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Roy UC, Bandyopadhyay P. Correlation between protein conformations and water structure and thermodynamics at high pressure: A molecular dynamics study of the Bovine Pancreatic Trypsin Inhibitor (BPTI) protein. J Chem Phys 2023; 158:095102. [PMID: 36889972 DOI: 10.1063/5.0124837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Pressure-induced perturbation of a protein structure leading to its folding-unfolding mechanism is an important yet not fully understood phenomenon. The key point here is the role of water and its coupling with protein conformations as a function of pressure. In the current work, using extensive molecular dynamics simulation at 298 K, we systematically examine the coupling between protein conformations and water structures of pressures of 0.001, 5, 10, 15, 20 kbar, starting from (partially) unfolded structures of the protein Bovine Pancreatic Trypsin Inhibitor (BPTI). We also calculate localized thermodynamics at those pressures as a function of protein-water distance. Our findings show that both protein-specific and generic effects of pressure are operating. In particular, we found that (1) the amount of increase in water density near the protein depends on the protein structural heterogeneity; (2) the intra-protein hydrogen bond decreases with pressure, while the water-water hydrogen bond per water in the first solvation shell (FSS) increases; protein-water hydrogen bonds also found to increase with pressure, (3) with pressure hydrogen bonds of waters in the FSS getting twisted; and (4) water's tetrahedrality in the FSS decreases with pressure, but it is dependent on the local environment. Thermodynamically, at higher pressure, the structural perturbation of BPTI is due to the pressure-volume work, while the entropy decreases with the increase of pressure due to the higher translational and rotational rigidity of waters in the FSS. The local and subtle effects of pressure, found in this work, are likely to be typical of pressure-induced protein structure perturbation.
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Affiliation(s)
- Umesh C Roy
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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2
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Wang Y, Sheng Y, Zhang Y, Geng F, Cao J. Effect of High Pressure/Heating Combination on the Structure and Texture of Chinese Traditional Pig Trotter Stewed with Soy Sauce. Foods 2022; 11:foods11152248. [PMID: 35954017 PMCID: PMC9368740 DOI: 10.3390/foods11152248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/09/2022] [Accepted: 07/17/2022] [Indexed: 02/01/2023] Open
Abstract
In order to clarify the effect of a high pressure/heating combination on the texture of Chinese traditional pig trotter with soy sauce, textural parameters (springiness, chewiness, hardness, and gumminess), the secondary structures, cross-links, decorin (DCN), glycosaminoglycans (GAGs) levels, and the histochemical morphology of collagen fibers under different treatments (0.1 MPa, 150 MPa, 300 MPa, 0.1 MPa + 50 °C, 150 MPa + 50 °C, and 300 MPa + 50 °C) were assessed. At room temperature, the 150 and 300 MPa treatments increased the hardness and chewiness of the pig trotter with weak denaturation of collagen proteins compared with the control group. Textural parameters were improved at 300 MPa + 50 °C, accompanied by an ultrastructural collapse of collagen fibers, the reduction in cross-links, DCN and GAGs levels, and unfolded triple-helix structure. We concluded that the positive effects on the textural parameters of pig trotters by a combination of treatments could be attributed to the collapse of collagen structure.
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Affiliation(s)
- Ying Wang
- Department of Food Science and Technology, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China; (Y.W.); (Y.Z.)
| | - Yanan Sheng
- Department of Food Science and Technology, Ningbo University, Ningbo 315211, China;
| | - Yuemei Zhang
- Department of Food Science and Technology, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China; (Y.W.); (Y.Z.)
| | - Fang Geng
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biologicalengineering, Chengdu University, Chengdu 610106, China;
| | - Jinxuan Cao
- Department of Food Science and Technology, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China; (Y.W.); (Y.Z.)
- Correspondence: ; Tel.: +86-18758823803
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3
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Maiti A, Daschakraborty S. Can Urea and Trimethylamine- N-oxide Prevent the Pressure-Induced Phase Transition of Lipid Membrane? J Phys Chem B 2022; 126:1426-1440. [PMID: 35139638 DOI: 10.1021/acs.jpcb.1c08891] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Organisms dwelling in ocean trenches are exposed to the high hydrostatic pressure of ocean water. Increasing pressure can alter the membrane packing density and fluidity and trigger the fluid-to-gel phase transition. To combat environmental stress, the organisms synthesize small polar solutes, which are known as osmolytes. Urea and trimethylamine-N-oxide (TMAO) are two such solutes found in deep-sea creatures. While TMAO stabilizes protein, urea induces protein denaturation. These solutes strongly influence the packing density and membrane fluidity of the lipid bilayer at different conditions. But can these solutes affect the pressure-induced phase transition of the lipid membrane? In the present work, we have studied the effect of these two solutes on pressure-induced fluid-to-gel phase transition based on the all-atom molecular dynamics (MD) simulation approach. A high-pressure-stimulated fluid-to-gel phase transition of the membrane is seen at 800 bar, which is consistent with previous experiments. We have also observed that in the low-pressure region (1-400 bar), urea slightly increases the membrane fluidity where TMAO decreases the same. However, the phase transition pressure remains almost unchanged on the addition of urea while TMAO shifts the phase transition toward a lower pressure. We have found that the hydrogen (H)-bond interaction between lipid and urea plays an important role in preserving the fluidity of the membrane in the low-pressure zone. However, at a higher pressure, both water and urea are excluded from the membrane surface. TMAO is also excluded from the interfacial region of the membrane at all pressures. Exclusion from the membrane surface further triggers the phase transition of the lipid membrane from the fluid to gel phase at a high pressure.
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Affiliation(s)
- Archita Maiti
- Department of Chemistry, Indian Institute of Technology Patna, Bihar 801106, India
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4
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Usman M, Sahar A, Inam‐Ur‐Raheem M, Rahman UU, Sameen A, Aadil RM. Gelatin extraction from fish waste and potential applications in food sector. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.15286] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Muhammad Usman
- National Institute of Food Science and Technology University of Agriculture Faisalabad 38000 Pakistan
| | - Amna Sahar
- National Institute of Food Science and Technology University of Agriculture Faisalabad 38000 Pakistan
- Department of Food Engineering University of Agriculture Faisalabad 38000 Pakistan
| | - Muhammad Inam‐Ur‐Raheem
- National Institute of Food Science and Technology University of Agriculture Faisalabad 38000 Pakistan
| | - Ubaid ur Rahman
- School of Food and Agricultural Sciences University of Management and Technology Lahore Pakistan
| | - Aysha Sameen
- National Institute of Food Science and Technology University of Agriculture Faisalabad 38000 Pakistan
| | - Rana Muhammad Aadil
- National Institute of Food Science and Technology University of Agriculture Faisalabad 38000 Pakistan
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5
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Huang Y, Zhang X, Suo H. Interaction between β-lactoglobulin and EGCG under high-pressure by molecular dynamics simulation. PLoS One 2021; 16:e0255866. [PMID: 34932559 PMCID: PMC8691620 DOI: 10.1371/journal.pone.0255866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/29/2021] [Indexed: 11/19/2022] Open
Abstract
The binding between β-lactoglobulin and epigallocatechin gallate (EGCG) under the pressure of 600 MPa was explored using molecular docking and molecular dynamics (MD) simulation. EGCG bound mainly in two regions with site 1 in internal cavity of the β-barrel and site 2 on the surface of protein. 150 ns MD was performed starting from the structure with the optimal binding energy at the two sites in molecular docking, respectively. It was found that the protein fluctuated greatly when small molecule bound to site 2 at 0.1 MPa, and the protein fluctuation and solvent accessible surface area became smaller under high-pressure. The binding of small molecules made the protein structure more stable with increasing of α-helix and β-sheet, while high-pressure destroyed α-helix of protein. The binding energy of small molecules at site 1was stronger than that at site 2 under 0.1 MPa, with stronger van der Waals and hydrophobic interaction at site 1 while more hydrogen bonds were present at site 2. The binding energy of both sites weakened under high-pressure, especially at site 1, causing the binding force to be weaker at site 1 than that at site 2 under high-pressure.
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Affiliation(s)
- Yechuan Huang
- College of Bioengineering, Jingchu University of Technology, Jingmen, PR China
- * E-mail: ,
| | - Xicai Zhang
- College of Bioengineering, Jingchu University of Technology, Jingmen, PR China
| | - Huayi Suo
- College of Food Science, Southwest University, Chongqing, PR China
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6
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Rai DK, Gillilan RE, Huang Q, Miller R, Ting E, Lazarev A, Tate MW, Gruner SM. High-pressure small-angle X-ray scattering cell for biological solutions and soft materials. J Appl Crystallogr 2021; 54:111-122. [PMID: 33841059 PMCID: PMC7941318 DOI: 10.1107/s1600576720014752] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/06/2020] [Indexed: 11/10/2022] Open
Abstract
Pressure is a fundamental thermodynamic parameter controlling the behavior of biological macromolecules. Pressure affects protein denaturation, kinetic parameters of enzymes, ligand binding, membrane permeability, ion trans-duction, expression of genetic information, viral infectivity, protein association and aggregation, and chemical processes. In many cases pressure alters the molecular shape. Small-angle X-ray scattering (SAXS) is a primary method to determine the shape and size of macromolecules. However, relatively few SAXS cells described in the literature are suitable for use at high pressures and with biological materials. Described here is a novel high-pressure SAXS sample cell that is suitable for general facility use by prioritization of ease of sample loading, temperature control, mechanical stability and X-ray background minimization. Cell operation at 14 keV is described, providing a q range of 0.01 < q < 0.7 Å-1, pressures of 0-400 MPa and an achievable temperature range of 0-80°C. The high-pressure SAXS cell has recently been commissioned on the ID7A beamline at the Cornell High Energy Synchrotron Source and is available to users on a peer-reviewed proposal basis.
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Affiliation(s)
- Durgesh K. Rai
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Richard E. Gillilan
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Robert Miller
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
- Department of Chemistry, Cornell University, Ithaca, NY 14853, USA
| | - Edmund Ting
- Pressure BioSciences Inc., South Easton, MA 02375, USA
| | | | - Mark W. Tate
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - Sol M. Gruner
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
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7
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Gasic AG, Cheung MS. A Tale of Two Desolvation Potentials: An Investigation of Protein Behavior under High Hydrostatic Pressure. J Phys Chem B 2020; 124:1619-1627. [DOI: 10.1021/acs.jpcb.9b10734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Andrei G. Gasic
- Department of Physics, University of Houston, Houston, Texas 77204, United States
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Margaret S. Cheung
- Department of Physics, University of Houston, Houston, Texas 77204, United States
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
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8
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Uralcan B, Debenedetti PG. Computational Investigation of the Effect of Pressure on Protein Stability. J Phys Chem Lett 2019; 10:1894-1899. [PMID: 30939023 DOI: 10.1021/acs.jpclett.9b00545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Previous studies show parabolic or elliptical regions of protein stability in the pressure-temperature ( P, T) plane. The construction of stability diagrams requires accessing a sufficiently broad ( P, T) range, which is often frustrated by ice formation in experiments and sampling challenges in simulations. We perform a fully atomistic computational study of the miniprotein Trp-cage over the range of temperatures 210 ≤ T ≤ 420 K and pressures P ≤ 5 kbar and construct the corresponding stability diagram. At ambient temperature, pressure shifts the conformational states toward unfolding. Below 250 K, the native fold's stability depends nonmonotonically on pressure. While cold unfolding and thermal denaturation differ significantly at ambient pressure, they exhibit progressive similarity at elevated pressures. At ambient pressure, cold denaturation is an enthalpically driven process that preserves significant elements of Trp-cage's secondary structure. In contrast, cold unfolding at elevated pressures involves a more substantial loss of secondary and tertiary structure, similar to thermal denaturation.
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Affiliation(s)
- Betul Uralcan
- Department of Chemical and Biological Engineering , Princeton University , Princeton , New Jersey 08544 , United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering , Princeton University , Princeton , New Jersey 08544 , United States
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9
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Espinosa YR, Caffarena ER, Grigera JR. The role of hydrophobicity in the cold denaturation of proteins under high pressure: A study on apomyoglobin. J Chem Phys 2019; 150:075102. [PMID: 30795674 DOI: 10.1063/1.5080942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
An exciting debate arises when microscopic mechanisms involved in the denaturation of proteins at high pressures are explained. In particular, the issue emerges when the hydrophobic effect is invoked, given that hydrophobicity cannot elucidate by itself the volume changes measured during protein unfolding. In this work, we study by the use of molecular dynamics simulations and essential dynamics analysis the relation between the solvation dynamics, volume, and water structure when apomyoglobin is subjected to a hydrostatic pressure regime. Accordingly, the mechanism of cold denaturation of proteins under high-pressure can be related to the disruption of the hydrogen-bond network of water favoring the coexistence of two states, low-density and high-density water, which directly implies in the formation of a molten globule once the threshold of 200 MPa has been overcome.
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Affiliation(s)
- Yanis R Espinosa
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP), Calle 59 Nro 789, B1900BTE La Plata, Argentina
| | - Ernesto R Caffarena
- Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Manguinhos, CEP 21040-360 Rio de Janeiro, Brazil
| | - J Raúl Grigera
- CEQUINOR, Universidad de La Plata and CONICET, 47 y 115, B1900 La Plata, Argentina
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10
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Affiliation(s)
- Filip Persson
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Bertil Halle
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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11
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Uralcan B, Kim SB, Markwalter CE, Prud’homme RK, Debenedetti PG. A Computational Study of the Ionic Liquid-Induced Destabilization of the Miniprotein Trp-Cage. J Phys Chem B 2018; 122:5707-5715. [DOI: 10.1021/acs.jpcb.8b01722] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Betul Uralcan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Sang Beom Kim
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Chester E. Markwalter
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Robert K. Prud’homme
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G. Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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12
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Hölzl C, Kibies P, Imoto S, Frach R, Suladze S, Winter R, Marx D, Horinek D, Kast SM. Design principles for high–pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures. J Chem Phys 2016; 144:144104. [DOI: 10.1063/1.4944991] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Christoph Hölzl
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Patrick Kibies
- Physikalische Chemie III, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Sho Imoto
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Roland Frach
- Physikalische Chemie III, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Saba Suladze
- Physikalische Chemie I, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Roland Winter
- Physikalische Chemie I, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Horinek
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Stefan M. Kast
- Physikalische Chemie III, Technische Universität Dortmund, 44227 Dortmund, Germany
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13
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Vilseck JZ, Tirado-Rives J, Jorgensen WL. Determination of partial molar volumes from free energy perturbation theory. Phys Chem Chem Phys 2015; 17:8407-15. [PMID: 25589343 PMCID: PMC4872387 DOI: 10.1039/c4cp05304d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood-Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm(3) mol(-1). The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute-solvent interactions.
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Affiliation(s)
- Jonah Z Vilseck
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA.
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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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15
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Wakai N, Takemura K, Morita T, Kitao A. Mechanism of deep-sea fish α-actin pressure tolerance investigated by molecular dynamics simulations. PLoS One 2014; 9:e85852. [PMID: 24465747 PMCID: PMC3896411 DOI: 10.1371/journal.pone.0085852] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 12/03/2013] [Indexed: 12/01/2022] Open
Abstract
The pressure tolerance of monomeric α-actin proteins from the deep-sea fish Coryphaenoides armatus and C. yaquinae was compared to that of non-deep-sea fish C. acrolepis, carp, and rabbit/human/chicken actins using molecular dynamics simulations at 0.1 and 60 MPa. The amino acid sequences of actins are highly conserved across a variety of species. The actins from C. armatus and C. yaquinae have the specific substitutions Q137K/V54A and Q137K/L67P, respectively, relative to C. acrolepis, and are pressure tolerant to depths of at least 6000 m. At high pressure, we observed significant changes in the salt bridge patterns in deep-sea fish actins, and these changes are expected to stabilize ATP binding and subdomain arrangement. Salt bridges between ATP and K137, formed in deep-sea fish actins, are expected to stabilize ATP binding even at high pressure. At high pressure, deep-sea fish actins also formed a greater total number of salt bridges than non-deep-sea fish actins owing to the formation of inter-helix/strand and inter-subdomain salt bridges. Free energy analysis suggests that deep-sea fish actins are stabilized to a greater degree by the conformational energy decrease associated with pressure effect.
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Affiliation(s)
- Nobuhiko Wakai
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Takemura
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Takami Morita
- Research Center for Fisheries Oceanography and Marine Ecosystem, National Research Institute of Fisheries Sciences, Fisheries Research Agency, Kanagawa, Japan
| | - Akio Kitao
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
- * E-mail:
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16
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Pal S, Bandyopadhyay S. Thermal unfolding of barstar and the properties of interfacial water around the unfolded forms. J Chem Phys 2013; 139:235101. [DOI: 10.1063/1.4844255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Abstract
Using a newly developed microsecond pressure-jump apparatus, we monitor the refolding kinetics of the helix-stabilized five-helix bundle protein λ*YA, the Y22W/Q33Y/G46,48A mutant of λ-repressor fragment 6-85, from 3 μs to 5 ms after a 1,200-bar P-drop. In addition to a microsecond phase, we observe a slower 1.4-ms phase during refolding to the native state. Unlike temperature denaturation, pressure denaturation produces a highly reversible helix-coil-rich state. This difference highlights the importance of the denatured initial condition in folding experiments and leads us to assign a compact nonnative helical trap as the reason for slower P-jump-induced refolding. To complement the experiments, we performed over 50 μs of all-atom molecular dynamics P-drop refolding simulations with four different force fields. Two of the force fields yield compact nonnative states with misplaced α-helix content within a few microseconds of the P-drop. Our overall conclusion from experiment and simulation is that the pressure-denatured state of λ*YA contains mainly residual helix and little β-sheet; following a fast P-drop, at least some λ*YA forms misplaced helical structure within microseconds. We hypothesize that nonnative helix at helix-turn interfaces traps the protein in compact nonnative conformations. These traps delay the folding of at least some of the population for 1.4 ms en route to the native state. Based on molecular dynamics, we predict specific mutations at the helix-turn interfaces that should speed up refolding from the pressure-denatured state, if this hypothesis is correct.
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18
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Using simulations to provide the framework for experimental protein folding studies. Arch Biochem Biophys 2012; 531:128-35. [PMID: 23266569 DOI: 10.1016/j.abb.2012.12.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 12/10/2012] [Accepted: 12/14/2012] [Indexed: 12/27/2022]
Abstract
Molecular dynamics simulations are a powerful theoretical tool to model the protein folding process in atomistic details under realistic conditions. Combined with a number of experimental techniques, simulations provide a detailed picture of how a protein folds or unfolds in the presence of explicit solvent and other molecular species, such as cosolvents, osmolytes, cofactors, active binding partners or inert crowding agents. The denaturing effects of temperature, pressure and external mechanical forces can also be probed. Qualitative and quantitative agreement with experiment contributes to a comprehensive molecular picture of protein states along the folding/unfolding pathway. The variety of systems examined reveals key features of the protein folding process.
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19
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Perezzan R, Rey A. Simulating protein unfolding under pressure with a coarse-grained model. J Chem Phys 2012; 137:185102. [DOI: 10.1063/1.4765057] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
It has been known for nearly 100 years that pressure unfolds proteins, yet the physical basis of this effect is not understood. Unfolding by pressure implies that the molar volume of the unfolded state of a protein is smaller than that of the folded state. This decrease in volume has been proposed to arise from differences between the density of bulk water and water associated with the protein, from pressure-dependent changes in the structure of bulk water, from the loss of internal cavities in the folded states of proteins, or from some combination of these three factors. Here, using 10 cavity-containing variants of staphylococcal nuclease, we demonstrate that pressure unfolds proteins primarily as a result of cavities that are present in the folded state and absent in the unfolded one. High-pressure NMR spectroscopy and simulations constrained by the NMR data were used to describe structural and energetic details of the folding landscape of staphylococcal nuclease that are usually inaccessible with existing experimental approaches using harsher denaturants. Besides solving a 100-year-old conundrum concerning the detailed structural origins of pressure unfolding of proteins, these studies illustrate the promise of pressure perturbation as a unique tool for examining the roles of packing, conformational fluctuations, and water penetration as determinants of solution properties of proteins, and for detecting folding intermediates and other structural details of protein-folding landscapes that are invisible to standard experimental approaches.
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