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Alvarado YJ, Olivarez Y, Lossada C, Vera-Villalobos J, Paz JL, Vera E, Loroño M, Vivas A, Torres FJ, Jeffreys LN, Hurtado-León ML, González-Paz L. Interaction of the new inhibitor paxlovid (PF-07321332) and ivermectin with the monomer of the main protease SARS-CoV-2: A volumetric study based on molecular dynamics, elastic networks, classical thermodynamics and SPT. Comput Biol Chem 2022; 99:107692. [PMID: 35640480 PMCID: PMC9107165 DOI: 10.1016/j.compbiolchem.2022.107692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 02/04/2023]
Abstract
The COVID-19 pandemic has accelerated the study of drugs, most notably ivermectin and more recently Paxlovid (PF-07321332) which is in phase III clinical trials with experimental data showing covalent binding to the viral protease Mpro. Theoretical developments of catalytic site-directed docking support thermodynamically feasible non-covalent binding to Mpro. Here we show that Paxlovid binds non-covalently at regions other than the catalytic sites with energies stronger than reported and at the same binding site as the ivermectin B1a homologue, all through theoretical methodologies, including blind docking. We volumetrically characterize the non-covalent interaction of the ivermectin homologues (avermectins B1a and B1b) and Paxlovid with the mMpro monomer, through molecular dynamics and scaled particle theory (SPT). Using the fluctuation-dissipation theorem (FDT), we estimated the electric dipole moment fluctuations at the surface of each of complex involved in this study, with similar trends to that observed in the interaction volume. Using fluctuations of the intrinsic volume and the number of flexible fragments of proteins using anisotropic and Gaussian elastic networks (ANM+GNM) suggests the complexes with ivermectin are more dynamic and flexible than the unbound monomer. In contrast, the binding of Paxlovid to mMpro shows that the mMpro-PF complex is the least structurally dynamic of all the species measured in this investigation. The results support a differential molecular mechanism of the ivermectin and PF homologues in the mMpro monomer. Finally, the results showed that Paxlovid despite beingbound in different sites through covalent or non-covalent forms behaves similarly in terms of its structural flexibility and volumetric behaviour.
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Affiliation(s)
- Ysaias José Alvarado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Bolivarian Republic of Venezuela.
| | - Yosmari Olivarez
- Universidad del Zulia (LUZ). Facultad Experimental de Ciencias (FEC), Departamento de Quimica, Laboratorio de Electronica Molecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Carla Lossada
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Joan Vera-Villalobos
- Facultad de Ciencias Naturales y Matemáticas, Departamento de Química y Ciencias Ambientales, Laboratorio de Análisis Químico Instrumental (LAQUINS), Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Eddy Vera
- Universidad del Zulia (LUZ). Facultad Experimental de Ciencias (FEC), Departamento de Quimica, Laboratorio de Electronica Molecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Marcos Loroño
- Departamento Académico de Química Analítica e Instrumental, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Alejandro Vivas
- Universidad del Zulia (LUZ). Facultad Experimental de Ciencias (FEC), Departamento de Quimica, Laboratorio de Electronica Molecular, 4001 Maracaibo, Bolivarian Republic of Venezuela
| | - Fernando Javier Torres
- Grupo de Química Computacional y Teórica (QCT-UR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Grupo de Química Computacional y Teórica (QCT-USFQ), Instituto de Simulación Computacional (ISC-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Laura N Jeffreys
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - María Laura Hurtado-León
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), Maracaibo 4001, Zulia, Bolivarian Republic of Venezuela
| | - Lenin González-Paz
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), Maracaibo 4001, Zulia, Bolivarian Republic of Venezuela; Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Estudios Botanicos y Agroforestales, (CEBA), Laboratorio de Proteccion Vegetal, 4001 Maracaibo, Bolivarian Republic of Venezuela.
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2
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Jirasek F, Garcia EJ, Hackemann E, Galeotti N, Hasse H. Influence of pH and Salts on Partial Molar Volume of Lysozyme and Bovine Serum Albumin in Aqueous Solutions. Chem Eng Technol 2018; 41:2337-2345. [PMID: 31007400 PMCID: PMC6472598 DOI: 10.1002/ceat.201800242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/27/2018] [Accepted: 09/03/2018] [Indexed: 11/12/2022]
Abstract
The partial molar volume of lysozyme and bovine serum albumin in aqueous solutions at different pH values and in aqueous solutions containing sodium chloride, ammonium chloride, sodium sulfate, or ammonium sulfate at different concentrations at pH 7.0 was investigated experimentally at 298.15 K and 1 bar. It was found that the influence of the pH value and the salts on the partial molar volume of the proteins is small, but trends were measurable. Furthermore, the partial molar volume of lysozyme in pure water at different pH values and in aqueous solutions with different sodium chloride concentrations at pH 7.0 was predicted by molecular simulations. The predictions are in good agreement with the experimental data.
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Affiliation(s)
- Fabian Jirasek
- University of KaiserslauternLaboratory of Engineering Thermodynamics (LTD)Erwin-Schrödinger-Strasse 4467663KaiserslauternGermany
| | - Edder J. Garcia
- University of KaiserslauternLaboratory of Engineering Thermodynamics (LTD)Erwin-Schrödinger-Strasse 4467663KaiserslauternGermany
| | - Eva Hackemann
- University of KaiserslauternLaboratory of Engineering Thermodynamics (LTD)Erwin-Schrödinger-Strasse 4467663KaiserslauternGermany
| | - Nadia Galeotti
- University of KaiserslauternLaboratory of Engineering Thermodynamics (LTD)Erwin-Schrödinger-Strasse 4467663KaiserslauternGermany
| | - Hans Hasse
- University of KaiserslauternLaboratory of Engineering Thermodynamics (LTD)Erwin-Schrödinger-Strasse 4467663KaiserslauternGermany
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3
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Galassi VV, Del Popolo MG, Fischer TM, Wilke N. Molecular Explanation for the Abnormal Flux of Material into a Hot Spot in Ester Monolayers. J Phys Chem B 2017; 121:5621-5632. [PMID: 28493697 DOI: 10.1021/acs.jpcb.7b00949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Langmuir monolayers of certain surfactants show a negative derivative of the surface pressure with respect to temperature. In these monolayers, a local temperature gradient leads to local yielding of the solid phase to a kinetically flowing liquid, so that the material flows toward the hotter regions that act as sinks. The accumulation of material leads to the formation of nonequilibrium multilamellar bubbles of different sizes. Here we investigate the molecular factors leading to such a peculiar behavior. First, we identify the required structural molecular moieties, and second we vary the composition of the subphase in order to analyze its influence. We conclude that esters appear to be unique in two key aspects: they form monolayers whose compression isotherms shift to lower areas as the temperature increases, and thus collapse into a hot spot; and they bind weakly to the aqueous subphase, i.e., water does not attach to the monolayer at the molecular level, but only supports it. Molecular simulations for a selected system confirm and help explain the observed behavior: surfactant molecules form a weak hydrogen bonding network, which is disrupted upon heating, and also the molecular tilting changes with temperature, leading to changes in the film density.
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Affiliation(s)
- Vanesa V Galassi
- CONICET, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo , Mendoza M5502JMA, Argentina
| | - Mario G Del Popolo
- CONICET, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo , Mendoza M5502JMA, Argentina
| | - Thomas M Fischer
- Institut für Experimentalphysik, Universität Bayreuth , 95440 Bayreuth, Germany
| | - Natalia Wilke
- Institut für Experimentalphysik, Universität Bayreuth , 95440 Bayreuth, Germany.,Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC-CONICET), Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba , Córdoba X5000HUA, Argentina
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4
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Guerra MER, Fadel V, Maltarollo VG, Baldissera G, Honorio KM, Ruggiero JR, Dos Santos Cabrera MP. MD simulations and multivariate studies for modeling the antileishmanial activity of peptides. Chem Biol Drug Des 2017; 90:501-510. [PMID: 28267894 DOI: 10.1111/cbdd.12970] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/29/2017] [Accepted: 02/21/2017] [Indexed: 11/30/2022]
Abstract
Leishmaniasis, a protozoan-caused disease, requires alternative treatments with minimized side-effects and less prone to resistance development. Antimicrobial peptides represent a possible choice to be developed. We report on the prospection of structural parameters of 23 helical antimicrobial and leishmanicidal peptides as a tool for modeling and predicting the activity of new peptides. This investigation is based on molecular dynamic simulations (MD) in mimetic membrane environment, as most of these peptides share the feature of interacting with phospholipid bilayers. To overcome the lack of experimental data on peptides' structures, we started simulations from designed 100% α-helices. This procedure was validated through comparisons with NMR data and the determination of the structure of Decoralin-amide. From physicochemical features and MD results, descriptors were raised and statistically related to the minimum inhibitory concentration against Leishmania by the multivariate data analysis technique. This statistical procedure confirmed five descriptors combined by different loadings in five principal components. The leishmanicidal activity depends on peptides' charge, backbone solvation, volume, and solvent-accessible surface area. The generated model possesses good predictability (q2 = 0.715, r2 = 0.898) and is indicative for the most and the least active peptides. This is a novel theoretical path for structure-activity studies combining computational methods that identify and prioritize the promising peptide candidates.
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Affiliation(s)
| | - Valmir Fadel
- Departamento de Física, Universidade Estadual Paulista, São José do Rio Preto, SP, Brazil
| | | | | | - Kathia Maria Honorio
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, SP, Brazil
| | - José Roberto Ruggiero
- Departamento de Física, Universidade Estadual Paulista, São José do Rio Preto, SP, Brazil
| | - Marcia Perez Dos Santos Cabrera
- Departamento de Física, Universidade Estadual Paulista, São José do Rio Preto, SP, Brazil.,Departamento de Química e Ciências Ambientais, Universidade Estadual Paulista, São José do Rio Preto, SP, Brazil
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Del Galdo S, Marracino P, D'Abramo M, Amadei A. In silico characterization of protein partial molecular volumes and hydration shells. Phys Chem Chem Phys 2016; 17:31270-7. [PMID: 26549621 DOI: 10.1039/c5cp05891k] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In this paper we present a computational approach, based on NVT molecular dynamics trajectories, that allows the direct evaluation of the protein partial molecular volume. The results obtained for five different globular proteins demonstrate the accuracy of this computational procedure in reproducing protein partial molecular volumes, providing quantitative characterization of the hydration shell in terms of the protein excluded volume, hydration shell ellipsoidal volume and related solvent density. Remarkably, our data indicate for the hydration shell a ≈10% solvent density increase with respect to the liquid water bulk density, in excellent agreement with the available experimental data.
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Affiliation(s)
- Sara Del Galdo
- Department of Chemical Science and Technology, University of Roma Tor Vergata, via della Ricerca Scientifica, 00133 Roma, Italy.
| | - Paolo Marracino
- Department of Information Engineering, Electronics and Telecommunications, University of Roma Sapienza, via Eudossiana 18, 00184 Roma, Italy
| | - Marco D'Abramo
- Department of Chemistry, University of Roma Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Andrea Amadei
- Department of Chemical Science and Technology, University of Roma Tor Vergata, via della Ricerca Scientifica, 00133 Roma, Italy.
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6
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Voloshin VP, Medvedev NN, Smolin N, Geiger A, Winter R. Exploring volume, compressibility and hydration changes of folded proteins upon compression. Phys Chem Chem Phys 2015; 17:8499-508. [PMID: 25685984 DOI: 10.1039/c5cp00251f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the physical basis of the structure, stability and function of proteins in solution, including extreme environmental conditions, requires knowledge of their temperature and pressure dependent volumetric properties. One physical-chemical property of proteins that is still little understood is their partial molar volume and its dependence on temperature and pressure. We used molecular dynamics simulations of aqueous solutions of a typical monomeric folded protein, staphylococcal nuclease (SNase), to study and analyze the pressure dependence of the apparent volume, Vapp, and its components by the Voronoi-Delaunay method. We show that the strong decrease of Vapp with pressure (βT = 0.95 × 10(-5) bar(-1), in very good agreement with the experimental value) is essentially due to the compression of the molecular volume, VM, ultimately, of its internal voids, V. Changes of the intrinsic volume (defined as the Voronoi volume of the molecule), the contribution of the solvent to the apparent volume, and of the contribution of the boundary voids between the protein and the solvent have also been studied and quantified in detail. The pressure dependences of the volumetric characteristics obtained are compared with the temperature dependent behavior of these quantities and with corresponding results for a natively unfolded polypeptide.
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Affiliation(s)
- Vladimir P Voloshin
- Institute of Chemical Kinetics and Combustion, SB RAS, 630090 Novosibirsk, Russia
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Ploetz EA, Smith PE. Infinitely dilute partial molar properties of proteins from computer simulation. J Phys Chem B 2014; 118:12844-54. [PMID: 25325571 PMCID: PMC4234426 DOI: 10.1021/jp508632h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A detailed understanding of temperature and pressure effects on an infinitely dilute protein's conformational equilibrium requires knowledge of the corresponding infinitely dilute partial molar properties. Established molecular dynamics methodologies generally have not provided a way to calculate these properties without either a loss of thermodynamic rigor, the introduction of nonunique parameters, or a loss of information about which solute conformations specifically contributed to the output values. Here we implement a simple method that is thermodynamically rigorous and possesses none of the above disadvantages, and we report on the method's feasibility and computational demands. We calculate infinitely dilute partial molar properties for two proteins and attempt to distinguish the thermodynamic differences between a native and a denatured conformation of a designed miniprotein. We conclude that simple ensemble average properties can be calculated with very reasonable amounts of computational power. In contrast, properties corresponding to fluctuating quantities are computationally demanding to calculate precisely, although they can be obtained more easily by following the temperature and/or pressure dependence of the corresponding ensemble averages.
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Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University , 213 CBC Building, Manhattan, Kansas 66506-0401, United States
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Voloshin VP, Kim AV, Medvedev NN, Winter R, Geiger A. Calculation of the volumetric characteristics of biomacromolecules in solution by the Voronoi–Delaunay technique. Biophys Chem 2014; 192:1-9. [DOI: 10.1016/j.bpc.2014.05.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 05/15/2014] [Accepted: 05/15/2014] [Indexed: 11/16/2022]
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9
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Medvedev NN, Voloshin VP, Kim AV, Anikeenko AV, Geiger A. Culation of partial molar volume and its components for molecular dynamics models of dilute solutions. J STRUCT CHEM+ 2014. [DOI: 10.1134/s0022476613080088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Fast Calculation of the Empty Volume in Molecular Systems by the Use of Voronoi-Delaunay Subsimplexes. TRANSACTIONS ON COMPUTATIONAL SCIENCE XXII 2014. [DOI: 10.1007/978-3-642-54212-1_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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Oleinikova A, Brovchenko I. Thermodynamic Properties of Hydration Water around Solutes: Effect of Solute Size and Water–Solute Interaction. J Phys Chem B 2012; 116:14650-9. [DOI: 10.1021/jp306781y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- A. Oleinikova
- Physical Chemistry, Dortmund University of Technology, Otto-Hahn-Str. 6, Dortmund, D-44227,
Germany
| | - I. Brovchenko
- Physical Chemistry, Dortmund University of Technology, Otto-Hahn-Str. 6, Dortmund, D-44227,
Germany
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12
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Voloshin VP, Medvedev NN, Andrews MN, Burri RR, Winter R, Geiger A. Volumetric Properties of Hydrated Peptides: Voronoi–Delaunay Analysis of Molecular Simulation Runs. J Phys Chem B 2011; 115:14217-28. [DOI: 10.1021/jp2050788] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimir P. Voloshin
- Institute of Chemical Kinetics and Combustion, SB RAS, 630090 Novosibirsk, Russia
| | - Nikolai N. Medvedev
- Institute of Chemical Kinetics and Combustion, SB RAS, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | | | - R. Reddy Burri
- Physikalische Chemie, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Roland Winter
- Physikalische Chemie, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Alfons Geiger
- Physikalische Chemie, Technische Universität Dortmund, 44221 Dortmund, Germany
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Brovchenko I, Andrews MN, Oleinikova A. Thermal stability of the hydrogen-bonded water network in the hydration shell of islet amyloid polypeptide. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2011; 23:155105. [PMID: 21451234 DOI: 10.1088/0953-8984/23/15/155105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The effect of temperature on the connectivity of hydrogen bonds in the hydration shells of the islet amyloid polypeptides (IAPPs) is studied by means of computer simulations. The hydrogen-bonded network of hydration water homogeneously envelopes a peptide at low temperature and breaks into an ensemble of small clusters upon heating. This thermal break occurs via a percolation transition, which is not found to be sensitive to the chemical modifications of IAPP (IAPP with and without a disulfide bridge, human and rat IAPP). The radius of gyration of IAPP starts to increase when the hydration water network breaks upon heating. The fluctuations of the number of intra-peptide hydrogen bonds show negative correlation with the fraction of molecules in the largest cluster of hydration water. The thermal stability of the network of hydration water is enhanced upon increasing number of intra-peptide hydrogen bonds, which makes the peptide surface more hydrophobic. The thermal stabilities of the hydrogen-bonded water networks in the hydration shells of IAPPs and of several other biomolecules are found to be rather similar: the network breaks between 300 and 330 K, i.e., in the temperature interval where the biological activity of living organisms is maximal.
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Affiliation(s)
- I Brovchenko
- Physical Chemistry, Dortmund University of Technology, Otto-Hahn-Straße 6, Dortmund, D-44227, Germany.
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Andrews MN, Winter R. Comparing the structural properties of human and rat islet amyloid polypeptide by MD computer simulations. Biophys Chem 2010; 156:43-50. [PMID: 21266296 DOI: 10.1016/j.bpc.2010.12.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Revised: 12/26/2010] [Accepted: 12/26/2010] [Indexed: 10/18/2022]
Abstract
Conformational properties of the full-length human and rat islet amyloid polypeptide 1-37 (amyloidogenic hIAPP and non-amyloidogenic rIAPP, respectively) were studied at 310 and 330 K by MD simulations both for the cysteine (reduced IAPP) and cystine (oxidized IAPP) moieties. At all temperatures studied, IAPP does not adopt a well-defined conformation and is essentially random coil in solution, although transient helices appear forming along the peptide between residues 8 and 22, particularly in the reduced form. Above the water percolation transition (at 320 K), the reduced hIAPP moiety presents a considerably diminished helical content remaining unstructured, while the natural cystine moiety reaches a rather compact state, presenting a radius of gyration that is almost 10% smaller and characterized by intrapeptide H-bonds that form many β-bridges in the C-terminal region. This compact conformation presents a short end-to-end distance and seems to form through the formation of β-sheet conformations in the C-terminal region with a minimization of the Y/F distances in a two-step mechanism: the first step taking place when the Y37/F23 distance is ~1.1 nm, and subsequently Y37/F15 reaches its minimum of ~0.86 nm. rIAPP, which does not aggregate, also presents transient helical conformations. A particularly stable helix is located in proximity of the C-terminal region, starting from residues L27 and P28. Our MD simulations show that P28 in rIAPP influences the secondary structure of IAPP by stabilizing the peptide in helical conformations. When this helix is not present, the peptide presents bends or H-bonded turns at P28 that seem to inhibit the formation of the β-bridges seen in hIAPP. Conversely, hIAPP is highly disordered in the C-terminal region, presenting transient isolated β-strand conformations, particularly at higher temperatures and when the natural disulfide bond is present. Such conformational differences found in our simulations could be responsible for the different aggregational propensities of the two different homologues. In fact, the fragment 30-37, which is identical in both homologues, is known to aggregate in vitro, hence the overall sequence must be responsible for the amyloidogenicity of hIAPP. The increased helicity in rIAPP induced by the serine-to-proline variation at residue 28 seems to be a plausible inhibitor of its aggregation.
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Affiliation(s)
- Maximilian N Andrews
- Faculty of Chemistry, Physical Chemistry I—Biophysical Chemistry, TU Dortmund University, Germany.
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