201
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Ansari N, Rizzi V, Carloni P, Parrinello M. Water-Triggered, Irreversible Conformational Change of SARS-CoV-2 Main Protease on Passing from the Solid State to Aqueous Solution. J Am Chem Soc 2021; 143:12930-12934. [PMID: 34398611 PMCID: PMC8386029 DOI: 10.1021/jacs.1c05301] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Indexed: 11/30/2022]
Abstract
The main protease from SARS-CoV-2 is a homodimer. Yet, a recent 0.1-ms-long molecular dynamics simulation performed by D. E. Shaw's research group shows that it readily undergoes a symmetry-breaking event on passing from the solid state to aqueous solution. As a result, the subunits present distinct conformations of the binding pocket. By analyzing this long simulation, we uncover a previously unrecognized role of water molecules in triggering the transition. Interestingly, each subunit presents a different collection of long-lived water molecules. Enhanced sampling simulations performed here, along with machine learning approaches, further establish that the transition to the asymmetric state is essentially irreversible.
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Affiliation(s)
- Narjes Ansari
- Italian
Institute of Technology, Via E. Melen 83, 16152 Genova, Italy
| | - Valerio Rizzi
- Italian
Institute of Technology, Via E. Melen 83, 16152 Genova, Italy
| | - Paolo Carloni
- Computational
Biomedicine, Institute for Advanced Simulation (IAS-5) and Institute
of Neuroscience and Medicine (INM-9), and JARA-Institute “Molecular
Neuroscience and Neuroimaging” (INM-11), Forschungszentrum Jülich, Jülich 52425, Germany
- Physics
Department, RWTH Aachen University, Aachen 52074, Germany
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202
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Samways ML, Taylor RD, Bruce Macdonald HE, Essex JW. Water molecules at protein-drug interfaces: computational prediction and analysis methods. Chem Soc Rev 2021; 50:9104-9120. [PMID: 34184009 DOI: 10.1039/d0cs00151a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The fundamental importance of water molecules at drug-protein interfaces is now widely recognised and a significant feature in structure-based drug design. Experimental methods for analysing the role of water in drug binding have many challenges, including the accurate location of bound water molecules in crystal structures, and problems in resolving specific water contributions to binding thermodynamics. Computational analyses of binding site water molecules provide an alternative, and in principle complete, structural and thermodynamic picture, and their use is now commonplace in the pharmaceutical industry. In this review, we describe the computational methodologies that are available and discuss their strengths and weaknesses. Additionally, we provide a critical analysis of the experimental data used to validate the methods, regarding the type and quality of experimental structural data. We also discuss some of the fundamental difficulties of each method and suggest directions for future study.
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Affiliation(s)
- Marley L Samways
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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203
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Roy P, Sengupta N. Hydration of a small protein under carbon nanotube confinement: Adsorbed substates induce selective separation of the dynamical response. J Chem Phys 2021; 154:204702. [PMID: 34241160 DOI: 10.1063/5.0047078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The co-involvement of biological molecules and nanomaterials has increasingly come to the fore in modern-day applications. While the "bio-nano" (BN) interface presents physico-chemical characteristics that are manifestly different from those observed in isotropic bulk conditions, the underlying molecular reasons remain little understood; this is especially true of anomalies in interfacial hydration. In this paper, we leverage atomistic simulations to study differential adsorption characteristics of a small protein on the inner (concave) surface of a single-walled carbon nanotube whose diameter exceeds dimensions conducive to single-file water movement. Our findings indicate that the extent of adsorption is decided by the degree of foldedness of the protein conformational substate. Importantly, we find that partially folded substates, but not the natively folded one, induce reorganization of the protein hydration layer into an inner layer water closer to the nanotube axis and an outer layer water in the interstitial space near the nanotube walls. Further analyses reveal sharp dynamical differences between water molecules in the two layers as observed in the onset of increased heterogeneity in rotational relaxation and the enhanced deviation from Fickian behavior. The vibrational density of states reveals that the dynamical distinctions are correlated with differences in crucial bands in the power spectra. The current results set the stage for further systematic studies of various BN interfaces vis-à-vis control of hydration properties.
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Affiliation(s)
- Priti Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
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204
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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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205
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Samaranayake CP, Sastry SK. Molecular dynamics evidence for nonthermal effects of electric fields on pectin methylesterase activity. Phys Chem Chem Phys 2021; 23:14422-14432. [PMID: 34180917 DOI: 10.1039/d0cp05950a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Experimental studies relevant to the nonthermal effects of electric fields on biological systems are emerging. However, these effects are poorly understood at the molecular level. The present study investigates pectin methylesterase, a cell wall modifying enzyme in plants, exposed to various electric field strengths. Molecular dynamics (MD) of the enzyme were studied with and without (thermal-only) electric field applications. The measurements were interpreted on the basis of equivalent energy input to gain insights into the effect of electric field treatment time at a constant temperature (50 °C). Results reveal that electric fields exert nonthermal effects on both local and global protein structure. In 1 μs simulations, the results show significant (P ≤ 0.05) shrinkage of the catalytic domain and shortening of enzyme-water hydrogen bond lifetime by a 50 V cm-1 electric field. Unwinding of the helical segments, altered intra- and intermolecular hydrogen bond patterns, and increased hydration are also caused by the 50 V cm-1 electric field. This study serves to understand the electric field influence on the functional role of proteins.
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Affiliation(s)
- Chaminda P Samaranayake
- Department of Food, Agricultural and Biological Engineering, The Ohio State University, 590 Woody Hayes Drive, Columbus, Ohio 43210, USA.
| | - Sudhir K Sastry
- Department of Food, Agricultural and Biological Engineering, The Ohio State University, 590 Woody Hayes Drive, Columbus, Ohio 43210, USA.
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206
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Wang D, Tian Y, Jiang L. Abnormal Properties of Low-Dimensional Confined Water. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100788. [PMID: 34176214 DOI: 10.1002/smll.202100788] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/25/2021] [Indexed: 06/13/2023]
Abstract
Water molecules confined to low-dimensional spaces exhibit unusual properties compared to bulk water. For example, the alternating hydrophilic and hydrophobic nanodomains on flat silicon wafer can induce the abnormal spreading of water (contact angles near 0°) which is caused by the 2D capillary effect. Hence, exploring the physicochemical properties of confined water from the nanoscale is of great value for understanding the challenges in material science and promoting the applications of nanomaterials in the fields of mass transport, nanofluidic designing, and fuel cell. The knowledge framework of confined water can also help to better understand the complex functions of the hydration layer of biomolecules, and even trace the origin of life. In this review, the physical properties, abnormal behaviors, and functions of the confined water are mainly summarized through several common low-dimensional water formats in the fields of solid/air-water interface, nanochannel confinement, and biological hydration layer. These researches indicate that the unusual behaviors of the confined water depend strongly on the confinement size and the interaction between the molecules and confining surface. These diverse properties of confined water open a new door to materials science and may play an important role in the future development of biology.
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Affiliation(s)
- Dianyu Wang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Ye Tian
- Key Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Lei Jiang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
- Key Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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207
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Lie AL, Pan X, White TW, Vaghefi E, Donaldson PJ. Age-Dependent Changes in Total and Free Water Content of In Vivo Human Lenses Measured by Magnetic Resonance Imaging. Invest Ophthalmol Vis Sci 2021; 62:33. [PMID: 34293079 PMCID: PMC8300047 DOI: 10.1167/iovs.62.9.33] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Purpose To use magnetic resonance imaging (MRI) to measure age-dependent changes in total and free water in human lenses in vivo. Methods Sixty-four healthy adults aged 18 to 86 years were recruited, fitted with a 32-channel head receiver coil, and placed in a 3 Tesla clinical MR scanner. Scans of the crystalline lens were obtained using a volumetric interpolated breath-hold examination sequence with dual flip angles, which were corrected for field inhomogeneity post-acquisition using a B1-map obtained using a turbo-FLASH sequence. The spatial distribution and content of corrected total (ρlens) and free (T1) water along the lens optical axis were extracted using custom-written code. Results Lens total water distribution and content did not change with age (all P > 0.05). In contrast to total water, a gradient in free water content that was highest in the periphery relative to the center was present in lenses across all ages. However, this initially parabolic free water gradient gradually developed an enhanced central plateau, as indicated by increasing profile shape parameter values (anterior: 0.067/y, P = 0.004; posterior: 0.050/y, P = 0.020) and central free water content (1.932 ms/y, P = 0.022) with age. Conclusions MRI can obtain repeatable total and free water measurements of in vivo human lenses. The observation that the lens steady-state free, but not total, water gradient is abolished with age raises the possibility that alterations in protein-water interactions are an underlying cause of the degradation in lens optics and overall vision observed with aging.
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Affiliation(s)
- Alyssa L Lie
- School of Optometry and Vision Science, New Zealand National Eye Centre, University of Auckland, New Zealand
| | - Xingzheng Pan
- School of Optometry and Vision Science, New Zealand National Eye Centre, University of Auckland, New Zealand.,Department of Physiology, School of Medical Sciences, New Zealand National Eye Centre, University of Auckland, New Zealand
| | - Thomas W White
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, United States
| | - Ehsan Vaghefi
- School of Optometry and Vision Science, New Zealand National Eye Centre, University of Auckland, New Zealand
| | - Paul J Donaldson
- Department of Physiology, School of Medical Sciences, New Zealand National Eye Centre, University of Auckland, New Zealand
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208
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Melillo JH, Gabriel JP, Pabst F, Blochowicz T, Cerveny S. Dynamics of aqueous peptide solutions in folded and disordered states examined by dynamic light scattering and dielectric spectroscopy. Phys Chem Chem Phys 2021; 23:15020-15029. [PMID: 34190269 DOI: 10.1039/d1cp01893k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Characterizing the segmental dynamics of proteins, and intrinsically disordered proteins in particular, is a challenge in biophysics. In this study, by combining data from broadband dielectric spectroscopy (BDS) and both depolarized (DDLS) and polarized (PDLS) dynamic light scattering, we were able to determine the dynamics of a small peptide [ε-poly(lysine)] in water solutions in two different conformations (pure β-sheet at pH = 10 and a more disordered conformation at pH = 7). We found that the segmental (α-) relaxation, as probed by DDLS, is faster in the disordered state than in the folded conformation. The water dynamics, as detected by BDS, is also faster in the disordered state. In addition, the combination of BDS and DDLS results allows us to confirm the molecular origin of water-related processes observed by BDS. Finally, we discuss the origin of two slow processes (A and B processes) detected by DDLS and PDLS in both conformations and usually observed in other types of water solutions. For fully homogeneous ε-PLL solutions at pH = 10, the A-DLS process is assigned to the diffusion of individual β-sheets. The combination of both techniques opens a route for understanding the dynamics of peptides and other biological solutions.
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Affiliation(s)
- Jorge H Melillo
- Centro de Física de Materiales (CSIC-UPV/EHU)-Material Physics Centre (MPC), Paseo Manuel de Lardizabal 5 (20018), San Sebastián, Spain.
| | - Jan Philipp Gabriel
- School for Molecular Sciences, Arizona State University, Tempe, 85287, USA and Institute for Condensed Matter Physics, Technical University of Darmstadt, 64289 Darmstadt, Germany
| | - Florian Pabst
- Institute for Condensed Matter Physics, Technical University of Darmstadt, 64289 Darmstadt, Germany
| | - Thomas Blochowicz
- Institute for Condensed Matter Physics, Technical University of Darmstadt, 64289 Darmstadt, Germany
| | - Silvina Cerveny
- Centro de Física de Materiales (CSIC-UPV/EHU)-Material Physics Centre (MPC), Paseo Manuel de Lardizabal 5 (20018), San Sebastián, Spain. and Donostia International Physics Center, Paseo Manuel de Lardizabal 4 (20018), San Sebastián, Spain
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209
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Päslack C, Das CK, Schlitter J, Schäfer LV. Spectrally Resolved Estimation of Water Entropy in the Active Site of Human Carbonic Anhydrase II. J Chem Theory Comput 2021; 17:5409-5418. [PMID: 34259506 DOI: 10.1021/acs.jctc.1c00554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A major challenge in understanding ligand binding to biomacromolecules lies in dissecting the underlying thermodynamic driving forces at the atomic level. Quantifying the contributions of water molecules is often especially demanding, although they can play important roles in biomolecular recognition and binding processes. One example is human carbonic anhydrase II, whose active site harbors a conserved network of structural water molecules that are essential for enzymatic catalysis. Inhibitor binding disrupts this water network and changes the hydrogen-bonding patterns in the active site. Here, we use atomistic molecular dynamics simulations to compute the absolute entropy of the individual water molecules confined in the active site of hCAII using a spectrally resolved estimation (SRE) approach. The entropy decrease of water molecules that remain in the active site upon binding of a dorzolamide inhibitor is caused by changes in hydrogen bonding and stiffening of the hydrogen-bonding network. Overall, this entropy decrease is overcompensated by the gain due to the release of three water molecules from the active site upon inhibitor binding. The spectral density calculations enable the assignment of the changes to certain vibrational modes. In addition, the range of applicability of the SRE approximation is systematically explored by exploiting the gradually changing degree of immobilization of water molecules as a function of the distance to a phospholipid bilayer surface, which defines an "entropy ruler". These results demonstrate the applicability of SRE to biomolecular solvation, and we expect it to become a useful method for entropy calculations in biomolecular systems.
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Affiliation(s)
| | - Chandan K Das
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | | | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
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210
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Mondal S, Mukherjee S, Acharya S, Bagchi B. Unfolding of Dynamical Events in the Early Stage of Insulin Dimer Dissociation. J Phys Chem B 2021; 125:7958-7966. [PMID: 34260242 DOI: 10.1021/acs.jpcb.1c03104] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dissociation of an insulin dimer is an important biochemical event that could also serve as a prototype of dissociations in similar biomolecular assemblies. We use a recently developed multidimensional free energy landscape for insulin dimer dissociation to unearth the microscopic and mechanistic aspects of the initial stages of the process that could hold the key to understanding the stability and the rate. The following sequence of events occurs in the initial stages: (i) The backbone hydrogen bonds break partially at the antiparallel β-sheet junction, (ii) the two α-helices (chain B) move away from each other while several residues (chain A) move closer, and (iii) a flow of adjacent water molecules occurs into the junction region. Interestingly, the intermonomeric center-to-center distance does not increase, but the number of native contacts exhibits a sharp decrease. Subsequent steps involve further disengagement of hydrophobic groups. This process is slow because of an entropic bottleneck created by the existence of the large configuration space available in the native state (NS), which is inhabited by low-frequency conformational fluctuations. We carry out a density-of-states analyses in the dimer NS to unearth distinctive features not present in the monomers. These low-frequency modes are also responsible for a large entropic stabilization of the NS. Hydrophobic disengagement in the early stage leads to the formation of a twisted intermediate state which itself is a metastable minimum (IS-1). The subsequent progress leads to another dimeric complex (IS-2), which is on the dissociative pathway and characterized by a further decrease in the native contacts. The dissociation process provides insights into the workings of a biomolecular assembly.
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Affiliation(s)
- Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, C. V. Raman Road, Bengaluru, Karnataka 560 012, India
| | - Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, C. V. Raman Road, Bengaluru, Karnataka 560 012, India
| | - Subhajit Acharya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, C. V. Raman Road, Bengaluru, Karnataka 560 012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, C. V. Raman Road, Bengaluru, Karnataka 560 012, India
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211
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El Ahdab D, Lagardère L, Inizan TJ, Célerse F, Liu C, Adjoua O, Jolly LH, Gresh N, Hobaika Z, Ren P, Maroun RG, Piquemal JP. Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV-2 Main Protease Dimerization Interface. J Phys Chem Lett 2021; 12:6218-6226. [PMID: 34196568 PMCID: PMC8262171 DOI: 10.1021/acs.jpclett.1c01460] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/10/2021] [Indexed: 05/27/2023]
Abstract
Following our previous work ( Chem. Sci. 2021, 12, 4889-4907), we study the structural dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of microsecond adaptive sampling molecular dynamics simulations (50 μs) using the AMOEBA polarizable force field (PFF). This interface is structured by a complex H-bond network that is stable only at physiological pH. Structural correlations analysis between its residues and the catalytic site confirms the presence of a buried allosteric site. However, noticeable differences in allosteric connectivity are observed between PFFs and non-PFFs. Interfacial polarizable water molecules are shown to appear at the heart of this discrepancy because they are connected to the global interface H-bond network and able to adapt their dipole moment (and dynamics) to their diverse local physicochemical microenvironments. The water-interface many-body interactions appear to drive the interface volume fluctuations and to therefore mediate the allosteric interactions with the catalytic cavity.
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Affiliation(s)
- Dina El Ahdab
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
- Université Saint-Joseph de Beyrouth, UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, 1104 2020 Beirut, Lebanon
| | - Louis Lagardère
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
- Sorbonne Université, IP2CT, FR 2622 CNRS, 75005 Paris, France
| | | | - Fréderic Célerse
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
- Sorbonne Université, IPCM, UMR 8232 CNRS, 75005 Paris, France
| | - Chengwen Liu
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Olivier Adjoua
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
| | - Luc-Henri Jolly
- Sorbonne Université, IP2CT, FR 2622 CNRS, 75005 Paris, France
| | - Nohad Gresh
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
| | - Zeina Hobaika
- Université Saint-Joseph de Beyrouth, UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, 1104 2020 Beirut, Lebanon
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Richard G Maroun
- Université Saint-Joseph de Beyrouth, UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, 1104 2020 Beirut, Lebanon
| | - Jean-Philip Piquemal
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
- Institut Universitaire de France, 75005 Paris, France
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212
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Guyot S, Pottier L, Bertheau L, Dumont J, Dorelle Hondjuila Miokono E, Dupont S, Ragon M, Denimal E, Marin A, Hallsworth JE, Beney L, Gervais P. Increased xerotolerance of Saccharomyces cerevisiae during an osmotic pressure ramp over several generations. Microb Biotechnol 2021; 14:1445-1461. [PMID: 33739621 PMCID: PMC8313259 DOI: 10.1111/1751-7915.13789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 12/01/2022] Open
Abstract
Although mechanisms involved in response of Saccharomyces cerevisiae to osmotic challenge are well described for low and sudden stresses, little is known about how cells respond to a gradual increase of the osmotic pressure (reduced water activity; aw ) over several generations as it could encounter during drying in nature or in food processes. Using glycerol as a stressor, we propagated S. cerevisiae through a ramp of the osmotic pressure (up to high molar concentrations to achieve testing-to-destruction) at the rate of 1.5 MPa day-1 from 1.38 to 58.5 MPa (0.990-0.635 aw ). Cultivability (measured at 1.38 MPa and at the harvest osmotic pressure) and glucose consumption compared with the corresponding sudden stress showed that yeasts were able to grow until about 10.5 MPa (0.926 aw ) and to survive until about 58.5 MPa, whereas glucose consumption occurred until 13.5 MPa (about 0.915 aw ). Nevertheless, the ramp conferred an advantage since yeasts harvested at 10.5 and 34.5 MPa (0.778 aw ) showed a greater cultivability than glycerol-shocked cells after a subsequent shock at 200 MPa (0.234 aw ) for 2 days. FTIR analysis revealed structural changes in wall and proteins in the range 1.38-10.5 MPa, which would be likely to be involved in the resistance at extreme osmotic pressure.
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Affiliation(s)
- Stéphane Guyot
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, F-21000, France
| | - Laurence Pottier
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, F-21000, France
| | - Lucie Bertheau
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, F-21000, France
| | - Jennifer Dumont
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, F-21000, France
| | | | - Sébastien Dupont
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, F-21000, France
| | - Mélanie Ragon
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, F-21000, France
| | - Emmanuel Denimal
- Direction des Systèmes d'Information, AgroSup Dijon, 26 Boulevard Docteur Petitjean, Dijon, 21000, France
| | - Ambroise Marin
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, F-21000, France
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Laurent Beney
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, F-21000, France
| | - Patrick Gervais
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, F-21000, France
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213
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Yao Y, Zhou T, Färber R, Grossner U, Floudas G, Mezzenga R. Designing cryo-enzymatic reactions in subzero liquid water by lipidic mesophase nanoconfinement. NATURE NANOTECHNOLOGY 2021; 16:802-810. [PMID: 33941918 DOI: 10.1038/s41565-021-00893-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
Cryo-enzymology provides the possibility to develop unconventional biological reactions and detect intermediates in ultrafast enzymatic catalysis processes, but also illuminates the understanding of life principles in extremely cold environments. The scarcity of biological or biomimetic host systems that provide liquid water at subzero temperatures inhibits the prosperity of cryo-enzymology. Here we introduce cryo-enzymatic reactions in subzero water nanoconfined within lipid mesophases formed by conventional lipids. We show that the enzymatic reactions that ensue outperform the homologue catalytic processes run at standard temperatures. We use phytantriol-based lipidic mesophases (LMPs), within which water remains in the liquid state down to -120 °C, and combine crystallization and dynamic studies of the confined water to provide a fundamental understanding of the physical status of water at subzero temperatures, which sets the stage for cryo-enzymatic reactions in these environments. In the model horseradish peroxidase oxidization, the cation free-radical product is stabilized in LMPs at -20 °C, in contrast to the fast-consuming reactions at temperatures above 0 °C. Furthermore, the LMP system also supports the cascade reaction and lipase reaction at subzero temperatures, at which enzymatic reactions with both hydrophilic and hydrophobic substrates are successfully carried out. Our designed LMP system opens access to the nature of confined water in the biomimetic environment and provides a platform for low-temperature biomacromolecule reconstitution and the cryogenic control of enzymatic reactions in bionanotechnology.
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Affiliation(s)
- Yang Yao
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Tao Zhou
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Raphael Färber
- High Voltage Laboratory, ETH Zürich, Zürich, Switzerland
| | - Ulrike Grossner
- Advanced Power Semiconductor Laboratory, ETH Zürich, Zürich, Switzerland
| | - George Floudas
- Max Planck Institute for Polymer Research, Mainz, Germany
- Department of Physics, University of Ioannina, Ioannina, Greece
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland.
- Department of Materials, ETH Zürich, Zürich, Switzerland.
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214
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Plazanet M, Morfin I, Honkimäki V, Buslaps T, Petrillo C, Sacchetti F. Hydrogen-bond network distortion of water in the soft confinement of Nafion membrane. J Chem Phys 2021; 154:244503. [PMID: 34241357 DOI: 10.1063/5.0049625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A Compton spectroscopy investigation is carried out in hydrated Nafion membranes, enabling identification of distortions in the hydrogen-bond distribution of the polymer hydrating water by means of the subtle changes reflected by the Compton profiles. Indeed, deformations of the Compton profiles are observed when varying hydration, and two different bonding kinds are associated with the water molecules: at low hydration, water surrounds the sulfonic groups, while on increasing hydration, water molecules occupy the interstitial cavities formed upon swelling of the membrane. The analysis is proposed in terms of averaged OH bond length variation. A sizable contraction of the OH distance is observed at low hydration (∼0.09 Å), while at higher hydration levels, the contraction is smaller (∼0.02 Å) and the OH bond length is closer to bulk water. An evaluation of the electron kinetic energy indicates that the spatial changes associated with the water distribution correspond to a consistent binding energy increase. Distinct temperature dependences of each water population are observed, which can be straightly related to water desorption into ice on cooling below the freezing point.
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Affiliation(s)
- M Plazanet
- LIPhy, University Grenoble-Alpes and CNRS, UMR5588 Grenoble, France
| | - I Morfin
- LIPhy, University Grenoble-Alpes and CNRS, UMR5588 Grenoble, France
| | | | | | - C Petrillo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, I-06123 Perugia, Italy
| | - F Sacchetti
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, I-06123 Perugia, Italy
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215
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Macro N, Chen L, Yang Y, Mondal T, Wang L, Horovitz A, Zhong D. Slowdown of Water Dynamics from the Top to the Bottom of the GroEL Cavity. J Phys Chem Lett 2021; 12:5723-5730. [PMID: 34129341 PMCID: PMC8687601 DOI: 10.1021/acs.jpclett.1c01216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
The GroE molecular chaperone system is a critical protein machine that assists the folding of substrate proteins in its cavity. Water in the cavity is suspected to play a role in substrate protein folding, but the mechanism is currently unknown. Herein, we report measurements of water dynamics in the equatorial and apical domains of the GroEL cavity in the apo and football states, using site-specific tryptophanyl mutagenesis as an intrinsic optical probe with femtosecond resolution combined with molecular dynamics simulations. We observed clearly different water dynamics in the two domains with a slowdown of the cavity water from the apical to equatorial region in the football state. The results suggest that the GroEL cavity provides a unique water environment that may facilitate substrate protein folding.
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Affiliation(s)
- Nicolas Macro
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Long Chen
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yushan Yang
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Tridib Mondal
- Department
of Structural Biology, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Lijuan Wang
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amnon Horovitz
- Department
of Structural Biology, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Dongping Zhong
- Department
of Physics, The Ohio State University, Columbus, Ohio 43210, United States
- Department
of Chemistry and Biochemistry, Programs of Biophysics, Program of
Chemical Physics, and Program of Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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216
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Kumar SU, Priya Doss CG. Residue interaction networks of K-Ras protein with water molecules identifies the potential role of switch II and P-loop. Comput Biol Med 2021; 135:104597. [PMID: 34237589 DOI: 10.1016/j.compbiomed.2021.104597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/01/2021] [Accepted: 06/17/2021] [Indexed: 02/07/2023]
Abstract
The mutant K-Ras with aberrant signaling is the primary cause of several cancers. The proposed study investigated the influence of water molecules in K-Ras crystal structure, where they have a significant function by understanding their residue interaction networks (RINs). We analyzed the RINs of K-Ras with and without water molecules and determined their interaction properties. RINs were developed with the help of StructureViz2 and RINspector; further, the changes in K-Ras backbone flexibility were predicted with the DynaMine. We found that the residues K42, I142, and L159 are the hotspots from water, including the K-Ras-GTP complex with the highest residue centrality analysis (RCA) Z-score. The DynaMine prediction calculated the NMR S2 value for the frequently mutated positions G12, G13, and Q61 showing a minor shift in flexibility, which make up the P-Loop and switch II of the K-Ras protein. This flexibility shift can account for changes in conformational activity and the protein's GTPase activity, making it difficult to recognize by the effectors and exchange factors. Taken together, our study helps in understanding the functional importance of the water molecules in K-Ras protein and the impact of mutation that modulate the conformational state of the protein.
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Affiliation(s)
- S Udhaya Kumar
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - C George Priya Doss
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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217
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Voloshin VP, Medvedev NN. ORIENTATION OF WATER MOLECULES NEAR A GLOBULAR PROTEIN. J STRUCT CHEM+ 2021. [DOI: 10.1134/s002247662105005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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218
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Community evolution and frequent subgraph patterns affect the thermostability of B. subtilis lipase A. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.100984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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219
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Ishiyama T. Ab initio molecular dynamics study on energy relaxation path of hydrogen-bonded OH vibration in bulk water. J Chem Phys 2021; 154:204502. [PMID: 34241149 DOI: 10.1063/5.0050078] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The vibrational energy relaxation paths of hydrogen-bonded (H-bonded) OH excited in pure water and in isotopically diluted (deuterated) water are elucidated via non-equilibrium ab initio molecular dynamics (NE-AIMD) simulations. The present study extends the previous NE-AIMD simulation for the energy relaxation of an excited free OH vibration at an air/water interface [T. Ishiyama, J. Chem. Phys. 154, 104708 (2021)] to the energy relaxation of an excited H-bonded OH vibration in bulk water. The present simulation shows that the excited OH vibration in pure water dissipates its energy on a timescale of 0.1 ps, whereas that in deuterated water relaxes on a timescale of 0.7 ps, consistent with the experimental observations. To decompose these relaxation energies into the components due to intramolecular and intermolecular couplings, constraints are introduced on the vibrational modes except for the target path in the NE-AIMD simulation. In the case of pure water, 80% of the total relaxation is attributed to the pathway due to the resonant intermolecular OH⋯OH stretch coupling, and the remaining 17% and 3% are attributed to intramolecular couplings with the bend overtone and with the conjugate OH stretch, respectively. This result strongly supports a significant role for the Förster transfer mechanism of pure water due to the intermolecular dipole-dipole interactions. In the case of deuterated water, on the other hand, 36% of the total relaxation is due to the intermolecular stretch coupling, and all the remaining 64% arises from coupling with the intramolecular bend overtone.
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Affiliation(s)
- Tatsuya Ishiyama
- Department of Applied Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
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220
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Dhabal D, Jiang Z, Pallath A, Patel AJ. Characterizing the Interplay between Polymer Solvation and Conformation. J Phys Chem B 2021; 125:5434-5442. [PMID: 33978411 DOI: 10.1021/acs.jpcb.1c02191] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between solvation and conformation. Using specialized molecular simulations, here we perform such a characterization for a hydrophobic polymer solvated in water. We find that an external potential, which unfavorably perturbs the polymer hydration waters, can trigger a coil-to-globule or collapse transition, and that the relative stabilities of the collapsed and extended states can be quantified by the strength of the requisite potential. Our results also provide mechanistic insights into the collapse transition, highlighting that the bottleneck to polymer collapse is the formation of a sufficiently large cluster, and the collective dewetting of such a cluster. We also study the collapse of the hydrophobic polymer in octane, a nonpolar solvent, and interestingly, we find that the mechanistic details of the transition are qualitatively similar to that in water.
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Affiliation(s)
- Debdas Dhabal
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zhitong Jiang
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Akash Pallath
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Amish J Patel
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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221
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Ghazwani M, Alam P, Alqarni MH, Yusufoglu HS, Shakeel F. Solubilization of Trans-Resveratrol in Some Mono-Solvents and Various Propylene Glycol + Water Mixtures. Molecules 2021; 26:3091. [PMID: 34064283 PMCID: PMC8196874 DOI: 10.3390/molecules26113091] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 01/20/2023] Open
Abstract
This research deals with the determination of solubility, Hansen solubility parameters, dissolution properties, enthalpy-entropy compensation, and computational modeling of a naturally-derived bioactive compound trans-resveratrol (TRV) in water, methanol, ethanol, n-propanol, n-butanol, propylene glycol (PG), and various PG + water mixtures. The solubility of TRV in six different mono-solvents and various PG + water mixtures was determined at 298.2-318.2 K and 0.1 MPa. The measured experimental solubility values of TRV were regressed using six different computational/theoretical models, including van't Hoff, Apelblat, Buchowski-Ksiazczak λh, Yalkowsly-Roseman, Jouyban-Acree, and van't Hoff-Jouyban-Acree models, with average uncertainties of less than 3.0%. The maxima of TRV solubility in mole fraction was obtained in neat PG (2.62 × 10-2) at 318.2 K. However, the minima of TRV solubility in the mole fraction was recorded in neat water (3.12 × 10-6) at 298.2 K. Thermodynamic calculation of TRV dissolution properties suggested an endothermic and entropy-driven dissolution of TRV in all studied mono-solvents and various PG + water mixtures. Solvation behavior evaluation indicated an enthalpy-driven mechanism as the main mechanism for TRV solvation. Based on these data and observations, PG has been chosen as the best mono-solvent for TRV solubilization.
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Affiliation(s)
- Mohammed Ghazwani
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha 61441, Saudi Arabia;
| | - Prawez Alam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia; (P.A.); (M.H.A.); (H.S.Y.)
| | - Mohammed H. Alqarni
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia; (P.A.); (M.H.A.); (H.S.Y.)
| | - Hasan S. Yusufoglu
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia; (P.A.); (M.H.A.); (H.S.Y.)
| | - Faiyaz Shakeel
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
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222
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Molecular Tailoring Approach for the Estimation of Intramolecular Hydrogen Bond Energy. Molecules 2021; 26:molecules26102928. [PMID: 34069140 PMCID: PMC8155843 DOI: 10.3390/molecules26102928] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/29/2022] Open
Abstract
Hydrogen bonds (HBs) play a crucial role in many physicochemical and biological processes. Theoretical methods can reliably estimate the intermolecular HB energies. However, the methods for the quantification of intramolecular HB (IHB) energy available in the literature are mostly empirical or indirect and limited only to evaluating the energy of a single HB. During the past decade, the authors have developed a direct procedure for the IHB energy estimation based on the molecular tailoring approach (MTA), a fragmentation method. This MTA-based method can yield a reliable estimate of individual IHB energy in a system containing multiple H-bonds. After explaining and illustrating the methodology of MTA, we present its use for the IHB energy estimation in molecules and clusters. We also discuss the use of this method by other researchers as a standard, state-of-the-art method for estimating IHB energy as well as those of other noncovalent interactions.
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223
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Ortiz-Mahecha CA, Agudelo WA, Patarroyo MA, Patarroyo ME, Suárez CF. MHCBI: a pipeline for calculating peptide-MHC binding energy using semi-empirical quantum mechanical methods with explicit/implicit solvent models. Brief Bioinform 2021; 22:6274818. [PMID: 33979434 DOI: 10.1093/bib/bbab171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/10/2021] [Accepted: 03/30/2021] [Indexed: 11/12/2022] Open
Abstract
Experimentally estimating peptide-major histocompatibility complex (pMHC) binding affinity has been quite challenging due to the many receptors and the many potential ligands implicated in it. We have thus proposed a straightforward computational methodology considering the different mechanisms involved in pMHC binding to facilitate studying such receptor-ligand interactions. We have developed a pipeline using semi-empirical quantum mechanical methods for calculating pMHC class I and II molecules' binding energy (BE). This pipeline can systematize the methodology for calculating pMHC system BE, enabling the rational design of T-cell epitopes to be used as pharmaceuticals and vaccines.
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Affiliation(s)
| | | | | | | | - Carlos F Suárez
- Fundación Instituto de Inmunología de Colombia, Bogota DC, Colombia
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224
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Water-oriented magnetic anisotropy transition. Nat Commun 2021; 12:2738. [PMID: 33980833 PMCID: PMC8115317 DOI: 10.1038/s41467-021-23057-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 04/14/2021] [Indexed: 12/04/2022] Open
Abstract
Water reorientation is essential in a wide range of chemical and biological processes. However, the effects of such reorientation through rotation around the metal–oxygen bond on the chemical and physical properties of the resulting complex are usually ignored. Most studies focus on the donor property of water as a recognized σ donor-type ligand rather than a participant in the π interaction. Although a theoretical approach to study water-rotation effects on the functionality of a complex has recently been conducted, it has not been experimentally demonstrated. In this study, we determine that the magnetic anisotropy of a Co(II) complex can be effectively controlled by the slight rotation of coordinating water ligands, which is achieved by a two-step structural phase transition. When the water molecule is rotated by 21.2 ± 0.2° around the Co–O bond, the directional magnetic susceptibility of the single crystal changes by approximately 30% along the a-axis due to the rotation of the magnetic anisotropy axis through the modification of the π interaction between cobalt(II) and the water ligand. The theoretical calculations further support the hypothesis that the reorientation of water molecules is a key factor contributing to the magnetic anisotropy transition of this complex. Little is known about how the orientation of coordinated water molecules affects the magnetic properties of single molecule magnets. Here the authors combine experimental data and theoretical calculations to study how the rotation of water molecules alters the magnetic anisotropy of a pyrazine-based cobalt(II) complex.
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225
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Blanquart S, Groussin M, Le Roy A, Szöllosi GJ, Girard E, Franzetti B, Gouy M, Madern D. Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins : Deciphering Gene Trajectories and Changes in Biochemical Properties. Mol Biol Evol 2021; 38:3754-3774. [PMID: 33974066 PMCID: PMC8382911 DOI: 10.1093/molbev/msab146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Extreme halophilic Archaea thrive in high salt, where, through proteomic adaptation, they cope with the strong osmolarity and extreme ionic conditions of their environment. In spite of wide fundamental interest, however, studies providing insights into this adaptation are scarce, because of practical difficulties inherent to the purification and characterization of halophilic enzymes. In this work, we describe the evolutionary history of malate dehydrogenases (MalDH) within Halobacteria (a class of the Euryarchaeota phylum). We resurrected nine ancestors along the inferred halobacterial MalDH phylogeny, including the Last Common Ancestral MalDH of Halobacteria (LCAHa) and compared their biochemical properties with those of five modern halobacterial MalDHs. We monitored the stability of these various MalDHs, their oligomeric states and enzymatic properties, as a function of concentration for different salts in the solvent. We found that a variety of evolutionary processes such as amino acid replacement, gene duplication, loss of MalDH gene and replacement owing to horizontal transfer resulted in significant differences in solubility, stability and catalytic properties between these enzymes in the three Halobacteriales, Haloferacales and Natrialbales orders since the LCAHa MalDH.We also showed how a stability trade-off might favor the emergence of new properties during adaptation to diverse environmental conditions. Altogether, our results suggest a new view of halophilic protein adaptation in Archaea.
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Affiliation(s)
| | - Mathieu Groussin
- Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, Villeurbanne, F-69622, France.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Aline Le Roy
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, F-38000, France
| | - Gergely J Szöllosi
- Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, Villeurbanne, F-69622, France.,MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Budapest, H-1117, Hungary
| | - Eric Girard
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, F-38000, France
| | - Bruno Franzetti
- Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, F-38000, France
| | - Manolo Gouy
- Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, Villeurbanne, F-69622, France
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226
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Cui H, Eltoukhy L, Zhang L, Markel U, Jaeger K, Davari MD, Schwaneberg U. Less Unfavorable Salt Bridges on the Enzyme Surface Result in More Organic Cosolvent Resistance. Angew Chem Int Ed Engl 2021; 60:11448-11456. [PMID: 33687787 PMCID: PMC8252522 DOI: 10.1002/anie.202101642] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Indexed: 11/06/2022]
Abstract
Biocatalysis for the synthesis of fine chemicals is highly attractive but usually requires organic (co-)solvents (OSs). However, native enzymes often have low activity and resistance in OSs and at elevated temperatures. Herein, we report a smart salt bridge design strategy for simultaneously improving OS resistance and thermostability of the model enzyme, Bacillus subtilits Lipase A (BSLA). We combined comprehensive experimental studies of 3450 BSLA variants and molecular dynamics simulations of 36 systems. Iterative recombination of four beneficial substitutions yielded superior resistant variants with up to 7.6-fold (D64K/D144K) improved resistance toward three OSs while exhibiting significant thermostability (thermal resistance up to 137-fold, and half-life up to 3.3-fold). Molecular dynamics simulations revealed that locally refined flexibility and strengthened hydration jointly govern the highly increased resistance in OSs and at 50-100 °C. The salt bridge redesign provides protein engineers with a powerful and likely general approach to design OSs- and/or thermal-resistant lipases and other α/β-hydrolases.
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Affiliation(s)
- Haiyang Cui
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- DWI Leibniz-Institute for Interactive MaterialsForckenbeckstrasse 5052074AachenGermany
| | - Lobna Eltoukhy
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Lingling Zhang
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesWest 7th Avenue 32, Tianjin Airport Economic Area300308TianjinChina
| | - Ulrich Markel
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme TechnologyHeinrich Heine University DüsseldorfWilhelm Johnen Strasse52426JülichGermany
- Institute of Bio-and Geosciences IBG 1: BiotechnologyForschungszentrum Jülich GmbHWilhelm Johnen Strasse52426JülichGermany
| | - Mehdi D. Davari
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Ulrich Schwaneberg
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- DWI Leibniz-Institute for Interactive MaterialsForckenbeckstrasse 5052074AachenGermany
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227
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Cui H, Eltoukhy L, Zhang L, Markel U, Jaeger K, Davari MD, Schwaneberg U. Less Unfavorable Salt Bridges on the Enzyme Surface Result in More Organic Cosolvent Resistance. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Haiyang Cui
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
- DWI Leibniz-Institute for Interactive Materials Forckenbeckstrasse 50 52074 Aachen Germany
| | - Lobna Eltoukhy
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Lingling Zhang
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences West 7th Avenue 32, Tianjin Airport Economic Area 300308 Tianjin China
| | - Ulrich Markel
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme Technology Heinrich Heine University Düsseldorf Wilhelm Johnen Strasse 52426 Jülich Germany
- Institute of Bio-and Geosciences IBG 1: Biotechnology Forschungszentrum Jülich GmbH Wilhelm Johnen Strasse 52426 Jülich Germany
| | - Mehdi D. Davari
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
- DWI Leibniz-Institute for Interactive Materials Forckenbeckstrasse 50 52074 Aachen Germany
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228
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Yazdani M, Jia Z, Chen J. Hydrophobic dewetting in gating and regulation of transmembrane protein ion channels. J Chem Phys 2021; 153:110901. [PMID: 32962356 DOI: 10.1063/5.0017537] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water is at the heart of almost all biological phenomena, without which no life that we know of would have been possible. It is a misleadingly complex liquid that exists in near coexistence with the vapor phase under ambient conditions. Confinement within a hydrophobic cavity can tip this balance enough to drive a cooperative dewetting transition. For a nanometer-scale pore, the dewetting transition leads to a stable dry state that is physically open but impermeable to ions. This phenomenon is often referred to as hydrophobic gating. Numerous transmembrane protein ion channels have now been observed to utilize hydrophobic gating in their activation and regulation. Here, we review recent theoretical, simulation, and experimental studies that together have started to establish the principles of hydrophobic gating and discuss how channels of various sizes, topologies, and biological functions can utilize these principles to control the thermodynamic properties of water within their interior pores for gating and regulation. Exciting opportunities remain in multiple areas, particularly on direct experimental detection of hydrophobic dewetting in biological channels and on understanding how the cell may control the hydrophobic gating in regulation of ion channels.
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Affiliation(s)
- Mahdieh Yazdani
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Zhiguang Jia
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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229
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Abstract
Quantum-mechanically driven charge polarization and charge transfer are ubiquitous in biomolecular systems, controlling reaction rates, allosteric interactions, ligand-protein binding, membrane transport, and dynamically driven structural transformations. Molecular dynamics (MD) simulations of these processes require quantum mechanical (QM) information in order to accurately describe their reactive dynamics. However, current techniques-empirical force fields, subsystem approaches, ab initio MD, and machine learning-vary in their ability to achieve a consistent chemical description across multiple atom types, and at scale. Here we present a physics-based, atomistic force field, the ensemble DFT charge-transfer embedded-atom method, in which QM forces are described at a uniform level of theory across all atoms, avoiding the need for explicit solution of the Schrödinger equation or large, precomputed training data sets. Coupling between the electronic and atomistic length scales is effected through an ensemble density functional theory formulation of the embedded-atom method originally developed for elemental materials. Charge transfer is expressed in terms of ensembles of ionic state basis densities of individual atoms, and charge polarization, in terms of atomic excited-state basis densities. This provides a highly compact yet general representation of the force field, encompassing both local and system-wide effects. Charge rearrangement is realized through the evolution of ensemble weights, adjusted at each dynamical time step via chemical potential equalization.
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Affiliation(s)
- Susan R Atlas
- Department of Chemistry and Chemical Biology, Department of Physics and Astronomy, and Center for Quantum Information and Control, University of New Mexico, Albuquerque, New Mexico 87131, United States
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230
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Tokunaga Y, Tanaka M, Iida H, Kinoshita M, Tojima Y, Takeuchi K, Imashimizu M. Nonthermal excitation effects mediated by sub-terahertz radiation on hydrogen exchange in ubiquitin. Biophys J 2021; 120:2386-2393. [PMID: 33894216 PMCID: PMC8390810 DOI: 10.1016/j.bpj.2021.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/23/2021] [Accepted: 04/16/2021] [Indexed: 11/28/2022] Open
Abstract
Water dynamics in the hydration layers of biomolecules play crucial roles in a wide range of biological functions. A hydrated protein contains multiple components of diffusional and vibrational dynamics of water and protein, which may be coupled at ∼0.1-THz frequency (10-ps timescale) at room temperature. However, the microscopic description of biomolecular functions based on various modes of protein-water-coupled motions remains elusive. A novel approach for perturbing the hydration dynamics in the subterahertz frequency range and probing them at the atomic level is therefore warranted. In this study, we investigated the effect of klystron-based, intense 0.1-THz excitation on the slow dynamics of ubiquitin using NMR-based measurements of hydrogen-deuterium exchange. We demonstrated that the subterahertz irradiation accelerated the hydrogen-deuterium exchange of the amides located in the interior of the protein and hydrophobic surfaces while decelerating this exchange in the amides located in the surface loop and short 310 helix regions. This subterahertz-radiation-induced effect was qualitatively contradictory to the increased-temperature-induced effect. Our results suggest that the heterogeneous water dynamics occurring at the protein-water interface include components that are nonthermally excited by the subterahertz radiation. Such subterahertz-excited components may be linked to the slow function-related dynamics of the protein.
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Affiliation(s)
- Yuji Tokunaga
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahito Tanaka
- Research Institute for Measurement and Analytical Instrumentation, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hitoshi Iida
- Research Institute for Physical Measurement, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Moto Kinoshita
- Research Institute for Physical Measurement, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yuya Tojima
- Research Institute for Physical Measurement, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Koh Takeuchi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahiko Imashimizu
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
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231
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De Zitter E, Hugelier S, Duwé S, Vandenberg W, Tebo AG, Van Meervelt L, Dedecker P. Structure-Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System*. Angew Chem Int Ed Engl 2021; 60:10073-10081. [PMID: 33543524 DOI: 10.1002/anie.202015201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Indexed: 11/05/2022]
Abstract
Anisotropic environments can drastically alter the spectroscopy and photochemistry of molecules, leading to complex structure-function relationships. We examined this using fluorescent proteins as easy-to-modify model systems. Starting from a single scaffold, we have developed a range of 27 photochromic fluorescent proteins that cover a broad range of spectroscopic properties, including the determination of 43 crystal structures. Correlation and principal component analysis confirmed the complex relationship between structure and spectroscopy, but also allowed us to identify consistent trends and to relate these to the spatial organization. We find that changes in spectroscopic properties can come about through multiple underlying mechanisms, of which polarity, hydrogen bonding and presence of water molecules are key modulators. We anticipate that our findings and rich structure/spectroscopy dataset can open opportunities for the development and evaluation of new and existing protein engineering methods.
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Affiliation(s)
- Elke De Zitter
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium.,Present address: University Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Siewert Hugelier
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium
| | - Sam Duwé
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium.,Present address: Advanced Optical Microscopy Centre, Hasselt University, Agoralaan building C, 3590, Diepenbeek, Belgium
| | - Wim Vandenberg
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium
| | - Alison G Tebo
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, USA
| | - Luc Van Meervelt
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium
| | - Peter Dedecker
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium
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232
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Computing inelastic neutron scattering spectra from molecular dynamics trajectories. Sci Rep 2021; 11:7938. [PMID: 33846390 PMCID: PMC8041884 DOI: 10.1038/s41598-021-86771-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/18/2021] [Indexed: 11/20/2022] Open
Abstract
Inelastic neutron scattering (INS) provides a weighted density of phonon modes. Currently, INS spectra can only be interpreted for perfectly crystalline materials because of high computational cost for electronic simulations. INS has the potential to provide detailed morphological information if sufficiently large volumes and appropriate structural variety are simulated. Here, we propose a method that allows direct comparison between INS data with molecular dynamics simulations, a simulation method that is frequently used to simulate semicrystalline/amorphous materials. We illustrate the technique by analyzing spectra of a well-studied conjugated polymer, poly(3-hexylthiophene-2,5-diyl) (P3HT) and conclude that our technique provides improved volume and structural variety, but that the classical force field requires improvement before the morphology can be accurately interpreted.
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233
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Morphogenic fields: A coming of age. Explore (NY) 2021; 18:187-194. [PMID: 33903061 DOI: 10.1016/j.explore.2021.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 11/22/2022]
Abstract
Morphogenesis, the coming-into-being of living organisms, was first described in the 4th century BC by Aristotle, progenitor of biology and embryology. Over the centuries it has been the subject of innumerable commentaries by philosophers, theologians and scientists but no consensus has ever been reached as to its causes. In the late 19th century, along with the emergence of cellular and molecular biology, embryology underwent a renaissance and became a topic of great interest and research. Early on the discipline divided into two opposing factions, those who attempted to explain fetal development on the basis of cellular and molecular mechanisms, and those who invoked the presence of organizing fields. The morphogenic field was first articulated in the early decades of the 20th century by multiple researchers independently of each other. The field became an extremely useful conceptual tool by which to explain a wide range of developmental phenomena. While embryology and genetics originally formed a unified discipline, during the 1930s 40 s geneticists became progressively skeptical of the field notion. The discovery of the DNA structure by Watson and Crick in the early 1950s decisively settled matters and thereafter the two disciplines pursued different lines of inquiry. After World War II embryology and the field concept went into a decades-long decline. By the 1980s an increasing number of scientists began to critically reexamine the morphogenic field concept and it underwent a second renaissance. In this paper I examine the development and evolution of the field concept, both experimentally and conceptually, and highlight the failure of genetic mechanisms to explain morphogenesis. I provide three instances from the medical literature of developmental phenomena which are only explainable on the basis of morphogenic field dynamics and argue that the field concept must be readmitted into mainstream scientific discourse.
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234
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Piskulich ZA, Thompson WH. Examining the Role of Different Molecular Interactions on Activation Energies and Activation Volumes in Liquid Water. J Chem Theory Comput 2021; 17:2659-2671. [PMID: 33819026 DOI: 10.1021/acs.jctc.0c01217] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There are a large number of force fields available to model water in molecular dynamics simulations, which each have their own strengths and weaknesses in describing the behavior of the liquid. One particular weakness in many of these models is their description of dynamics away from ambient conditions, where their ability to reproduce measurements is mixed. To investigate this issue, we use the recently developed fluctuation theory for dynamics to directly evaluate measures of the local temperature and pressure dependence: the activation energy and the activation volume. We examine these activation parameters for hydrogen-bond jump exchange times, OH reorientation times, and diffusion coefficients calculated from the SPC/E, SPC/Fw, TIP3P-PME, TIP3P-PME/Fw, OPC3, TIP4P/2005, TIP4P/Ew, E3B2, and E3B3 water models. Activation energy decompositions available through the fluctuation theory approach provide mechanistic insight into the origins of different temperature dependences between the various models, as well as the influence of three-body effects and flexibility.
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Affiliation(s)
- Zeke A Piskulich
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Ward H Thompson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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235
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Biasin E, Fox ZW, Andersen A, Ledbetter K, Kjær KS, Alonso-Mori R, Carlstad JM, Chollet M, Gaynor JD, Glownia JM, Hong K, Kroll T, Lee JH, Liekhus-Schmaltz C, Reinhard M, Sokaras D, Zhang Y, Doumy G, March AM, Southworth SH, Mukamel S, Gaffney KJ, Schoenlein RW, Govind N, Cordones AA, Khalil M. Direct observation of coherent femtosecond solvent reorganization coupled to intramolecular electron transfer. Nat Chem 2021; 13:343-349. [PMID: 33589787 DOI: 10.1038/s41557-020-00629-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/14/2020] [Indexed: 01/31/2023]
Abstract
It is well known that the solvent plays a critical role in ultrafast electron-transfer reactions. However, solvent reorganization occurs on multiple length scales, and selectively measuring short-range solute-solvent interactions at the atomic level with femtosecond time resolution remains a challenge. Here we report femtosecond X-ray scattering and emission measurements following photoinduced charge-transfer excitation in a mixed-valence bimetallic (FeiiRuiii) complex in water, and their interpretation using non-equilibrium molecular dynamics simulations. Combined experimental and computational analysis reveals that the charge-transfer excited state has a lifetime of 62 fs and that coherent translational motions of the first solvation shell are coupled to the back electron transfer. Our molecular dynamics simulations identify that the observed coherent translational motions arise from hydrogen bonding changes between the solute and nearby water molecules upon photoexcitation, and have an amplitude of tenths of ångströms, 120-200 cm-1 frequency and ~100 fs relaxation time. This study provides an atomistic view of coherent solvent reorganization mediating ultrafast intramolecular electron transfer.
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Affiliation(s)
- Elisa Biasin
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
| | - Zachary W Fox
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Amity Andersen
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kathryn Ledbetter
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Kasper S Kjær
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Department of Physics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Julia M Carlstad
- Department of Chemistry, University of Washington, Seattle, WA, USA.,Department of Chemistry, University of California, Berkeley, CA, USA
| | - Matthieu Chollet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - James D Gaynor
- Department of Chemistry, University of Washington, Seattle, WA, USA.,Department of Chemistry, University of California, Berkeley, CA, USA
| | - James M Glownia
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Kiryong Hong
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Gas Metrology Group, Division of Chemical and Biological Metrology, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Thomas Kroll
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Jae Hyuk Lee
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Pohang Accelerator Laboratory, Pohang, Republic of Korea
| | | | - Marco Reinhard
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Dimosthenis Sokaras
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Yu Zhang
- Department of Chemistry, Physics, and Astronomy, University of California, Irvine, CA, USA.,Q-Chem, Pleasanton, CA, USA
| | - Gilles Doumy
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL, USA
| | - Anne Marie March
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL, USA
| | - Stephen H Southworth
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL, USA
| | - Shaul Mukamel
- Department of Chemistry, Physics, and Astronomy, University of California, Irvine, CA, USA
| | - Kelly J Gaffney
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Robert W Schoenlein
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Niranjan Govind
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Amy A Cordones
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
| | - Munira Khalil
- Department of Chemistry, University of Washington, Seattle, WA, USA.
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236
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Steinrücken E, Wissel T, Brodrecht M, Breitzke H, Regentin J, Buntkowsky G, Vogel M. 2H NMR study on temperature-dependent water dynamics in amino-acid functionalized silica nanopores. J Chem Phys 2021; 154:114702. [PMID: 33752372 DOI: 10.1063/5.0044141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We prepare various amino-acid functionalized silica pores with diameters of ∼6 nm and study the temperature-dependent reorientation dynamics of water in these confinements. Specifically, we link basic Lys, neutral Ala, and acidic Glu to the inner surfaces and combine 2H nuclear magnetic resonance spin-lattice relaxation and line shape analyses to disentangle the rotational motions of the surfaces groups and the crystalline and liquid water fractions coexisting below partial freezing. Unlike the crystalline phase, the liquid phase shows reorientation dynamics, which strongly depends on the chemistry of the inner surfaces. The water reorientation is slowest for the Lys functionalization, followed by Ala and Glu and, finally, the native silica pores. In total, the rotational correlation times of water at the different surfaces vary by about two orders of magnitude, where this span is largely independent of the temperature in the range ∼200-250 K.
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Affiliation(s)
- Elisa Steinrücken
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Till Wissel
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
| | - Martin Brodrecht
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
| | - Hergen Breitzke
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
| | - Julia Regentin
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Gerd Buntkowsky
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
| | - Michael Vogel
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
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237
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Kundu S, Chowdhury A, Nandi S, Bhattacharyya K, Patra A. Deciphering the evolution of supramolecular nanofibers in solution and solid-state: a combined microscopic and spectroscopic approach. Chem Sci 2021; 12:5874-5882. [PMID: 34168812 PMCID: PMC8179674 DOI: 10.1039/d0sc07050e] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/17/2021] [Indexed: 12/21/2022] Open
Abstract
Supramolecular self-assembly of small organic molecules has emerged as a powerful tool to construct well-defined micro- and nanoarchitecture through fine-tuning a range of intermolecular interactions. The size, shape, and optical properties of these nanostructures largely depend on the specific assembly of the molecular building units, temperature and polarity of the medium, and external stimuli. The engineering of supramolecular self-assembled nanostructures with morphology-dependent tunable emission is in high demand due to the promising scope in nanodevices and molecular machines. However, probing the evolution of molecular aggregates from the solution and directing the self-assembly process in a pre-defined fashion are challenging. In the present study, we have deciphered the sequential evolution of supramolecular nanofibers from solution to spherical and oblong-shaped nanoparticles through the variation of solvent polarity, tuning the hydrophobic-hydrophilic interactions. An intriguing case of molecular self-assembly has been elucidated employing a newly designed π-conjugated thiophene derivative (TPAn) through a combination of steady-state absorption, emission measurements, fluorescence correlation spectroscopy (FCS), and electron microscopy. The FCS analysis and microscopy results revealed that the small-sized nanofibers in the dispersion further agglomerated upon solvent evaporation, resulting in a network of nanofibers. Stimuli-responsive reversible interconversion between a network of nanofibers and spherical nanoaggregates was probed both in dispersion and solvent-evaporated state. The evolution of organic nanofibers and a subtle control over the self-assembly process demonstrated in the current investigation provide a general paradigm to correlate the size, shape, and emission properties of fluorescent molecular aggregates in complex heterogeneous media, including a human cell.
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Affiliation(s)
- Subhankar Kundu
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal By-Pass Road, Bhauri Bhopal 462066 Madhya Pradesh India
| | - Arkaprava Chowdhury
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal By-Pass Road, Bhauri Bhopal 462066 Madhya Pradesh India
| | - Somen Nandi
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal By-Pass Road, Bhauri Bhopal 462066 Madhya Pradesh India
| | - Kankan Bhattacharyya
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal By-Pass Road, Bhauri Bhopal 462066 Madhya Pradesh India
| | - Abhijit Patra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal By-Pass Road, Bhauri Bhopal 462066 Madhya Pradesh India
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238
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De Zitter E, Hugelier S, Duwé S, Vandenberg W, Tebo AG, Van Meervelt L, Dedecker P. Structure–Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Elke De Zitter
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
- Present address: University Grenoble Alpes CEA CNRS IBS 71 Avenue des Martyrs 38000 Grenoble France
| | - Siewert Hugelier
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
| | - Sam Duwé
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
- Present address: Advanced Optical Microscopy Centre Hasselt University Agoralaan building C 3590 Diepenbeek Belgium
| | - Wim Vandenberg
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
| | - Alison G. Tebo
- Janelia Research Campus Howard Hughes Medical Institute 19700 Helix Drive Ashburn Virginia 20147 USA
| | - Luc Van Meervelt
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
| | - Peter Dedecker
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
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239
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Päslack C, Schäfer LV, Heyden M. Protein flexibility reduces solvent-mediated friction barriers of ligand binding to a hydrophobic surface patch. Phys Chem Chem Phys 2021; 23:5665-5672. [PMID: 33656505 DOI: 10.1039/d1cp00181g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Solvent fluctuations have been explored in detail for idealized and rigid hydrophobic model systems, but so far it has remained unclear how internal protein motions and their coupling to the surrounding solvent affect the dynamics of ligand binding to biomolecular surfaces. Here, molecular dynamics simulations were used to elucidate the solvent-mediated binding of a model ligand to the hydrophobic surface patch of ubiquitin. The ligand's friction profiles reveal pronounced long-time correlations and enhanced friction in the vicinity of the protein, similar to idealized hydrophobic surfaces. Interestingly, these effects are shaped by internal protein motions. Protein flexibility modulates water density fluctuations near the hydrophobic surface patch and smooths out the friction profile of ligand binding.
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Affiliation(s)
- Christopher Päslack
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, D-44780 Bochum, Germany.
| | - Lars V Schäfer
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, D-44780 Bochum, Germany.
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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240
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Zhang Z, Ricci CG, Fan C, Cheng LT, Li B, McCammon JA. Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding. J Chem Theory Comput 2021; 17:2465-2478. [PMID: 33650860 DOI: 10.1021/acs.jctc.0c01109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We develop a hybrid approach that combines the Monte Carlo (MC) method, a variational implicit-solvent model (VISM), and a binary level-set method for the simulation of biomolecular binding in an aqueous solvent. The solvation free energy for the biomolecular complex is estimated by minimizing the VISM free-energy functional of all possible solute-solvent interfaces that are used as dielectric boundaries. This functional consists of the solute volumetric, solute-solvent interfacial, solute-solvent van der Waals interaction, and electrostatic free energy. A technique of shifting the dielectric boundary is used to accurately predict the electrostatic part of the solvation free energy. Minimizing such a functional in each MC move is made possible by our new and fast binary level-set method. This method is based on the approximation of surface area by the convolution of an indicator function with a compactly supported kernel and is implemented by simple flips of numerical grid cells locally around the solute-solvent interface. We apply our approach to the p53-MDM2 system for which the two molecules are approximated by rigid bodies. Our efficient approach captures some of the poses before the final bound state. All-atom molecular dynamics simulations with most of such poses quickly reach the final bound state. Our work is a new step toward realistic simulations of biomolecular interactions. With further improvement of coarse graining and MC sampling, and combined with other models, our hybrid approach can be used to study the free-energy landscape and kinetic pathways of ligand binding to proteins.
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Affiliation(s)
- Zirui Zhang
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - Clarisse G Ricci
- Department of Chemistry and Biochemistry and Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0365, United States
| | - Chao Fan
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - Li-Tien Cheng
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - Bo Li
- Department of Mathematics and Quantitative Biology Ph.D. Program, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry and Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0365, United States
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Dedic J, Okur HI, Roke S. Hyaluronan orders water molecules in its nanoscale extended hydration shells. SCIENCE ADVANCES 2021; 7:eabf2558. [PMID: 33658208 PMCID: PMC7929505 DOI: 10.1126/sciadv.abf2558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/14/2021] [Indexed: 05/17/2023]
Abstract
Hyaluronan (HA) is an anionic, highly hydrated bio-polyelectrolyte found in the extracellular environment, like the synovial fluid between joints. We explore the extended hydration shell structure of HA in water using femtosecond elastic second-harmonic scattering (fs-ESHS). HA enhances orientational water-water correlations. Angle-resolved fs-ESHS measurements and nonlinear optical modeling show that HA behaves like a flexible chain surrounded by extended shells of orientationally correlated water. We describe several ways to determine the concentration-dependent size and shape of a polyelectrolyte in water, using the amount of water oriented by the polyelectrolyte charges as a contrast agent. The spatial extent of the hydration shell is determined via temperature-dependent measurements and can reach up to 475 nm, corresponding to a length of 1600 water molecules. A strong isotope effect, stemming from nuclear quantum effects, is observed when light water (H2O) is replaced by heavy water (D2O), amounting to a factor of 4.3 in the scattered SH intensity.
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Affiliation(s)
- J Dedic
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute of Materials Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - H I Okur
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute of Materials Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department of Chemistry and National Nanotechnology Research Center (UNAM), Bilkent University, 06800 Ankara, Turkey
| | - S Roke
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute of Materials Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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242
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Edington SC, Liu S, Baiz CR. Infrared spectroscopy probes ion binding geometries. Methods Enzymol 2021; 651:157-191. [PMID: 33888203 DOI: 10.1016/bs.mie.2020.12.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Infrared (IR) spectroscopy is a well-established technique for probing the structure, behavior, and surroundings of molecules in their native environments. Its characteristics-most specifically high structural sensitivity, ready applicability to aqueous samples, and broad availability-make it a valuable enzymological technique, particularly for the interrogation of ion binding sites. While IR spectroscopy of the "garden variety" (steady state at room temperature with wild-type proteins) is versatile and powerful in its own right, the combination of IR spectroscopy with specialized experimental schemes for leveraging ultrafast time resolution, protein labeling, and other enhancements further extends this utility. This book chapter provides the fundamental physical background and literature context essential for harnessing IR spectroscopy in the general context of enzymology with specific focus on interrogation of ion binding. Studies of lanthanide ions binding to calmodulin are highlighted as illustrative examples of this process. Appropriate sample preparation, data collection, and spectral interpretation are discussed from a detail-oriented and practical perspective with the goal of facilitating the reader's rapid progression from reading words in a book to collecting and analyzing their own data in the lab.
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Affiliation(s)
- Sean C Edington
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Stephanie Liu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, United States
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, Austin, TX, United States.
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243
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Zhang Y, Haider K, Kaur D, Ngo VA, Cai X, Mao J, Khaniya U, Zhu X, Noskov S, Lazaridis T, Gunner MR. Characterizing the Water Wire in the Gramicidin Channel Found by Monte Carlo Sampling Using Continuum Electrostatics and in Molecular Dynamics Trajectories with Conventional or Polarizable Force Fields. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416520420016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Water molecules play a key role in all biochemical processes. They help define the shape of proteins, and they are reactant or product in many reactions and are released as ligands are bound. They facilitate the transfer of protons through transmembrane proton channel, pump and transporter proteins. Continuum electrostatics (CE) force fields used by program Multiconformation CE (MCCE) capture electrostatic interactions in biomolecules with an implicit solvent, which captures the averaged solvent water equilibrium properties. Hybrid CE methods can use explicit water molecules within the protein surrounded by implicit solvent. These hybrid methods permit the study of explicit hydrogen bond networks within the protein and allow analysis of processes such as proton transfer reactions. Yet hybrid CE methods have not been rigorously tested. Here, we present an explicit treatment of water molecules in the Gramicidin A (gA) channel using MCCE and compare the resulting distributions of water molecules and key hydration features against those obtained with explicit solvent Molecular Dynamics (MD) simulations with the nonpolarizable CHARMM36 and polarizable Drude force fields. CHARMM36 leads to an aligned water wire in the channel characterized by a large absolute net water dipole moment; the MCCE and Drude analysis lead to a small net dipole moment as the water molecules change orientation within the channel. The correct orientation is not as yet known, so these calculations identify an open question.
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Affiliation(s)
- Yingying Zhang
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Kamran Haider
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
| | - Divya Kaur
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Van A. Ngo
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Xiuhong Cai
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Junjun Mao
- Levich Institute, School of Engineering, City College of New York, City University of New York, New York, NY 10031, USA
| | - Umesh Khaniya
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Xuyu Zhu
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Sergei Noskov
- Department of Biological Sciences, Centre for Molecular Simulation, University of Calgary, Calgary, AB, Canada
| | - Themis Lazaridis
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, USA
- Department of Chemistry, City College of New York, City University of New York, New York, NY 10031, USA
| | - M. R. Gunner
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
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244
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Mi D, Cui J, Kuang S, Dong X, Lu H. Facile Atmospheric Generation of Water Radical Cations via
TiO
2
‐Nanoneedle Arrays for Aromatic Hydrocarbon Detection Based on Corona Discharge. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12220] [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)
- Dongbo Mi
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation East China University of Technology Nanchang 330013 China
| | - Jinhaojie Cui
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation East China University of Technology Nanchang 330013 China
| | - Siliang Kuang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry Jilin University Changchun 130012 China
| | - Xiaofeng Dong
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation East China University of Technology Nanchang 330013 China
| | - Haiyan Lu
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry Jilin University Changchun 130012 China
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245
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Ogata K. Investigation of Cooperative Modes for Collective Molecules Using Grid-Based Principal Component Analysis. J Phys Chem B 2021; 125:1072-1084. [PMID: 33492137 DOI: 10.1021/acs.jpcb.0c09615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A grid-based principal component analysis method (GBPCA) has been developed and implemented to investigate the modes of collective molecules present in the cube in the grid system from their trajectories using molecular dynamics (MD) simulation. This method is applied to the simulations of water, methane, and hydrated proteins. In the cases of single molecules, GBPCA demonstrates that while individual molecules interact with other molecules and move randomly, the collective molecules nevertheless produce cooperative principal component (PC) modes. Notably, these PC modes of the collective molecules formed vorticial or symmetrical structures, with some resembling torus-like structures. Such structures were observed not only in simulations with models that reproduced real molecules, such as water or methane, but also in simulations with artificial molecules that were modified to interact weakly or only repulsively. On the contrary, molecules without any interactions did not exhibit the cooperative PC modes that lead to the formation of specific structures. These results imply that when molecules subject to intermolecular forces are located in a space in which they can interact with one another, the PC modes of the collective molecules will form vorticial and torus-like structures. In the cases of hydrated proteins, the results reveal that the collective molecules in the protein and water molecules showed cooperative PC modes, forming vorticial or torus-like structures, as in the cases of the water or methane molecules. The PC modes of the water molecules close to the protein were influenced by the protein motion and indicated cooperative modes with the protein. Moreover, proteins with the same folds had similar PC mode structures. Besides, the PC modes of the proteins composed of multiple domains appeared independently in the protein domain. Hence, it can be understood that the cooperative motions of the collective molecules of the protein and surrounding water molecules contribute strongly to the protein's structure and function. These results are expected to help our understanding of the dynamics of molecules in the liquid state.
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Affiliation(s)
- Koji Ogata
- Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, 1-1-1 Daigaku-Dori, Sanyo-Onoda, Yamaguchi 859-0884, Japan
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246
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Bergazin TD, Ben-Shalom IY, Lim NM, Gill SC, Gilson MK, Mobley DL. Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo. J Comput Aided Mol Des 2021; 35:167-177. [PMID: 32968887 PMCID: PMC7904576 DOI: 10.1007/s10822-020-00344-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/16/2020] [Indexed: 11/26/2022]
Abstract
Water molecules can be found interacting with the surface and within cavities in proteins. However, water exchange between bulk and buried hydration sites can be slow compared to simulation timescales, thus leading to the inefficient sampling of the locations of water. This can pose problems for free energy calculations for computer-aided drug design. Here, we apply a hybrid method that combines nonequilibrium candidate Monte Carlo (NCMC) simulations and molecular dynamics (MD) to enhance sampling of water in specific areas of a system, such as the binding site of a protein. Our approach uses NCMC to gradually remove interactions between a selected water molecule and its environment, then translates the water to a new region, before turning the interactions back on. This approach of gradual removal of interactions, followed by a move and then reintroduction of interactions, allows the environment to relax in response to the proposed water translation, improving acceptance of moves and thereby accelerating water exchange and sampling. We validate this approach on several test systems including the ligand-bound MUP-1 and HSP90 proteins with buried crystallographic waters removed. We show that our BLUES (NCMC/MD) method enhances water sampling relative to normal MD when applied to these systems. Thus, this approach provides a strategy to improve water sampling in molecular simulations which may be useful in practical applications in drug discovery and biomolecular design.
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Affiliation(s)
| | - Ido Y Ben-Shalom
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Nathan M Lim
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - Sam C Gill
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA.
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.
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247
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Stasiulewicz M, Panuszko A, Śmiechowski M, Bruździak P, Maszota P, Stangret J. Effect of urea and glycine betaine on the hydration sphere of model molecules for the surface features of proteins. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.115090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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248
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Suvlu D, Thirumalai D, Rasaiah JC. Water-Mediated Interactions Determine Helix Formation of Peptides in Open Nanotubes. J Phys Chem B 2021; 125:817-824. [PMID: 33464101 DOI: 10.1021/acs.jpcb.0c10178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Water-mediated interactions (WMIs) play diverse roles in molecular biology. They are particularly relevant in geometrically confined spaces such as the interior of the chaperonin, at the interface between ligands and their binding partners, and in the ribosome tunnel. Inspired in part by the geometry of the ribosome tunnel, we consider confinement effects on the stability of peptides. We describe results from replica exchange molecular dynamics simulations of a system containing a 23-alanine or 23-serine polypeptide confined to nonpolar and polar nanotubes in the gas phase and when open to a water reservoir. We quantify the effect of water in determining the preferred conformational states of these polypeptides by calculating the difference in the solvation free energy for the helix and coil states in the open nanotube in the two phases. Our simulations reveal several possibilities. We find that nanoscopic confinement preferentially stabilizes the helical state of polypeptides with hydrophobic side chains, which is explained by the entropic stabilization mechanism proposed on the basis of polymer physics. Polypeptide chains with hydrophilic side chains can adopt helical structures within nanotubes, but helix formation is sensitive to the nature of the nanotube due to WMIs. We elaborate on the potential implications of our findings to the stability of peptides in the ribosome tunnel.
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Affiliation(s)
- Dylan Suvlu
- University of Maine, Orono, Maine 04469, United States
| | - D Thirumalai
- The University of Texas at Austin, Austin, Texas 78712, United States
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249
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Friesen S, Fedotova MV, Kruchinin SE, Buchner R. Hydration and dynamics of L-glutamate ion in aqueous solution. Phys Chem Chem Phys 2021; 23:1590-1600. [PMID: 33409510 DOI: 10.1039/d0cp05489e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Aqueous solutions of sodium l-glutamate (NaGlu) in the concentration range 0 < c/M ≤ 1.90 at 25 °C were investigated by dielectric relaxation spectroscopy (DRS) and statistical mechanics (1D-RISM and 3D-RISM calculations) to study the hydration and dynamics of the l-glutamate (Glu-) anion. Although at c → 0 water molecules beyond the first hydration shell are dynamically affected, Glu- hydration is rather fragile and for c ⪆ 0.3 M apparently restricted to H2O molecules hydrogen bonding to the carboxylate groups. These hydrating dipoles are roughly parallel to the anion moment, leading to a significantly enhanced effective dipole moment of Glu-. However, l-glutamate dynamics is determined by the rotational diffusion of individual anions under hydrodynamic slip boundary conditions. Thus, the lifetime of the hydrate complexes, as well as of possibly formed [Na+Glu-]0 ionpairs and l-glutamate aggregates, cannot exceed the characteristic timescale for Glu- rotation.
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Affiliation(s)
- Sergej Friesen
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany.
| | - Marina V Fedotova
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya St. 1, 153045 Ivanovo, Russian Federation.
| | - Sergey E Kruchinin
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya St. 1, 153045 Ivanovo, Russian Federation.
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany.
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250
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