1
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Galano‐Frutos JJ, Sancho J. Energy, water, and protein folding: A molecular dynamics-based quantitative inventory of molecular interactions and forces that make proteins stable. Protein Sci 2024; 33:e4905. [PMID: 38284492 PMCID: PMC10804899 DOI: 10.1002/pro.4905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 12/12/2023] [Accepted: 01/05/2024] [Indexed: 01/30/2024]
Abstract
Protein folding energetics can be determined experimentally on a case-by-case basis but it is not understood in sufficient detail to provide deep control in protein design. The fundamentals of protein stability have been outlined by calorimetry, protein engineering, and biophysical modeling, but these approaches still face great difficulty in elucidating the specific contributions of the intervening molecules and physical interactions. Recently, we have shown that the enthalpy and heat capacity changes associated to the protein folding reaction can be calculated within experimental error using molecular dynamics simulations of native protein structures and their corresponding unfolded ensembles. Analyzing in depth molecular dynamics simulations of four model proteins (CI2, barnase, SNase, and apoflavodoxin), we dissect here the energy contributions to ΔH (a key component of protein stability) made by the molecular players (polypeptide and solvent molecules) and physical interactions (electrostatic, van der Waals, and bonded) involved. Although the proteins analyzed differ in length, isoelectric point and fold class, their folding energetics is governed by the same quantitative pattern. Relative to the unfolded ensemble, the native conformations are enthalpically stabilized by comparable contributions from protein-protein and solvent-solvent interactions, and almost equally destabilized by interactions between protein and solvent molecules. The native protein surface seems to interact better with water than the unfolded one, but this is outweighed by the unfolded surface being larger. From the perspective of physical interactions, the native conformations are stabilized by van de Waals and Coulomb interactions and destabilized by conformational strain arising from bonded interactions. Also common to the four proteins, the sign of the heat capacity change is set by interactions between protein and solvent molecules or, from the alternative perspective, by Coulomb interactions.
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Affiliation(s)
- Juan José Galano‐Frutos
- Biocomputation and Complex Systems Physics Institute (BIFI)‐Joint Unit GBsC‐CSICUniversity of ZaragozaZaragozaSpain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de CienciasUniversity of ZaragozaZaragozaSpain
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)‐Joint Unit GBsC‐CSICUniversity of ZaragozaZaragozaSpain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de CienciasUniversity of ZaragozaZaragozaSpain
- Aragon Health Research Institute (IIS Aragón)ZaragozaSpain
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2
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Seto T. General anesthetic binding mode via hydration with weak affinity and molecular discrimination: General anesthetic dissolution in interfacial water of the common binding site of GABA A receptor. Biophys Physicobiol 2023; 20:e200005. [PMID: 38496235 PMCID: PMC10941959 DOI: 10.2142/biophysico.bppb-v20.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 01/23/2023] [Indexed: 01/25/2023] Open
Abstract
The GABAA receptor (GABAAR) is a target channel for the loss of awareness of general anesthesia. General anesthetic (GA) spans a wide range of chemical structures, such as monatomic molecules, barbital acids, phenols, ethers, and alkanes. GA has a weak binding affinity, and the affinity has a characteristic that correlates with the solubility in olive oil rather than the molecular shape. The GA binding site of GABAAR is common to GAs and exists in the transmembrane domain of the GABAAR intersubunit. In this study, the mechanism of GA binding, which allows binding of various GAs with intersubunit selectivity, was elucidated from the hydration analysis of the binding site. Regardless of the diverse GA chemical structures, a strong correlation was observed between the binding free energy and total dehydration number of the binding process. The GA binding free energy was more involved in the binding dehydration and showed molecular recognition that allowed for the binding of various GA structures via binding site hydration. We regarded the GA substitution for the interfacial water molecule of the binding site as a dissolution into the interfacial hydration layer. The elucidation of the GA binding mechanism mediated by hydration at the GABAAR common binding site provides a rationale for the combined use of anesthetics in medical practice and its combination adjustments via drug interactions.
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Affiliation(s)
- Tomoyoshi Seto
- Department of Anesthesiology, School of Medicine, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan
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3
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Kalayan J, Chakravorty A, Warwicker J, Henchman RH. Total free energy analysis of fully hydrated proteins. Proteins 2023; 91:74-90. [PMID: 35964252 PMCID: PMC10087023 DOI: 10.1002/prot.26411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
The total free energy of a hydrated biomolecule and its corresponding decomposition of energy and entropy provides detailed information about regions of thermodynamic stability or instability. The free energies of four hydrated globular proteins with different net charges are calculated from a molecular dynamics simulation, with the energy coming from the system Hamiltonian and entropy using multiscale cell correlation. Water is found to be most stable around anionic residues, intermediate around cationic and polar residues, and least stable near hydrophobic residues, especially when more buried, with stability displaying moderate entropy-enthalpy compensation. Conversely, anionic residues in the proteins are energetically destabilized relative to singly solvated amino acids, while trends for other residues are less clear-cut. Almost all residues lose intraresidue entropy when in the protein, enthalpy changes are negative on average but may be positive or negative, and the resulting overall stability is moderate for some proteins and negligible for others. The free energy of water around single amino acids is found to closely match existing hydrophobicity scales. Regarding the effect of secondary structure, water is slightly more stable around loops, of intermediate stability around β strands and turns, and least stable around helices. An interesting asymmetry observed is that cationic residues stabilize a residue when bonded to its N-terminal side but destabilize it when on the C-terminal side, with a weaker reversed trend for anionic residues.
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Affiliation(s)
- Jas Kalayan
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Arghya Chakravorty
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Jim Warwicker
- Manchester Institute of Biotechnology and School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Richard H Henchman
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
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4
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Hartl J, Friesen S, Johannsmann D, Buchner R, Hinderberger D, Blech M, Garidel P. Dipolar Interactions and Protein Hydration in Highly Concentrated Antibody Formulations. Mol Pharm 2022; 19:494-507. [PMID: 35073097 DOI: 10.1021/acs.molpharmaceut.1c00587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Molecular interaction mechanisms in high-concentrated protein systems are of fundamental importance for the rational development of biopharmaceuticals such as monoclonal antibody (mAb) formulations. In such high-concentrated protein systems, the intermolecular distances between mAb molecules are reduced to the size of the protein diameter (approx. 10 nm). Thus, protein-protein interactions are more pronounced at high concentrations; so a direct extrapolation of physicochemical properties obtained from measurements at a low protein concentration of the corresponding properties at a high protein concentration is highly questionable. Besides the charge-charge interaction, the effects of molecular crowding, dipolar interaction, changes in protein hydration, and self-assembling tendency become more relevant. Here, protein hydration, protein dipole moment, and protein-protein interactions were studied in protein concentrations up to 200 mg/mL (= 1.3 mM) in different formulations for selected mAbs using dielectric relaxation spectroscopy (DRS). These data are correlated with the second virial coefficient, A2, the diffusion interaction parameter, kD, the elastic shear modulus, G', and the dynamic viscosity, η. When large contributions of dipolar protein-protein interactions were observed, the tendency of self-assembling and an increase in solution viscosity were detected. These effects were examined using specific buffer conditions. Furthermore, different types of protein-water interactions were identified via DRS, whereby the effect of high protein concentration on protein hydration was investigated for different high-concentrated liquid formulations (HCLFs).
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Affiliation(s)
- Josef Hartl
- Institute of Chemistry, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Sergej Friesen
- Institute of Physical and Theoretical Chemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Diethelm Johannsmann
- Institute of Physical Chemistry, Clausthal University of Technology, 38678 Clausthal-Zellerfeld, Germany
| | - Richard Buchner
- Institute of Physical and Theoretical Chemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, 88397 Biberach an der Riss, Germany
| | - Patrick Garidel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, 88397 Biberach an der Riss, Germany
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5
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Racca JD, Chatterjee D, Chen YS, Rai RK, Yang Y, Georgiadis MM, Haas E, Weiss MA. Tenuous transcriptional threshold of human sex determination. II. SRY exploits water-mediated clamp at the edge of ambiguity. Front Endocrinol (Lausanne) 2022; 13:1029177. [PMID: 36568077 PMCID: PMC9771472 DOI: 10.3389/fendo.2022.1029177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
Y-encoded transcription factor SRY initiates male differentiation in therian mammals. This factor contains a high-mobility-group (HMG) box, which mediates sequence-specific DNA binding with sharp DNA bending. A companion article in this issue described sex-reversal mutations at box position 72 (residue 127 in human SRY), invariant as Tyr among mammalian orthologs. Although not contacting DNA, the aromatic ring seals the domain's minor wing at a solvent-exposed junction with a basic tail. A seeming paradox was posed by the native-like biochemical properties of inherited Swyer variant Y72F: its near-native gene-regulatory activity is consistent with the father's male development, but at odds with the daughter's XY female somatic phenotype. Surprisingly, aromatic rings (Y72, F72 or W72) confer higher transcriptional activity than do basic or polar side chains generally observed at solvated DNA interfaces (Arg, Lys, His or Gln). Whereas biophysical studies (time-resolved fluorescence resonance energy transfer and heteronuclear NMR spectroscopy) uncovered only subtle perturbations, dissociation of the Y72F complex was markedly accelerated relative to wild-type. Studies of protein-DNA solvation by molecular-dynamics (MD) simulations of an homologous high-resolution crystal structure (SOX18) suggest that Y72 para-OH anchors a network of water molecules at the tail-DNA interface, perturbed in the variant in association with nonlocal conformational fluctuations. Loss of the Y72 anchor among SRY variants presumably "unclamps" its basic tail, leading to (a) rapid DNA dissociation despite native affinity and (b) attenuated transcriptional activity at the edge of sexual ambiguity. Conservation of Y72 suggests that this water-mediated clamp operates generally among SRY and metazoan SOX domains.
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Affiliation(s)
- Joseph D. Racca
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
- *Correspondence: Joseph D. Racca, ; Michael A. Weiss,
| | - Deepak Chatterjee
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yen-Shan Chen
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Ratan K. Rai
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yanwu Yang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Millie M. Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Elisha Haas
- Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
| | - Michael A. Weiss
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
- *Correspondence: Joseph D. Racca, ; Michael A. Weiss,
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6
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Nakagawa H, Tamada T. Hydration and its Hydrogen Bonding State on a Protein Surface in the Crystalline State as Revealed by Molecular Dynamics Simulation. Front Chem 2021; 9:738077. [PMID: 34733819 PMCID: PMC8558535 DOI: 10.3389/fchem.2021.738077] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/29/2021] [Indexed: 11/13/2022] Open
Abstract
Protein hydration is crucial for the stability and molecular recognition of a protein. Water molecules form a hydration water network on a protein surface via hydrogen bonds. This study examined the hydration structure and hydrogen bonding state of a protein, staphylococcal nuclease, at various hydration levels in its crystalline state by all-atom molecular dynamics (MD) simulation. Hydrophilic residues were more hydrated than hydrophobic residues. As the water content increases, both types of residues were uniformly more hydrated. The number of hydrogen bonds per single water asymptotically approaches 4, the same as bulk water. The distances and angles of hydrogen bonds in hydration water in the protein crystal were almost the same as those in the tetrahedral structure of bulk water regardless of the hydration level. The hydrogen bond structure of hydration water observed by MD simulations of the protein crystalline state was compared to the Hydrogen and Hydration Database for Biomolecule from experimental protein crystals.
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Affiliation(s)
- Hiroshi Nakagawa
- Materials Science Research Center, Japan Atomic Energy Agency, Ibaraki, Japan.,J-PARC Center, Japan Atomic Energy Agency, Ibaraki, Japan
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Ibaraki, Japan
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7
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Kalayan J, Curtis RA, Warwicker J, Henchman RH. Thermodynamic Origin of Differential Excipient-Lysozyme Interactions. Front Mol Biosci 2021; 8:689400. [PMID: 34179093 PMCID: PMC8226134 DOI: 10.3389/fmolb.2021.689400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/25/2021] [Indexed: 01/15/2023] Open
Abstract
Understanding the intricate interplay of interactions between proteins, excipients, ions and water is important to achieve the effective purification and stable formulation of protein therapeutics. The free energy of lysozyme interacting with two kinds of polyanionic excipients, citrate and tripolyphosphate, together with sodium chloride and TRIS-buffer, are analysed in multiple-walker metadynamics simulations to understand why tripolyphosphate causes lysozyme to precipitate but citrate does not. The resulting multiscale decomposition of energy and entropy components for water, sodium chloride, excipients and lysozyme reveals that lysozyme is more stabilised by the interaction of tripolyphosphate with basic residues. This is accompanied by more sodium ions being released into solution from tripolyphosphate than for citrate, whilst the latter instead has more water molecules released into solution. Even though lysozyme aggregation is not directly probed in this study, these different mechanisms are suspected to drive the cross-linking between lysozyme molecules with vacant basic residues, ultimately leading to precipitation.
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Affiliation(s)
- Jas Kalayan
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.,Department of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Robin A Curtis
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.,Departments of Chemical Engineering and Analytical Science, The University of Manchester, Manchester, United Kingdom
| | - Jim Warwicker
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.,Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.,Department of Chemistry, The University of Manchester, Manchester, United Kingdom.,Faculty of Medicine and Health, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
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8
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Abstract
Water molecules in the immediate vicinity of biomacromolecules and biomimetic organized assemblies often exhibit a markedly distinct behavior from that of their bulk counterparts. The overall sluggish behavior of biological water substantially affects the stability and integrity of biomolecules, as well as the successful execution of various crucial water-mediated biochemical phenomena. In this Minireview, insights are provided into the features of truncated hydrogen-bond networks that grant biological water its unique characteristics. In particular, experimental results and theoretical investigations, based on chemical kinetics, are presented that have shed light on the dynamics and energetics governing such characteristics. It is emphasized how such details help us to understand the energetics of biological water, an aspect relatively less explored than its dynamics. For instance, when biological water at hydrophilic or charged protein surfaces was explored, the free energy of H-bond breakage was found to be of the order of 0.4 kcal mol-1 higher than that of bulk water.
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Affiliation(s)
- Aniruddha Adhikari
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea.,Department of Physics, UNIST, 44919, Ulsan, Republic of Korea
| | - Won-Woo Park
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea
| | - Oh-Hoon Kwon
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea.,Center for Soft and Living Matter, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
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9
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Kearney BM, Schwabe M, Marcus KC, Roberts DM, Dechene M, Swartz P, Mattos C. DRoP: Automated detection of conserved solvent-binding sites on proteins. Proteins 2019; 88:152-165. [PMID: 31294888 DOI: 10.1002/prot.25781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 06/19/2019] [Accepted: 07/06/2019] [Indexed: 11/08/2022]
Abstract
Water and ligand binding play critical roles in the structure and function of proteins, yet their binding sites and significance are difficult to predict a priori. Multiple solvent crystal structures (MSCS) is a method where several X-ray crystal structures are solved, each in a unique solvent environment, with organic molecules that serve as probes of the protein surface for sites evolved to bind ligands, while the first hydration shell is essentially maintained. When superimposed, these structures contain a vast amount of information regarding hot spots of protein-protein or protein-ligand interactions, as well as conserved water-binding sites retained with the change in solvent properties. Optimized mining of this information requires reliable structural data and a consistent, objective analysis tool. Detection of related solvent positions (DRoP) was developed to automatically organize and rank the water or small organic molecule binding sites within a given set of structures. It is a flexible tool that can also be used in conserved water analysis given multiple structures of any protein independent of the MSCS method. The DRoP output is an HTML format list of the solvent sites ordered by conservation rank in its population within the set of structures, along with renumbered and recolored PDB files for visualization and facile analysis. Here, we present a previously unpublished set of MSCS structures of bovine pancreatic ribonuclease A (RNase A) and use it together with published structures to illustrate the capabilities of DRoP.
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Affiliation(s)
- Bradley M Kearney
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts.,Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina
| | - Michael Schwabe
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Kendra C Marcus
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Daniel M Roberts
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina
| | - Michelle Dechene
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina
| | - Paul Swartz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts.,Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina
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10
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Setny P, Wiśniewska MD. Water-mediated conformational preselection mechanism in substrate binding cooperativity to protein kinase A. Proc Natl Acad Sci U S A 2018; 115:3852-7. [PMID: 29581285 DOI: 10.1073/pnas.1720024115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Substrate binding cooperativity in protein kinase A (PKA) seems to involve allosteric coupling between the two binding sites. It received significant attention, but its molecular basis still remains not entirely clear. Based on long molecular dynamics of PKA and its complexes, we characterized an allosteric pathway that links ATP binding to the redistribution of states adopted by a protein substrate positioning segment in favor of those that warrant correct binding. We demonstrate that the cooperativity mechanism critically depends on the presence of water in two distinct, buried hydration sites. One holds just a single water molecule, which acts as a switchable hydrogen bond bridge along the allosteric pathway. The second, filled with partially disordered solvent, is essential for providing a smooth free energy landscape underlying conformational transitions of the peptide binding region. Our findings remain in agreement with experimental data, also concerning the cooperativity abolishing effect of the Y204A mutation, and indicate a plausible molecular mechanism contributing to experimentally observed binding cooperativity of the two substrates.
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11
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Sharma V, Jambrina PG, Kaukonen M, Rosta E, Rich PR. Insights into functions of the H channel of cytochrome c oxidase from atomistic molecular dynamics simulations. Proc Natl Acad Sci U S A 2017; 114:E10339-E10348. [PMID: 29133387 PMCID: PMC5715751 DOI: 10.1073/pnas.1708628114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Proton pumping A-type cytochrome c oxidase (CcO) terminates the respiratory chains of mitochondria and many bacteria. Three possible proton transfer pathways (D, K, and H channels) have been identified based on structural, functional, and mutational data. Whereas the D channel provides the route for all pumped protons in bacterial A-type CcOs, studies of bovine mitochondrial CcO have led to suggestions that its H channel instead provides this route. Here, we have studied H-channel function by performing atomistic molecular dynamics simulations on the entire, as well as core, structure of bovine CcO in a lipid-solvent environment. The majority of residues in the H channel do not undergo large conformational fluctuations. Its upper and middle regions have adequate hydration and H-bonding residues to form potential proton-conducting channels, and Asp51 exhibits conformational fluctuations that have been observed crystallographically. In contrast, throughout the simulations, we do not observe transient water networks that could support proton transfer from the N phase toward heme a via neutral His413, regardless of a labile H bond between Ser382 and the hydroxyethylfarnesyl group of heme a In fact, the region around His413 only became sufficiently hydrated when His413 was fixed in its protonated imidazolium state, but its calculated pKa is too low for this to provide the means to create a proton transfer pathway. Our simulations show that the electric dipole moment of residues around heme a changes with the redox state, hence suggesting that the H channel could play a more general role as a dielectric well.
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Affiliation(s)
- Vivek Sharma
- Department of Physics, University of Helsinki, FI-00014, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Pablo G Jambrina
- Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Markus Kaukonen
- Department of Physics, University of Helsinki, FI-00014, Helsinki, Finland
| | - Edina Rosta
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Peter R Rich
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
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12
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Giliberti V, Badioli M, Nucara A, Calvani P, Ritter E, Puskar L, Aziz EF, Hegemann P, Schade U, Ortolani M, Baldassarre L. Heterogeneity of the Transmembrane Protein Conformation in Purple Membranes Identified by Infrared Nanospectroscopy. Small 2017; 13:1701181. [PMID: 28960799 DOI: 10.1002/smll.201701181] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/02/2017] [Indexed: 06/07/2023]
Abstract
Cell membranes are intrinsically heterogeneous, as the local protein and lipid distribution is critical to physiological processes. Even in template systems embedding a single protein type, like purple membranes, there can be a different local response to external stimuli or environmental factors, resulting in heterogeneous conformational changes. Despite the dramatic advances of microspectroscopy techniques, the identification of the conformation heterogeneity is still a challenging task. Tip-enhanced infrared nanospectroscopy is here used to identify conformational changes connected to the hydration state of the transmembrane proteins contained in a 50 nm diameter cell membrane area, without the need for fluorescent labels. In dried purple membrane monolayers, areas with fully hydrated proteins are found among large numbers of molecules with randomly distributed hydration states. Infrared nanospectroscopy results are compared to the spectra obtained with diffraction-limited infrared techniques based on the use of synchrotron radiation, in which the diffraction limit still prevents the observation of nanoscale heterogeneity.
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Affiliation(s)
- Valeria Giliberti
- Istituto Italiano di Tecnologia, Center for Life NanoScience, Viale Regina Elena 291, I-00161, Roma, Italy
| | - Michela Badioli
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
| | - Alessandro Nucara
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
| | - Paolo Calvani
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
| | - Eglof Ritter
- Humboldt-Universität zu Berlin, Institut für Biologie, Invalidenstraße 42, D-10115, Berlin, Germany
| | - Ljiljana Puskar
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489, Berlin, Germany
| | - Emad Flear Aziz
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489, Berlin, Germany
| | - Peter Hegemann
- Humboldt-Universität zu Berlin, Institut für Biologie, Invalidenstraße 42, D-10115, Berlin, Germany
| | - Ulrich Schade
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489, Berlin, Germany
| | - Michele Ortolani
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
| | - Leonetta Baldassarre
- Istituto Italiano di Tecnologia, Center for Life NanoScience, Viale Regina Elena 291, I-00161, Roma, Italy
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
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13
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Sirotkin VA, Kuchierskaya AA. α-chymotrypsin in water-acetone and water-dimethyl sulfoxide mixtures: Effect of preferential solvation and hydration. Proteins 2017; 85:1808-1819. [PMID: 28612358 DOI: 10.1002/prot.25334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/02/2017] [Accepted: 06/07/2017] [Indexed: 11/10/2022]
Abstract
We investigated water/organic solvent sorption and residual enzyme activity to simultaneously monitor preferential solvation/hydration of protein macromolecules in the entire range of water content at 25°C. We applied this approach to estimate protein destabilization/stabilization due to the preferential interactions of bovine pancreatic α-chymotrypsin with water-acetone (moderate-strength H-bond acceptor) and water-DMSO (strong H-bond acceptor) mixtures. There are three concentration regimes for the dried α-chymotrypsin. α-Chymotrypsin is preferentially hydrated at high water content. The residual enzyme activity values are close to 100%. At intermediate water content, the dehydrated α-chymotrypsin has a higher affinity for acetone/DMSO than for water. Residual enzyme activity is minimal in this concentration range. The acetone/DMSO molecules are preferentially excluded from the protein surface at the lowest water content, resulting in preferential hydration. The residual catalytic activity in the water-poor acetone is ∼80%, compared with that observed after incubation in pure water. This effect is very small for the water-poor DMSO. Two different schemes are operative for the hydrated enzyme. At high and intermediate water content, α-chymotrypsin exhibits preferential hydration. However, at intermediate water content, in contrast to the dried enzyme, the initially hydrated α-chymotrypsin possesses increased preferential hydration parameters. At low water content, no residual enzyme activity was observed. Preferential binding of DMSO/acetone to α-chymotrypsin was detected. Our data clearly demonstrate that the hydrogen bond accepting ability of organic solvents and the protein hydration level constitute key factors in determining the stability of protein-water-organic solvent systems.
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Affiliation(s)
- Vladimir A Sirotkin
- Department of Physical Chemistry, Kazan Federal University, A.M. Butlerov Institute of Chemistry, Kazan, 420008, Russia
| | - Alexandra A Kuchierskaya
- Department of Physical Chemistry, Kazan Federal University, A.M. Butlerov Institute of Chemistry, Kazan, 420008, Russia
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14
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Tompa K, Bokor M, Ágner D, Iván D, Kovács D, Verebélyi T, Tompa P. Hydrogen Mobility and Protein-Water Interactions in Proteins in the Solid State. Chemphyschem 2017; 18:677-682. [PMID: 28066974 DOI: 10.1002/cphc.201601136] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Indexed: 11/10/2022]
Abstract
In this work the groundwork is laid for characterizing the mobility of hydrogen-hydrogen pairs (proton-proton radial vectors) in proteins in the solid state that contain only residual water. In this novel approach, we introduce new ways of analyzing and interpreting data: 1) by representing hydrogen mobility (HM) and melting diagram (MD) data recorded by wide-line 1 H NMR spectroscopic analysis as a function of fundamental temperature (thermal excitation energy); 2) by suggesting a novel mode of interpretation of these parameters that sheds light on details of protein-water interactions, such as the exact amount of water molecules and the distribution of barrier potentials pertaining to their rotational and surface translational mobility; 3) by relying on directly determined physical observables. We illustrate the power of this approach by studying the behavior of two proteins, the structured enzyme lysozyme and the intrinsically disordered ERD14.
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Affiliation(s)
- Kálmán Tompa
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, H-1122, Budapest, Konkoly-Thege út 29-33., Hungary
| | - Mónika Bokor
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, H-1122, Budapest, Konkoly-Thege út 29-33., Hungary
| | - Dorina Ágner
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, H-1122, Budapest, Konkoly-Thege út 29-33., Hungary
| | - Dávid Iván
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, H-1122, Budapest, Konkoly-Thege út 29-33., Hungary.,Department of Physics, Faculty of Natural Sciences, Budapest University of Technology and Economics, H-1521, Budapest, Budafoki út 8., Hungary
| | - Dénes Kovács
- VIB Structural Biology Research Center (SBRC), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Tamás Verebélyi
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, H-1122, Budapest, Konkoly-Thege út 29-33., Hungary
| | - Péter Tompa
- VIB Structural Biology Research Center (SBRC), Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
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15
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Ahmed IA, Gai F. Simple method to introduce an ester infrared probe into proteins. Protein Sci 2017; 26:375-381. [PMID: 27813296 DOI: 10.1002/pro.3076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 10/25/2016] [Accepted: 10/28/2016] [Indexed: 01/09/2023]
Abstract
The ester carbonyl stretching vibration has recently been shown to be a sensitive and convenient infrared (IR) probe of protein electrostatics due to the linear dependence of its frequency on local electric field. While an ester moiety can be easily incorporated into peptides via solid-phase synthesis, currently there is no method available to site-specifically incorporate it into a large protein. Herein, we show that it is possible to use a cysteine alkylation reaction to achieve this goal and demonstrate the feasibility of this simple method by successfully incorporating a methyl ester group (CH2 COOCH3 ) into a model peptide (YGGCGG), two amyloid-forming peptides derived from the insulin B chain and Aβ, and bovine serum albumin (BSA). IR results obtained with those peptide and protein systems further confirm the utility of this vibrational probe in monitoring, for example, the structural integrity of amyloid fibrils and ligand binding-induced changes in protein local hydration status.
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Affiliation(s)
- Ismail A Ahmed
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
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16
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Leptihn S, Gottschalk J, Kuhn A. T7 ejectosome assembly: A story unfolds. Bacteriophage 2016; 6:e1128513. [PMID: 27144087 DOI: 10.1080/21597081.2015.1128513] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/01/2015] [Accepted: 12/02/2015] [Indexed: 10/22/2022]
Abstract
T7 phage DNA is transported from the capsid into the host cytoplasm across the cell wall by an ejectosome comprised of the viral proteins gp14, gp15 and gp16. Prior to infection, these proteins form the so-called internal core in the mature virion. Gp16 was shown to associate with pure phospholipid bilayers while gp15 bound to DNA. A complex of both proteins appears as spiral-like rods in electron micrographs. It was also shown that the proteins gp15 and gp16 have the propensity to regain their full structure after thermal unfolding. From these observations it was concluded that (partial) unfolding of the proteins occurs during the translocation through the narrow portal of the phage capsid. After leaving the phage head, the proteins refold to form the ejectosome channel across the periplasm of the host. In this work, we analyzed the structure of gp15 and gp16 in presence of lipids and their stability toward chemical denaturants. A model to explain how the ejectosome might assemble in the host cell is discussed.
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Affiliation(s)
- Sebastian Leptihn
- Institute of Microbiology and Molecular Biology, University of Hohenheim , Stuttgart, Germany
| | - Julia Gottschalk
- Institute of Microbiology and Molecular Biology, University of Hohenheim , Stuttgart, Germany
| | - Andreas Kuhn
- Institute of Microbiology and Molecular Biology, University of Hohenheim , Stuttgart, Germany
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17
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Harpole KW, O'Brien ES, Clark MA, McKnight CJ, Vugmeyster L, Wand AJ. The unusual internal motion of the villin headpiece subdomain. Protein Sci 2015; 25:423-32. [PMID: 26473993 DOI: 10.1002/pro.2831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 10/12/2015] [Indexed: 11/06/2022]
Abstract
The thermostable 36-residue subdomain of the villin headpiece (HP36) is the smallest known cooperatively folding protein. Although the folding and internal dynamics of HP36 and close variants have been extensively studied, there has not been a comprehensive investigation of side-chain motion in this protein. Here, the fast motion of methyl-bearing amino acid side chains is explored over a range of temperatures using site-resolved solution nuclear magnetic resonance deuterium relaxation. The squared generalized order parameters of methyl groups extensively spatially segregate according to motional classes. This has not been observed before in any protein studied using this methodology. The class segregation is preserved from 275 to 305 K. Motions detected in Helix 3 suggest a fast timescale of conformational heterogeneity that has not been previously observed but is consistent with a range of folding and dynamics studies. Finally, a comparison between the order parameters in solution with previous results based on solid-state nuclear magnetic resonance deuterium line shape analysis of HP36 in partially hydrated powders shows a clear disagreement for half of the sites. This result has significant implications for the interpretation of data derived from a variety of approaches that rely on partially hydrated protein samples.
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Affiliation(s)
- Kyle W Harpole
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 19104-6059
| | - Evan S O'Brien
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 19104-6059
| | - Matthew A Clark
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska, 99508
| | - C James McKnight
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts, 02118
| | - Liliya Vugmeyster
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska, 99508.,Department of Chemistry, University of Colorado at Denver, Denver, Colorado, 80204
| | - A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 19104-6059
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18
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Biedermannová L, Schneider B. Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures. ACTA ACUST UNITED AC 2015; 71:2192-202. [PMID: 26527137 PMCID: PMC4631476 DOI: 10.1107/s1399004715015679] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/20/2015] [Indexed: 12/22/2022]
Abstract
The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.
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Affiliation(s)
- Lada Biedermannová
- Laboratory of Biomolecular Recognition, Institute of Biotechnology CAS, Videnska 1083, 142 20 Prague, Czech Republic
| | - Bohdan Schneider
- Laboratory of Biomolecular Recognition, Institute of Biotechnology CAS, Videnska 1083, 142 20 Prague, Czech Republic
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19
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O'Brien ES, Nucci NV, Fuglestad B, Tommos C, Wand AJ. Defining the Apoptotic Trigger: THE INTERACTION OF CYTOCHROME c AND CARDIOLIPIN. J Biol Chem 2015; 290:30879-87. [PMID: 26487716 DOI: 10.1074/jbc.m115.689406] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 11/06/2022] Open
Abstract
The interaction between cytochrome c and the anionic lipid cardiolipin has been proposed as a primary event in the apoptotic signaling cascade. Numerous studies that have examined the interaction of cytochrome c with cardiolipin embedded in a variety of model phospholipid membranes have suggested that partial unfolding of the protein is a precursor to the apoptotic response. However, these studies lacked site resolution and used model systems with negligible or a positive membrane curvature, which is distinct from the large negative curvature of the invaginations of the inner mitochondrial membrane where cytochrome c resides. We have used reverse micelle encapsulation to mimic the potential effects of confinement on the interaction of cytochrome c with cardiolipin. Encapsulation of oxidized horse cytochrome c in 1-decanoyl-rac-glycerol/lauryldimethylamine-N-oxide/hexanol reverse micelles prepared in pentane yields NMR spectra essentially identical to the protein in free aqueous solution. The structure of encapsulated ferricytochrome c was determined to high precision (<r.m.s. deviation>bb ∼ 0.23 Å) using NMR-based methods and is closely similar to the cryogenic crystal structure (<r.m.s. deviation>bb ∼ 1.2 Å). Incorporation of cardiolipin into the reverse micelle surfactant shell causes localized chemical shift perturbations of the encapsulated protein, providing the first view of the cardiolipin/cytochrome c interaction interface at atomic resolution. Three distinct sites of interaction are detected: the so-called A- and L-sites, plus a previously undocumented interaction centered on residues Phe-36, Gly-37, Thr-58, Trp-59, and Lys-60. Importantly, in distinct contrast to earlier studies of this interaction, the protein is not significantly disturbed by the binding of cardiolipin in the context of the reverse micelle.
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Affiliation(s)
- Evan S O'Brien
- From the Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059
| | - Nathaniel V Nucci
- From the Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059
| | - Brian Fuglestad
- From the Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059
| | - Cecilia Tommos
- From the Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059
| | - A Joshua Wand
- From the Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059
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20
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Abstract
The heterotrimeric SecY translocon complex is required for the cotranslational assembly of membrane proteins in bacteria and archaea. The insertion of transmembrane (TM) segments during nascent-chain passage through the translocon is generally viewed as a simple partitioning process between the water-filled translocon and membrane lipid bilayer, suggesting that partitioning is driven by the hydrophobic effect. Indeed, the apparent free energy of partitioning of unnatural aliphatic amino acids on TM segments is proportional to accessible surface area, which is a hallmark of the hydrophobic effect [Öjemalm K, et al. (2011) Proc Natl Acad Sci USA 108(31):E359-E364]. However, the apparent partitioning solvation parameter is less than one-half the value expected for simple bulk partitioning, suggesting that the water in the translocon departs from bulk behavior. To examine the state of water in a SecY translocon complex embedded in a lipid bilayer, we carried out all-atom molecular-dynamics simulations of the Pyrococcus furiosus SecYE, which was determined to be in a "primed" open state [Egea PF, Stroud RM (2010) Proc Natl Acad Sci USA 107(40):17182-17187]. Remarkably, SecYE remained in this state throughout our 450-ns simulation. Water molecules within SecY exhibited anomalous diffusion, had highly retarded rotational dynamics, and aligned their dipoles along the SecY transmembrane axis. The translocon is therefore not a simple water-filled pore, which raises the question of how anomalous water behavior affects the mechanism of translocon function and, more generally, the partitioning of hydrophobic molecules. Because large water-filled cavities are found in many membrane proteins, our findings may have broader implications.
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21
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Abstract
The network of hydrogen bonds characteristic of bulk water is significantly disturbed at the protein-water interface, where local fields induce mutually frustrated dipolar domains with potentially novel structure and dynamics. Here the dipolar susceptibility of hydration shells of lysozyme is studied by molecular dynamics simulations in a broad range of temperatures, 140-300 K. The real part of the susceptibility passes through a broad maximum as a function of temperature. The maximum shifts to higher temperatures with increasing frequency of the dielectric experiment. This phenomenology is consistent with that reported for bulk relaxor ferroelectrics, where it is related to the formation of dipolar nanodomains. Nanodomains in the hydration shell extend 12-15 Å from the protein surface into the bulk. Their dynamics are significantly slower than the dynamics of bulk water. The domains dynamically freeze into a ferroelectric glass below 160 K, at which point the Arrhenius plot of the dipolar relaxation time becomes significantly steeper.
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22
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Meister K, Strazdaite S, DeVries AL, Lotze S, Olijve LL, Voets IK, Bakker HJ. Observation of ice-like water layers at an aqueous protein surface. Proc Natl Acad Sci U S A 2014; 111:17732-6. [PMID: 25468976 DOI: 10.1073/pnas.1414188111] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We study the properties of water at the surface of an antifreeze protein with femtosecond surface sum frequency generation spectroscopy. We find clear evidence for the presence of ice-like water layers at the ice-binding site of the protein in aqueous solution at temperatures above the freezing point. Decreasing the temperature to the biological working temperature of the protein (0 °C to -2 °C) increases the amount of ice-like water, while a single point mutation in the ice-binding site is observed to completely disrupt the ice-like character and to eliminate antifreeze activity. Our observations indicate that not the protein itself but ordered ice-like water layers are responsible for the recognition and binding to ice.
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23
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Nucci NV, Fuglestad B, Athanasoula EA, Wand AJ. Role of cavities and hydration in the pressure unfolding of T4 lysozyme. Proc Natl Acad Sci U S A 2014; 111:13846-51. [PMID: 25201963 DOI: 10.1073/pnas.1410655111] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is well known that high hydrostatic pressures can induce the unfolding of proteins. The physical underpinnings of this phenomenon have been investigated extensively but remain controversial. Changes in solvation energetics have been commonly proposed as a driving force for pressure-induced unfolding. Recently, the elimination of void volumes in the native folded state has been argued to be the principal determinant. Here we use the cavity-containing L99A mutant of T4 lysozyme to examine the pressure-induced destabilization of this multidomain protein by using solution NMR spectroscopy. The cavity-containing C-terminal domain completely unfolds at moderate pressures, whereas the N-terminal domain remains largely structured to pressures as high as 2.5 kbar. The sensitivity to pressure is suppressed by the binding of benzene to the hydrophobic cavity. These results contrast to the pseudo-WT protein, which has a residual cavity volume very similar to that of the L99A-benzene complex but shows extensive subglobal reorganizations with pressure. Encapsulation of the L99A mutant in the aqueous nanoscale core of a reverse micelle is used to examine the hydration of the hydrophobic cavity. The confined space effect of encapsulation suppresses the pressure-induced unfolding transition and allows observation of the filling of the cavity with water at elevated pressures. This indicates that hydration of the hydrophobic cavity is more energetically unfavorable than global unfolding. Overall, these observations point to a range of cooperativity and energetics within the T4 lysozyme molecule and illuminate the fact that small changes in physical parameters can significantly alter the pressure sensitivity of proteins.
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24
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Vajda T, Perczel A. Role of water in protein folding, oligomerization, amyloidosis and miniprotein. J Pept Sci 2014; 20:747-59. [PMID: 25098401 DOI: 10.1002/psc.2671] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 06/03/2014] [Accepted: 06/06/2014] [Indexed: 01/02/2023]
Abstract
The essential involvement of water in most fundamental extra-cellular and intracellular processes of proteins is critically reviewed and evaluated in this article. The role of water in protein behavior displays structural ambivalence; it can protect the disordered peptide-chain by hydration or helps the globular chain-folding, but promotes also the protein aggregation, as well (see: diseases). A variety of amyloid diseases begins as benign protein monomers but develops then into toxic amyloid aggregates of fibrils. Our incomplete knowledge of this process emphasizes the essential need to reveal the principles of governing this oligomerization. To understand the biophysical basis of the simpler in vitro amyloid formation may help to decipher also the in vivo way. Nevertheless, to ignore the central role of the water's effect among these events means to receive an uncompleted picture of the true phenomenon. Therefore this review represents a stopgap role, because the most published studies--with a few exceptions--have been neglected the crucial importance of water in the protein research. The following questions are discussed from the water's viewpoint: (i) interactions between water and proteins, (ii) protein hydration/dehydration, (iii) folding of proteins and miniproteins, (iv) peptide/protein oligomerization, and (v) amyloidosis.
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Affiliation(s)
- Tamás Vajda
- MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University and Laboratory of Structural Chemistry & Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, 1117, Hungary
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25
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Zhao H, Chen Y, Rezabkova L, Wu Z, Wistow G, Schuck P. Solution properties of γ-crystallins: hydration of fish and mammal γ-crystallins. Protein Sci 2013; 23:88-99. [PMID: 24282025 DOI: 10.1002/pro.2394] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 11/06/2022]
Abstract
Lens γ crystallins are found at the highest protein concentration of any tissue, ranging from 300 mg/mL in some mammals to over 1000 mg/mL in fish. Such high concentrations are necessary for the refraction of light, but impose extreme requirements for protein stability and solubility. γ-crystallins, small stable monomeric proteins, are particularly associated with the lowest hydration regions of the lens. Here, we examine the solvation of selected γ-crystallins from mammals (human γD and mouse γS) and fish (zebrafish γM2b and γM7). The thermodynamic water binding coefficient B₁ could be probed by sucrose expulsion, and the hydrodynamic hydration shell of tightly bound water was probed by translational diffusion and structure-based hydrodynamic boundary element modeling. While the amount of tightly bound water of human γD was consistent with that of average proteins, the water binding of mouse γS was found to be relatively low. γM2b and γM7 crystallins were found to exhibit extremely low degrees hydration, consistent with their role in the fish lens. γM crystallins have a very high methionine content, in some species up to 15%. Structure-based modeling of hydration in γM7 crystallin suggests low hydration is associated with the large number of surface methionine residues, likely in adaptation to the extremely high concentration and low hydration environment in fish lenses. Overall, the degree of hydration appears to balance stability and tissue density requirements required to produce and maintain the optical properties of the lens in different vertebrate species.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, Bethesda, Maryland, 20892
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26
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Kearney BM, Johnson CW, Roberts DM, Swartz P, Mattos C. DRoP: a water analysis program identifies Ras-GTP-specific pathway of communication between membrane-interacting regions and the active site. J Mol Biol 2013; 426:611-29. [PMID: 24189050 DOI: 10.1016/j.jmb.2013.10.036] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 10/26/2013] [Accepted: 10/28/2013] [Indexed: 01/09/2023]
Abstract
Ras GTPase mediates several cellular signal transduction pathways and is found mutated in a large number of cancers. It is active in the GTP-bound state, where it interacts with effector proteins, and at rest in the GDP-bound state. The catalytic domain is tethered to the membrane, with which it interacts in a nucleotide-dependent manner. Here we present the program Detection of Related Solvent Positions (DRoP) for crystallographic water analysis on protein surfaces and use it to study Ras. DRoP reads and superimposes multiple Protein Data Bank coordinates, transfers symmetry-related water molecules to the position closest to the protein surface, and ranks the waters according to how well conserved and tightly clustered they are in the set of structures. Coloring according to this rank allows visualization of the results. The effector-binding region of Ras is hydrated with highly conserved water molecules at the interface between the P-loop, switch I, and switch II, as well as at the Raf-RBD binding pocket. Furthermore, we discovered a new conserved water-mediated H-bonding network present in Ras-GTP, but not in Ras-GDP, that links the nucleotide sensor residues R161 and R164 on helix 5 to the active site. The double mutant RasN85A/N86A, where the final link between helix 5 and the nucleotide is not possible, is a severely impaired enzyme, while the single mutant RasN86A, with partial connection to the active site, has a wild-type hydrolysis rate. DRoP was instrumental in determining the water-mediated connectivity networks that link two lobes of the catalytic domain in Ras.
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Affiliation(s)
- Bradley M Kearney
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Christian W Johnson
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Daniel M Roberts
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Paul Swartz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA.
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27
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Abstract
Cryogenic X-ray crystallography has heen applied to investigate thehydration structures of proteins. The amount of hydration water moleculesidentified at cryogenic temperature is more than twice those at ambienttemperature, and the structural models of proteins with a lot of hydrationwater molecules have provided much information to elucidate the static anddynamical characteristics of hydration structures of proteins. On proteinsurface, hydration water molecules distribute non-randomly and stillretain the tetrahedral hydrogen-bond geometry as well as in bulk solvent.In addition, water molecules form clathrate-like arrangements to cover thehydrophobic residues exposed to solvent. The standard interaction geometryenables the three-dimensional extension of hydrogen-bond networks aroundprotein molecules and, simultaneously, ensures the concerted reorganizationof hydration structures during the dynamical motion of proteins at work.The hydration structure analyses at cryogenic temperatures may contributeto understanding physical principles governing the dynamics of `molecularmachines' in aqueous environment.
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Affiliation(s)
- Masayoshi Nakasako
- Department of Physics, Faculty of Science and Engineering, Keio University and PRESTO-JST, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522 Japan
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28
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Abstract
The nature of water's interaction with biomolecules such as proteins has been difficult to examine in detail at atomic resolution. Solution NMR spectroscopy is potentially a powerful method for characterizing both the structural and temporal aspects of protein hydration but has been plagued by artifacts. Encapsulation of the protein of interest within the aqueous core of a reverse micelle particle results in a general slowing of water dynamics, significant reduction in hydrogen exchange chemistry and elimination of contributions from bulk water thereby enabling the use of nuclear Overhauser effects to quantify interactions between the protein surface and hydration water. Here we extend this approach to allow use of dipolar interactions between hydration water and hydrogens bonded to protein carbon atoms. By manipulating the molecular reorientation time of the reverse micelle particle through use of low viscosity liquid propane, the T(1ρ) relaxation time constants of (1)H bonded to (13)C were sufficiently lengthened to allow high quality rotating frame nuclear Overhauser effects to be obtained. These data supplement previous results obtained from dipolar interactions between the protein and hydrogens bonded to nitrogen and in aggregate cover the majority of the molecular surface of the protein. A wide range of hydration dynamics is observed. Clustering of hydration dynamics on the molecular surface is also seen. Regions of long-lived hydration water correspond with regions of the protein that participate in molecular recognition of binding partners suggesting that the contribution of the solvent entropy to the entropy of binding has been maximized through evolution.
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Affiliation(s)
- Nathaniel V. Nucci
- Johnson Research Foundation and Department of Biochemistry & Biophysics, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA 19104-6059
| | - Maxim S. Pometun
- Johnson Research Foundation and Department of Biochemistry & Biophysics, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA 19104-6059
| | - A. Joshua Wand
- Johnson Research Foundation and Department of Biochemistry & Biophysics, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA 19104-6059
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29
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SINEVA ELENAV, DAVYDOV DMITRIR. Constrained water access to the active site of cytochrome P450 from the piezophilic bacterium Photobacterium profundum. High Press Res 2010; 30:466-474. [PMID: 21475616 PMCID: PMC3070315 DOI: 10.1080/08957959.2010.535208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Living species inhabiting ocean deeps must adapt to high hydrostatic pressure. This adaptation, which must enable functioning under conditions of promoted protein hydration, is especially important for proteins such as cytochromes P450 that exhibit functionally important hydration-dehydration dynamics. Here we study the interactions of substrates with cytochrome P450-SS9, a putative fatty acid hydroxylase from the piezophilic bacterium Photobacterium profundum SS9, and characterize the protein's barotropic properties. Comparison of P450-SS9 with cytochrome P450BM-3, a mesophilic fatty acid hydroxylase, suggests that P450-SS9 is characterized by severely confined accessibility and low water occupancy of the active site. This feature may reveal a mechanism of structural adaptation of the piezophilic enzyme. We also demonstrate that saturated and unsaturated fatty acids exert opposite effects on solvent accessibility and hydration of the active site. Modulation of the protein conformation by fatty acids is hypothesized to have an important physiological function in the piezophile.
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30
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Abstract
An efficient molecular simulation methodology has been developed to determine the positioning of water molecules in the binding site of a protein or protein-ligand complex. Occupancies and absolute binding free energies of water molecules are computed using a statistical thermodynamics approach. The methodology, referred to as Just Add Water Molecules (JAWS), features "theta-water" molecules that can appear and disappear on a binding-site grid. Key approximations render the technique far more efficient than conventional free energy simulations. Testing of JAWS on five diverse examples (neuraminidase, scytalone dehydratase, major urinary protein 1, beta-lactoglobulin, and COX-2) demonstrates its accuracy in locating hydration sites in comparison to results from high-resolution crystal structures. Possible applications include aid in refinement of protein crystal structures, drug lead optimization, setup of docking calculations, and simulations of protein-ligand complexes.
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Affiliation(s)
- Julien Michel
- Department of Chemistry, Yale University, New Haven CT-06520, USA
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31
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Diakova G, Goddard YA, Korb JP, Bryant RG. Changes in protein structure and dynamics as a function of hydration from (1)H second moments. J Magn Reson 2007; 189:166-72. [PMID: 17920315 PMCID: PMC2390912 DOI: 10.1016/j.jmr.2007.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Revised: 09/11/2007] [Accepted: 09/12/2007] [Indexed: 05/25/2023]
Abstract
We report the proton second moment obtained directly from the Free Induction Decay (FID) of the NMR signal of variously hydrated bovine serum albumin (BSA) and hen egg white lysozyme (HEWL) and from the width of the NMR Z-spectrum of the cross-linked protein gels of different concentrations. The second moment of the proteins decreases in a continuous stepwise way as a function of increasing water content, which suggests that the structural and dynamical changes occur in small incremental steps. Although the second moment is dominated by the short range distances of nearest neighbors, the changes in the second moment show that the protein structure becomes more open with increasing hydration level. A difference between the apparent liquid content of the sample as found from decomposition of the FID and the analytically determined water content demonstrates that water absorbed in the early stages of hydration is motionally immobilized and magnetically indistinguishable from rigid protein protons while at high hydration levels some protein side-chain protons move rapidly contributing to liquid-like component of the NMR signal.
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Affiliation(s)
- Galina Diakova
- Chemistry Department, University of Virginia, Charlottesville, VA 22904-4319, USA
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32
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Abstract
To minimize radiation damage, crystal structures of biological macromolecules are usually determined after rapid cooling to cryogenic temperatures, some 150-200 K below the normal physiological range. The biological relevance of such structures relies on the assumption that flash-cooling is sufficiently fast to kinetically trap the macromolecule and associated solvent in a room-temperature equilibrium state. To test this assumption, we use a two-state model to calculate the structural changes expected during rapid cooling of a typical protein crystal. The analysis indicates that many degrees of freedom in a flash-cooled protein crystal are quenched at temperatures near 200 K, where local conformational and association equilibria may be strongly shifted toward low-enthalpy states. Such cryoartifacts should be most important for strongly solvent-coupled processes, such as hydration of nonpolar cavities and surface regions, conformational switching of solvent-exposed side chains, and weak ligand binding. The dynamic quenching that emerges from the model considered here can also rationalize the glass transition associated with the atomic fluctuations in the protein.
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Affiliation(s)
- Bertil Halle
- Department of Biophysical Chemistry, Lund University, SE-22100 Lund, Sweden.
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