirms that His155 and His187 are the residues whose protonation is involved in the conformational rearrangement of huPrP in mildly acidic condition, and (2) shows how their protonation leads to the destructuration of the C-terminal part of HB and to the loss of the last turn of HA that represent the crucial microscopic steps of the rearrangement. © 2006 Wiley-Liss, Inc.

Affiliations ▼
*** IBB - CNR Affiliation

Dipartimento di Chimica, Universitá Federico II, Complesso di Monte S. Angelo, Napoli, Italy

Istituto di Biostrutture e Bioimmagini, CNR, Napoli, Italy

Details ▼
Impact factor: 3.73, 5-year impact factor: 2.964

Paper type: Journal Article,

Keywords: Conformational Transition, Electrostatic Calculation, Histidine Titration, Molecular Dynamics, Pkα, Prion Protein, Acid Base Balance, Article, Carboxy Terminal Sequence, Human, Molecular Model, Priority Journal, Protein Conformation, Protein Domain, Protein Structure, Proton Transport, Simulation, Titrimetry, Amino Acid Sequence, Computer Simulation, Hydrogen-Ion Concentration, Kinetics, Magnetic Resonance Spectroscopy, Peptide Fragments,

Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-33744784306&partnerID=40&md5=c76d800af03abb3d316886e04176bebb

References ▼
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Griffith, J. S., Self-replication and scrapie (1967) Nature, 215, pp. 1043-104

Prusiner, S. B., Molecular biology of prion diseases (1991) Science, 252, pp. 1515-1522

Prusiner, S. B., McKinley, M. P., Bowman, K. A., Bolton, D. C., Bendheim, P. E., Groth, D. F., Glenner, G. G., Scrapie prions aggregate to form amyloid-like birefringent rods (1983) Cell, 35, pp. 349-358

Donne, D. G., Viles, J. H., Groth, D., Mehlhorn, I., James, T. L., Cohen, F. E., Prusiner, S. B., Structure of the recombinant full-length hamster prion protein PrP (29-231): The N terminus is highly flexible (1997) Proc Natl Acad Sci USA, 94, pp. 13452-13457

Knaus, K. J., Morillas, M., Swietnicki, W., Malone, M., Surewicz, W., Yee, V. C., Crystal structure of the human prion protein reveals a mechanism for oligomerization (2001) Nat Struct Biol, 8, pp. 770-774

Haire, L. F., Whyte, S. M., Vasisht, N., Gill, A. C., Verma, C., Dodson, E. J., Dodson, G. G., The crystal structure of the globular domain of sheep prion protein (2004) J Mol Biol, 336, pp. 1175-1183

Pan, K. M., Baldwin, M., Nguyen, J., Gasset, M., Serban, A., Groth, D., Huang, Z., Conversion of -helixes into -sheets features in the formation of the scrapie prion proteins (1993) Proc Natl Acad Sci USA, 90, pp. 10962-10966

Leffers, K. W., Schell, J., Jansen, K., Lucassen, R., Kaimann, T., Nagel-Steger, L., Tatzelt, J., The structural transition of the prion protein into its pathogenic conformation is induced by unmasking hydrophobic sites (2004) J Mol Biol, 344, pp. 839-853

Armen, R. S., DeMarco, M. L., Alonso, D. O., Daggett, V., Pauling and Corey's -pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease (2004) Proc Natl Acad Sci USA, 101, pp. 11622-11627

Kelly, J. W., The environmental dependency of protein folding best explains prion and amyloid diseases (1998) Proc Natl Acad Sci USA, 95, pp. 930-932

Jackson, G. S., Hill, A. F., Joseph, C., Hosszu, L., Power, A., Waltho, J. P., Clarke, A. R., Multiple folding pathways for heterologously expressed human prion protein (1999) Biochim Biophys Acta, 1431, pp. 1-13

Alonso, D. O. V., DeArmond, S. J., Cohen, F. E., Daggett, V., Mapping the early steps in the pH-induced conformational conversion of the prion protein (2001) Proc Natl Acad Sci USA, 98, pp. 2985-2989

Alonso, D. O. V., An, C., Daggett, V., Simulations of biomolecules: Characterization of the early steps in the pH-induced conformational conversion of the hamster, bovine and human forms of the prion protein (2002) Philos Trans R Soc Lond A, 360, pp. 1165-1178

Pauly, P. C., Harris, D. A., Copper stimulates endocytosis of the prion protein (1998) J Biol Chem, 273, pp. 33107-33110

Hornshaw, M. P., McDermott, J. R., Candy, J. M., Copper binding to the N-terminal tandem repeat regions of mammalian and avian prion protein (1995) Biochem Biophys Res Commun, 207, pp. 621-629

St ckel, J., Safar, J., Wallace, A. C., Cohen, F. E., Pnisiner, S. B., Prion protein selectively binds copper (II) ions (1998) Biochemistry, 37, pp. 7185-7193

Cereghetti, G. M., Schweiger, A., Glockshuber, R., Van Doorslaer, S., Stability and Cu (II) binding of prion protein variants related to inherited human prion diseases (2003) Biophys J, 84, pp. 1985-1997

Cereghetti, M. G., Schweiger, A., Glockshuber, R., Van Doorslaer, S., Electron paramagnetic resonance evidence for binding of Cu2+ to the C-terminal domain of the murine prion protein (2001) Biophys J, 81, pp. 516-525

Ullmann, G. M., Knapp, E. -W., Electrostatic models for computing protonation and redox equilibria in proteins (1999) Eur Biophys J, 28, pp. 533-551

Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz Jr., K. M., Furguson, D. M., Spellmeyer, D. C., Kollman, P. A., A second generation force field for the simulation of proteins, nucleic acids, and organic molecules (1995) J Am Chem Soc, 117, pp. 5179-5197

Van Gunsteren, W. F., Berendsen, H. J. C., (1987) Gromos87 Manual, , Biomos BV, Niienborgh 4, 9747 AG Groningen, The Netherlands

Van Buuren, A. R., Marrink, S. J., Berendsen, H. J. C., A molecular dynamics study of the decane/water interface (1993) J Phys Chem, 97, pp. 9206-9212

Georgescu, R. E., Alexov, E. G., Gunner, M. R., Combining conformational flexibility and continuum electrostatics for calculating pK s in proteins (2002) Biophysical J, 83, pp. 1731-1748

Van Vlijmen, H. W., Schaefer, M., Karplus, M., Improving the accuracy of protein pK calculations: Conformational averaging versus the average structure (1998) Proteins, 33, pp. 145-158

You, T. J., Bashford, D., Conformation and hydrogen ion titration of proteins: A continuum electrostatic model with conformational flexibility (1995) Biophys J, 69, pp. 1721-1733

Ullmann, G. M., Noodelmann, L., Case, D. A., Density functional calculation of pK values and redox potentials in the bovine Rieske iron-sulfur protein (2002) J Biol Inorg Chem, 7, pp. 632-639

Ironside, J. W., Prion diseases in man (1998) J Pathol, 186, pp. 227-234

Wlodek, S. T., Antosiewicz, J., McCammon, J. A., Prediction of titration properties of structures of a protein derived from molecular dynamics trajectories (1997) Protein Sci, 6, pp. 373-382


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4 Records (4 excluding Abstracts and Conferences).
Total impact factor: 12.554 (12.554 excluding Abstracts and Conferences).
Total 5-year impact factor: 13.336 (13.336 excluding Abstracts and Conferences).



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