1
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Omwansu W, Musembi R, Derese S. Graph-based analysis of H-bond networks and unsupervised learning reveal conformational coupling in prion peptide segments. Phys Chem Chem Phys 2024. [PMID: 39291469 DOI: 10.1039/d4cp02123a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
In this study, we employed a comprehensive computational approach to investigate the physical chemistry of the water networks surrounding hydrated peptide segments, as derived from molecular dynamics simulations. Our analysis uncovers a complex interplay of direct and water-mediated hydrogen bonds that intricately weave through the peptides. We demonstrate that these hydrogen bond networks encode critical information about the peptides' conformational behavior, with the dimensionality of these networks showing sensitivity to the peptides' conformations. Additionally, we estimated the free-energy landscape of the peptides across various conformations, revealing that their structures are predominantly characterized by unfolded, partially folded, and folded configurations, resulting in broad and rugged free-energy surfaces due to the numerous degrees of freedom contributed by the surrounding solvent. Importantly, the structured nature of this free-energy landscape becomes obscured when conventional collective variables, such as the number of hydrogen bonds, are used. Our findings provide new insights into the molecular mechanisms that couple protein and solvent degrees of freedom, highlighting their significance in the functioning of biological systems.
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Affiliation(s)
- Wycliffe Omwansu
- Department of Physics, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya.
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Robinson Musembi
- Department of Physics, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya.
| | - Solomon Derese
- Department of Chemistry, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
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2
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Reid KM, Poudel H, Leitner DM. Dynamics of Hydrogen Bonds between Water and Intrinsically Disordered and Structured Regions of Proteins. J Phys Chem B 2023; 127:7839-7847. [PMID: 37672685 DOI: 10.1021/acs.jpcb.3c03102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Recent studies indicate more restricted dynamics of water around intrinsically disordered proteins (IDPs) than structured proteins. We examine here the dynamics of hydrogen bonds between water molecules and two proteins, small ubiquitin-related modifier-1 (SUMO-1) and ubiquitin-conjugating enzyme E2I (UBC9), which we compare around intrinsically disordered regions (IDRs) and structured regions of these proteins. It has been recognized since some time that excluded volume effects, which influence access of water molecules to hydrogen-bonding sites, and the strength of hydrogen bonds between water and protein affect hydrogen bond lifetimes. While we find those two properties to mediate lifetimes of hydrogen bonds between water and protein residues in this study, we also find that the lifetimes are affected by the concentration of charged groups on other nearby residues. These factors are more important in determining the hydrogen bond lifetimes than whether a residue hydrogen bonding with water belongs to an IDR or to a structured region.
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Affiliation(s)
- Korey M Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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3
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Xiong D, Xu Q, Tian L, Bai J, Yang L, Jia J, Liu X, Yang X, Duan X. Mechanism of improving solubility and emulsifying properties of wheat gluten protein by pH cycling treatment and its application in powder oils. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2022.108132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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4
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Lupi L, Bracco B, Sassi P, Corezzi S, Morresi A, Fioretto D, Comez L, Paolantoni M. Hydration Dynamics of Model Peptides with Different Hydrophobic Character. Life (Basel) 2022; 12:life12040572. [PMID: 35455063 PMCID: PMC9031890 DOI: 10.3390/life12040572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022] Open
Abstract
The multi-scale dynamics of aqueous solutions of the hydrophilic peptide N-acetyl-glycine-methylamide (NAGMA) have been investigated through extended frequency-range depolarized light scattering (EDLS), which enables the broad-band detection of collective polarizability anisotropy fluctuations. The results have been compared to those obtained for N-acetyl-leucinemethylamide (NALMA), an amphiphilic peptide which shares with NAGMA the same polar backbone, but also contains an apolar group. Our study indicates that the two model peptides induce similar effects on the fast translational dynamics of surrounding water. Both systems slow down the mobility of solvating water molecules by a factor 6–8, with respect to the bulk. Moreover, the two peptides cause a comparable far-reaching spatial perturbation extending to more than two hydration layers in diluted conditions. The observed concentration dependence of the hydration number is explained considering the random superposition of different hydration shells, while no indication of solute aggregation phenomena has been found. The results indicate that the effect on the dynamics of water solvating the amphiphilic peptide is dominated by the hydrophilic backbone. The minor impact of the hydrophobic moiety on hydration features is consistent with structural findings derived by Fourier transform infrared (FTIR) measurements, performed in attenuated total reflectance (ATR) configuration. Additionally, we give evidence that, for both systems, the relaxation mode in the GHz frequency range probed by EDLS is related to solute rotational dynamics. The rotation of NALMA occurs at higher timescales, with respect to the rotation of NAGMA; both processes are significantly slower than the structural dynamics of hydration water, suggesting that solute and solvent motions are uncoupled. Finally, our results do not indicate the presence of super-slow water (relaxation times in the order of tens of picoseconds) around the peptides investigated.
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Affiliation(s)
- Laura Lupi
- Dipartimento di Matematica e Fisica, Università Roma Tre, 00146 Rome, Italy;
| | - Brenda Bracco
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.); (A.M.)
| | - Paola Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.); (A.M.)
| | - Silvia Corezzi
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (S.C.); (D.F.)
| | - Assunta Morresi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.); (A.M.)
| | - Daniele Fioretto
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (S.C.); (D.F.)
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 060123 Perugia, Italy
| | - Lucia Comez
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 060123 Perugia, Italy
- Correspondence: (L.C.); (M.P.)
| | - Marco Paolantoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.); (A.M.)
- Correspondence: (L.C.); (M.P.)
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5
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Reid KM, Singh AK, Bikash CR, Wei J, Tal-Gan Y, Vinh NQ, Leitner DM. The origin and impact of bound water around intrinsically disordered proteins. Biophys J 2022; 121:540-551. [PMID: 35074392 PMCID: PMC8874019 DOI: 10.1016/j.bpj.2022.01.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/14/2021] [Accepted: 01/13/2022] [Indexed: 12/29/2022] Open
Abstract
Proteins and water couple dynamically over a wide range of time scales. Motivated by their central role in protein function, protein-water dynamics and thermodynamics have been extensively studied for structured proteins, where correspondence to structural features has been made. However, properties controlling intrinsically disordered protein (IDP)-water dynamics are not yet known. We report results of megahertz-to-terahertz dielectric spectroscopy and molecular dynamics simulations of a group of IDPs with varying charge content along with structured proteins of similar size. Hydration water around IDPs is found to exhibit more heterogeneous rotational and translational dynamics compared with water around structured proteins of similar size, yielding on average more restricted dynamics around individual residues of IDPs, charged or neutral, compared with structured proteins. The on-average slower water dynamics is found to arise from excess tightly bound water in the first hydration layer, which is related to greater exposure to charged groups. The more tightly bound water to IDPs correlates with the smaller hydration shell found experimentally, and affects entropy associated with protein-water interactions, the contribution of which we estimate based on the dielectric measurements and simulations. Water-IDP dynamic coupling at terahertz frequencies is characterized by the dielectric measurements and simulations.
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Affiliation(s)
- Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada
| | - Abhishek K. Singh
- Department of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia
| | | | - Jessica Wei
- Department of Chemistry, University of Nevada, Reno, Nevada
| | - Yftah Tal-Gan
- Department of Chemistry, University of Nevada, Reno, Nevada
| | - Nguyen Q. Vinh
- Department of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia,Corresponding author
| | - David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada,Corresponding author
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6
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Laity PR, Holland C. Seeking Solvation: Exploring the Role of Protein Hydration in Silk Gelation. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27020551. [PMID: 35056868 PMCID: PMC8781151 DOI: 10.3390/molecules27020551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/31/2021] [Accepted: 01/11/2022] [Indexed: 02/05/2023]
Abstract
The mechanism by which arthropods (e.g., spiders and many insects) can produce silk fibres from an aqueous protein (fibroin) solution has remained elusive, despite much scientific investigation. In this work, we used several techniques to explore the role of a hydration shell bound to the fibroin in native silk feedstock (NSF) from Bombyx mori silkworms. Small angle X-ray and dynamic light scattering (SAXS and DLS) revealed a coil size (radius of gyration or hydrodynamic radius) around 12 nm, providing considerable scope for hydration. Aggregation in dilute aqueous solution was observed above 65 °C, matching the gelation temperature of more concentrated solutions and suggesting that the strength of interaction with the solvent (i.e., water) was the dominant factor. Infrared (IR) spectroscopy indicated decreasing hydration as the temperature was raised, with similar changes in hydration following gelation by freezing or heating. It was found that the solubility of fibroin in water or aqueous salt solutions could be described well by a relatively simple thermodynamic model for the stability of the protein hydration shell, which suggests that the affected water is enthalpically favoured but entropically penalised, due to its reduced (vibrational or translational) dynamics. Moreover, while the majority of this investigation used fibroin from B. mori, comparisons with published work on silk proteins from other silkworms and spiders, globular proteins and peptide model systems suggest that our findings may be of much wider significance.
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7
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Mollazadeh S, Yazdimamaghani M, Yazdian-Robati R, Pirhadi S. New insight into the structural changes of apoferritin pores in the process of doxorubicin loading at an acidic pH: Molecular dynamics simulations. Comput Biol Med 2021; 141:105158. [PMID: 34952337 DOI: 10.1016/j.compbiomed.2021.105158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 11/19/2022]
Abstract
Apoferritin (APO-Fr) is one of the most investigated proteins proposed as an advanced structure for drug delivery systems. Herein, molecular dynamics simulation was employed to compare the opening of 3-fold and 4-fold pores in APO-Fr during the partial disassembly process at an acidic pH. We showed that more hydrophilic residues in the surface of 3-fold pores compared to 4-fold pores facilitate increased flexibility and a higher tendency to open. In particular, dissociation is induced by the presence of Doxorubicin (DOX) close to 3-fold pores. Our simulations showed loaded DOXs on the APO-Fr surface were mainly involved in the hydrogen bond interactions with the hydrophilic residues, suggesting the difficulty of hydrophobic drugs loading in APO-Fr with the partial disassembly process. However, π-π interactions as well as hydrogen bonds between protein and DOXs were mediated by the basic and acidic amino acids such as HIP128, GLU17, and LYS143 at the open pores, providing penetration of DOXs into the H-Apo-Fr. We conclude that increased drug encapsulations and loading capacity of hydrophobic drugs into the cavity of APO-Fr are feasible by further disassembly of openings to access the internal hydrophobic portions of the protein.
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Affiliation(s)
- Shirin Mollazadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical, Iran
| | - Mostafa Yazdimamaghani
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Rezvan Yazdian-Robati
- Pharmaceutical Sciences Research Centre, Mazandaran University of Medical Sciences, Sari, Iran; Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Somayeh Pirhadi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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8
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Hydration and aggregation in aqueous xylitol solutions in the wide temperature range. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions. Int J Mol Sci 2021; 22:ijms22179350. [PMID: 34502252 PMCID: PMC8431001 DOI: 10.3390/ijms22179350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
The biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide) and diglycine, by means of FTIR spectroscopy and molecular dynamics simulations. We isolated the spectroscopic share of water molecules that are simultaneously under the influence of peptide and osmolyte and determined the structural and energetic properties of these water molecules. Our experimental and computational results revealed that the changes in the structure of water around peptides, caused by the presence of stabilizing or destabilizing osmolyte, are significantly different for both NAGMA and diglycine. The main factor determining the influence of osmolytes on peptides is the structural-energetic similarity of their hydration spheres. We showed that the chosen peptides can serve as models for various fragments of the protein surface: NAGMA for the protein backbone and diglycine for the protein surface with polar side chains.
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10
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Santra M, Seal A, Bhattacharjee K, Chakrabarty S. Structural and dynamical heterogeneity of water trapped inside Na +-pumping KR2 rhodopsin in the dark state. J Chem Phys 2021; 154:215101. [PMID: 34240976 DOI: 10.1063/5.0044904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Photoisomerization in the retinal leads to a channel opening in rhodopsins that triggers translocation or pumping of ions/protons. Crystal structures of rhodopsins contain several structurally conserved water molecules. It has been suggested that water plays an active role in facilitating the ion pumping/translocation process by acting as a lubricant in these systems. In this paper, we systematically investigate the localization, structure, dynamics, and energetics of the water molecules along the channel for the resting/dark state of KR2 rhodopsin. By employing several microseconds long atomistic molecular dynamics simulation of this trans-membrane protein system, we demonstrate the presence of five distinct water containing pockets/cavities separated by gateways controlled by protein side-chains. There exists a strong hydrogen bonded network involving these buried water molecules and functionally important key residues. We present evidence of significant structural and dynamical heterogeneity in the water molecules present in these cavities, with very rare exchange between them. The exchange time scale of such buried water with the bulk has an extremely wide range, from tens of nanoseconds to >1.5 µs. The translational and rotational dynamics of buried water are found to be strongly dependent on the protein cavity size and local interactions with a classic signature of trapped diffusion and rotational anisotropy.
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Affiliation(s)
- Mantu Santra
- School of Chemical and Materials Sciences, Indian Institute of Technology Goa, Ponda, Goa 403401, India
| | - Aniruddha Seal
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, Odisha, India
| | - Kankana Bhattacharjee
- Department of Chemical, Biological & Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, West Bengal, India
| | - Suman Chakrabarty
- Department of Chemical, Biological & Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, West Bengal, India
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11
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Shiraga K, Urabe M, Matsui T, Kikuchi S, Ogawa Y. Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor. Phys Chem Chem Phys 2020; 22:19468-19479. [PMID: 32761010 DOI: 10.1039/d0cp02265a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The biological functions of proteins depend on harmonization with hydration water surrounding them. Indeed, the dynamical transition of proteins, such as thermal denaturation, is dependent on the changes in the mobility of hydration water. However, the role of hydration water during dynamical transition is yet to be fully understood due to technical limitations in precisely characterizing the amount of hydration water. A state-of-the-art CMOS dielectric sensor consisting of 65 GHz LC resonators addressed this issue by utilizing the feature that oscillation frequency sensitively shifts in response to the complex dielectric constant at 65 GHz with extremely high precision. This study aimed to establish an analytical algorithm to derive the hydration number from the measured frequency shift and to demonstrate the transition of hydration number upon the thermal denaturation of human serum albumin. The determined hydration number in the native state drew a "global" hydration picture beyond the first solvation shell, with substantially reduced uncertainty of the hydration number (about ±1%). This allowed the detection of a rapid increase in the hydration number at about 55 °C during the heating process, which was in excellent phase with the irreversible rupture of the α-helical structure into solvent-exposed extended chains, whereas the hydration number did not trace the forward path in the subsequent cooling process. Our result indicates that the weakening of water hydrogen bonds trigger the unfolding of the protein structure first, followed by the changes in the number of hydration water as a consequence of thermal denaturation.
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Affiliation(s)
- Keiichiro Shiraga
- RIKEN Center for Integrative Medical Sciences (IMS), Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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12
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Mandal M, Das A, Mukhopadhyay C. Ubiquitin folds via a flip-twist-lock mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140299. [DOI: 10.1016/j.bbapap.2019.140299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/14/2019] [Accepted: 10/01/2019] [Indexed: 01/08/2023]
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13
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Schirò G, Weik M. Role of hydration water in the onset of protein structural dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:463002. [PMID: 31382251 DOI: 10.1088/1361-648x/ab388a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Proteins are the molecular workhorses in a living organism. Their 3D structures are animated by a multitude of equilibrium fluctuations and specific out-of-equilibrium motions that are required for proteins to be biologically active. When studied as a function of temperature, functionally relevant dynamics are observed at and above the so-called protein dynamical transition (~240 K) in hydrated, but not in dry proteins. In this review we present and discuss the main experimental and computational results that provided evidence for the dynamical transition, with a focus on the role of hydration water dynamics in sustaining functional protein dynamics. The coupling and mutual influence of hydration water dynamics and protein dynamics are discussed and the hypotheses illustrated that have been put forward to explain the physical origin of their onsets.
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Affiliation(s)
- Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
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14
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Thompson MC, Barad BA, Wolff AM, Sun Cho H, Schotte F, Schwarz DMC, Anfinrud P, Fraser JS. Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme. Nat Chem 2019; 11:1058-1066. [PMID: 31527847 PMCID: PMC6815256 DOI: 10.1038/s41557-019-0329-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 08/09/2019] [Indexed: 12/21/2022]
Abstract
Correlated motions of proteins are critical to function, but these features are difficult to resolve using traditional structure determination techniques. Time-resolved X-ray methods hold promise for addressing this challenge, but have relied on the exploitation of exotic protein photoactivity, and are therefore not generalizable. Temperature jumps, through thermal excitation of the solvent, have been utilized to study protein dynamics using spectroscopic techniques, but their implementation in X-ray scattering experiments has been limited. Here, we perform temperature-jump small- and wide-angle X-ray scattering measurements on a dynamic enzyme, cyclophilin A, demonstrating that these experiments are able to capture functional intramolecular protein dynamics on the microsecond timescale. We show that cyclophilin A displays rich dynamics following a temperature jump, and use the resulting time-resolved signal to assess the kinetics of conformational changes. Two relaxation processes are resolved: a fast process is related to surface loop motions, and a slower process is related to motions in the core of the protein that are critical for catalytic turnover.
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Affiliation(s)
- Michael C Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin A Barad
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Alexander M Wolff
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Hyun Sun Cho
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Friedrich Schotte
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel M C Schwarz
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Philip Anfinrud
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
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15
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López‐Martínez M, López‐Ortiz M, Antinori ME, Wientjes E, Nin‐Hill A, Rovira C, Croce R, Díez‐Pérez I, Gorostiza P. Electrochemically Gated Long‐Distance Charge Transport in Photosystem I. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Montse López‐Martínez
- Department of Material Science and Physical ChemistryUniversity of Barcelona Martí i Franquès, 1 08028 Barcelona Spain
- Institute for Bioengineering of Catalonia (IBEC)The Barcelona Institute of Science and Technology Baldiri Reixac 10–12 08028 Barcelona Spain
- Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) 28029 Madrid Spain
- Present address: Institut für Angewandte PhysikTU Wien Vienna Austria
| | - Manuel López‐Ortiz
- Institute for Bioengineering of Catalonia (IBEC)The Barcelona Institute of Science and Technology Baldiri Reixac 10–12 08028 Barcelona Spain
- Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) 28029 Madrid Spain
| | - Maria Elena Antinori
- Institute for Bioengineering of Catalonia (IBEC)The Barcelona Institute of Science and Technology Baldiri Reixac 10–12 08028 Barcelona Spain
- Present address: Smart Materials, NanophysicsIstituto Italiano di Tecnologia Genova Italy
| | - Emilie Wientjes
- Laboratory of BiophysicsWageningen University 6700 ET Wageningen The Netherlands
| | - Alba Nin‐Hill
- Inorganic and Organic Chemistry Department & Institute of Theoretical and Computational Chemistry (IQTCUB)University of Barcelona (UB) Martí i Franquès, 1 Barcelona 08028 Spain
| | - Carme Rovira
- Inorganic and Organic Chemistry Department & Institute of Theoretical and Computational Chemistry (IQTCUB)University of Barcelona (UB) Martí i Franquès, 1 Barcelona 08028 Spain
- Catalan Institution for Research and Advanced Studies (ICREA) 08010 Barcelona Spain
| | - Roberta Croce
- Biophysics of Photosynthesis. Dep. Physics and AstronomyFaculty of SciencesVrije Universiteit Amsterdam De Boelelaan 1081 1081 HV Amsterdam The Netherlands
| | - Ismael Díez‐Pérez
- Department of Material Science and Physical ChemistryUniversity of Barcelona Martí i Franquès, 1 08028 Barcelona Spain
- Present address: Department of Chemistry, Faculty of Natural & Mathematical SciencesKing's College London London UK
| | - Pau Gorostiza
- Institute for Bioengineering of Catalonia (IBEC)The Barcelona Institute of Science and Technology Baldiri Reixac 10–12 08028 Barcelona Spain
- Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) 28029 Madrid Spain
- Catalan Institution for Research and Advanced Studies (ICREA) 08010 Barcelona Spain
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16
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López-Martínez M, López-Ortiz M, Antinori ME, Wientjes E, Nin-Hill A, Rovira C, Croce R, Díez-Pérez I, Gorostiza P. Electrochemically Gated Long-Distance Charge Transport in Photosystem I. Angew Chem Int Ed Engl 2019; 58:13280-13284. [PMID: 31310425 DOI: 10.1002/anie.201904374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/23/2019] [Indexed: 12/26/2022]
Abstract
The transport of electrons along photosynthetic and respiratory chains involves a series of enzymatic reactions that are coupled through redox mediators, including proteins and small molecules. The use of native and synthetic redox probes is key to understanding charge transport mechanisms and to the design of bioelectronic sensors and solar energy conversion devices. However, redox probes have limited tunability to exchange charge at the desired electrochemical potentials (energy levels) and at different protein sites. Herein, we take advantage of electrochemical scanning tunneling microscopy (ECSTM) to control the Fermi level and nanometric position of the ECSTM probe in order to study electron transport in individual photosystem I (PSI) complexes. Current-distance measurements at different potentiostatic conditions indicate that PSI supports long-distance transport that is electrochemically gated near the redox potential of P700, with current extending farther under hole injection conditions.
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Affiliation(s)
- Montse López-Martínez
- Department of Material Science and Physical Chemistry, University of Barcelona, Martí i Franquès, 1, 08028, Barcelona, Spain.,Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain.,Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029, Madrid, Spain.,Present address: Institut für Angewandte Physik, TU Wien, Vienna, Austria
| | - Manuel López-Ortiz
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain.,Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029, Madrid, Spain
| | - Maria Elena Antinori
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain.,Present address: Smart Materials, Nanophysics, Istituto Italiano di Tecnologia, Genova, Italy
| | - Emilie Wientjes
- Laboratory of Biophysics, Wageningen University, 6700 ET, Wageningen, The Netherlands
| | - Alba Nin-Hill
- Inorganic and Organic Chemistry Department & Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona (UB), Martí i Franquès, 1, Barcelona, 08028, Spain
| | - Carme Rovira
- Inorganic and Organic Chemistry Department & Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona (UB), Martí i Franquès, 1, Barcelona, 08028, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
| | - Roberta Croce
- Biophysics of Photosynthesis. Dep. Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Ismael Díez-Pérez
- Department of Material Science and Physical Chemistry, University of Barcelona, Martí i Franquès, 1, 08028, Barcelona, Spain.,Present address: Department of Chemistry, Faculty of Natural & Mathematical Sciences, King's College London, London, UK
| | - Pau Gorostiza
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain.,Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029, Madrid, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
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17
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Sharma B, Chandra A. Conformation-Induced Dynamical Heterogeneity of Water in the Solvation Shell of Zwitterionic γ-Aminobutyric Acid. J Phys Chem B 2019; 123:7937-7946. [DOI: 10.1021/acs.jpcb.9b01771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Bikramjit Sharma
- Department of Chemistry, Indian Institute of Technology, Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology, Kanpur, Kanpur 208016, India
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18
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Yang KC, Cui FC, Shi C, Chen WD, Li YQ. Evolution of Conformation and Dynamics of Solvents in Hydration Shell along the Urea-induced Unfolding of Ubiquitin. CHINESE JOURNAL OF POLYMER SCIENCE 2019. [DOI: 10.1007/s10118-019-2238-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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19
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Salvi N, Abyzov A, Blackledge M. Solvent-dependent segmental dynamics in intrinsically disordered proteins. SCIENCE ADVANCES 2019; 5:eaax2348. [PMID: 31259246 PMCID: PMC6598773 DOI: 10.1126/sciadv.aax2348] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/22/2019] [Indexed: 05/04/2023]
Abstract
Protein and water dynamics have a synergistic relationship, which is particularly important for intrinsically disordered proteins (IDPs), although the details of this coupling remain poorly understood. Here, we combine temperature-dependent molecular dynamics simulations using different water models with extensive nuclear magnetic resonance (NMR) relaxation to examine the importance of distinct modes of solvent and solute motion for the accurate reproduction of site-specific dynamics in IDPs. We find that water dynamics play a key role in motional processes internal to "segments" of IDPs, stretches of primary sequence that share dynamic properties and behave as discrete dynamic units. We identify a relationship between the time scales of intrasegment dynamics and the lifetime of hydrogen bonds in bulk water. Correct description of these motions is essential for accurate reproduction of protein relaxation. Our findings open important perspectives for understanding the role of hydration water on the behavior and function of IDPs in solution.
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20
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Matveev VV. Cell theory, intrinsically disordered proteins, and the physics of the origin of life. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 149:114-130. [PMID: 30965040 DOI: 10.1016/j.pbiomolbio.2019.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/01/2019] [Accepted: 04/05/2019] [Indexed: 12/30/2022]
Abstract
Cell theory, as formulated by Theodor Schwann in 1839, introduced the idea that the cell is the main structural unit of living nature. Later, in solving the problem of cell multiplication, Rudolf Virchow expanded the cell theory with a postulate: all cells only arise from pre-existing cells. But what did the very first cell arise from? This paper proposes extending the Virchow's law by the assumption that between the nonliving protocell and the first living cell the continuity of fundamental physical properties (the principle of invariance of physical properties) is preserved. The protocell is understood here as a cell-shaped physical system on the basis of the self-organized biologically significant prebiotic macromolecules, primarily peptides, having a potential to transform into the living cell. Biophase is considered as the physical basis of the membraneless protocell, the internal environment of which is separated from the external environment due to the phase of adsorbed water. The evidence is given that the first protocells may have been formed on the basis of intrinsically disordered peptides. Data on the similarity of the physical properties of living cells and the following model systems are given: protein and artificial polymer solutions, coacervate droplets, and ion-exchange resin granules. Available data on the similarity of the physical properties of cell models and living cells allow us to rephrase the Virchow's postulate as follows: the physical properties of a living cell could only arise from pre-existing physical properties of the protocell.
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Affiliation(s)
- Vladimir V Matveev
- Laboratory of Cell Physiology, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave 4, St. Petersburg, 194064, Russia.
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21
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Sun CQ. Aqueous charge injection: solvation bonding dynamics, molecular nonbond interactions, and extraordinary solute capabilities. INT REV PHYS CHEM 2018. [DOI: 10.1080/0144235x.2018.1544446] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chang Q. Sun
- EBEAM, Yangtze Normal University, Chongqing, People's Republic of China
- NOVITAS, EEE, Nanyang Technological University, Singapore, Singapore
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22
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Budday D, Leyendecker S, van den Bedem H. Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion. J Chem Inf Model 2018; 58:2108-2122. [PMID: 30240209 DOI: 10.1021/acs.jcim.8b00267] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Elastic network models (ENMs) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have contributed significantly to insights into protein molecular mechanisms and function. However, despite a shared purpose of these approaches, the topological nature of rigidity analysis, and thereby the absence of motion modes, has impeded a direct comparison. Here, we present an alternative, kinematic approach to rigidity analysis, which circumvents these drawbacks. We introduce a novel protein hydrogen bond network spectral decomposition, which provides an orthonormal basis for collective motions modulated by noncovalent interactions, analogous to the eigenspectrum of normal modes. The zero modes decompose proteins into rigid clusters identical to those from topological rigidity, while nonzero modes rank protein motions by their hydrogen bond collective energy penalty. Our kinematic flexibility analysis bridges topological rigidity theory and ENM, enabling a detailed analysis of motion modes obtained from both approaches. Analysis of a large, structurally diverse data set revealed that collectivity of protein motions, reported by the Shannon entropy, is significantly reduced for rigidity theory compared to normal mode approaches. Strikingly, kinematic flexibility analysis suggests that the hydrogen bonding network encodes a protein-fold specific, spatial hierarchy of motions, which goes nearly undetected in ENM. This hierarchy reveals distinct motion regimes that rationalize experimental and simulated protein stiffness variations. Kinematic motion modes highly correlate with reported crystallographic B factors and molecular dynamics simulations of adenylate kinase. A formal expression for changes in free energy derived from the spectral decomposition indicates that motions across nearly 40% of modes obey enthalpy-entropy compensation. Taken together, our results suggest that hydrogen bond networks have evolved to modulate protein structure and dynamics, which can be efficiently probed by kinematic flexibility analysis.
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Affiliation(s)
- Dominik Budday
- Chair of Applied Dynamics , University of Erlangen-Nuremberg , 91058 Erlangen , Germany
| | - Sigrid Leyendecker
- Chair of Applied Dynamics , University of Erlangen-Nuremberg , 91058 Erlangen , Germany
| | - Henry van den Bedem
- Biosciences Division, SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 , United States.,Department of Bioengineering and Therapeutic Sciences , University of California , San Francisco , California 94158 , United States
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23
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Affiliation(s)
- Shridhar K. Sathe
- Department of Nutrition, Food & Exercise Sciences (NFES); Florida State University; 120 Convocation Way, Tallahassee FL 32306-1493 USA
| | - Valerie D. Zaffran
- Department of Nutrition, Food & Exercise Sciences (NFES); Florida State University; 120 Convocation Way, Tallahassee FL 32306-1493 USA
| | - Sahil Gupta
- Department of Nutrition, Food & Exercise Sciences (NFES); Florida State University; 120 Convocation Way, Tallahassee FL 32306-1493 USA
| | - Tengfei Li
- Department of Nutrition, Food & Exercise Sciences (NFES); Florida State University; 120 Convocation Way, Tallahassee FL 32306-1493 USA
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24
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Thyparambil AA, Bazin I, Guiseppi-Elie A. Molecular Modeling and Simulation Tools in the Development of Peptide-Based Biosensors for Mycotoxin Detection: Example of Ochratoxin. Toxins (Basel) 2017. [PMCID: PMC5744115 DOI: 10.3390/toxins9120395] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mycotoxin contamination of food and feed is now ubiquitous. Exposures to mycotoxin via contact or ingestion can potentially induce adverse health outcomes. Affordable mycotoxin-monitoring systems are highly desired but are limited by (a) the reliance on technically challenging and costly molecular recognition by immuno-capture technologies; and (b) the lack of predictive tools for directing the optimization of alternative molecular recognition modalities. Our group has been exploring the development of ochratoxin detection and monitoring systems using the peptide NFO4 as the molecular recognition receptor in fluorescence, electrochemical and multimodal biosensors. Using ochratoxin as the model mycotoxin, we share our perspective on addressing the technical challenges involved in biosensor fabrication, namely: (a) peptide receptor design; and (b) performance evaluation. Subsequently, the scope and utility of molecular modeling and simulation (MMS) approaches to address the above challenges are described. Informed and enabled by phage display, the subsequent application of MMS approaches can rationally guide subsequent biomolecular engineering of peptide receptors, including bioconjugation and bioimmobilization approaches to be used in the fabrication of peptide biosensors. MMS approaches thus have the potential to reduce biosensor development cost, extend product life cycle, and facilitate multi-analyte detection of mycotoxins, each of which positively contributes to the overall affordability of mycotoxin biosensor monitoring systems.
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Affiliation(s)
- Aby A. Thyparambil
- Center for Bioelectronics, Biosensors and Biochips (C3B), Texas A&M University, College Station, TX 77843, USA;
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Ingrid Bazin
- Laboratoire de Génie de l’Environnement Industriel( LGEI), Institut Mines Telecom (IMT) Mines Ales, University of Montpellier, 30100 Ales, France;
| | - Anthony Guiseppi-Elie
- Center for Bioelectronics, Biosensors and Biochips (C3B), Texas A&M University, College Station, TX 77843, USA;
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, TX 77843, USA
- ABTECH Scientific, Inc., Biotechnology Research Park, 800 East Leigh Street, Richmond, VA 23219, USA
- Correspondence: ; Tel.: +1-979-458-1239; Fax: +1-979-458-8219
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25
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Pandey HD, Leitner DM. Thermodynamics of Hydration Water around an Antifreeze Protein: A Molecular Simulation Study. J Phys Chem B 2017; 121:9498-9507. [DOI: 10.1021/acs.jpcb.7b05892] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hari Datt Pandey
- Department of Chemistry and
Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
| | - David M. Leitner
- Department of Chemistry and
Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
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