1
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Sabei A, Hognon C, Martin J, Frezza E. Dynamics of Protein-RNA Interfaces Using All-Atom Molecular Dynamics Simulations. J Phys Chem B 2024; 128:4865-4886. [PMID: 38740056 DOI: 10.1021/acs.jpcb.3c07698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Facing the current challenges posed by human health diseases requires the understanding of cell machinery at a molecular level. The interplay between proteins and RNA is key for any physiological phenomenon, as well protein-RNA interactions. To understand these interactions, many experimental techniques have been developed, spanning a very wide range of spatial and temporal resolutions. In particular, the knowledge of tridimensional structures of protein-RNA complexes provides structural, mechanical, and dynamical pieces of information essential to understand their functions. To get insights into the dynamics of protein-RNA complexes, we carried out all-atom molecular dynamics simulations in explicit solvent on nine different protein-RNA complexes with different functions and interface size by taking into account the bound and unbound forms. First, we characterized structural changes upon binding and, for the RNA part, the change in the puckering. Second, we extensively analyzed the interfaces, their dynamics and structural properties, and the structural waters involved in the binding, as well as the contacts mediated by them. Based on our analysis, the interfaces rearranged during the simulation time showing alternative and stable residue-residue contacts with respect to the experimental structure.
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Affiliation(s)
- Afra Sabei
- Université Paris Cité, CiTCoM, CNRS, Paris F-75006, France
| | - Cécilia Hognon
- Université Paris Cité, CiTCoM, CNRS, Paris F-75006, France
| | - Juliette Martin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5086 MMSB, Lyon 69367, France
- Laboratory of Biology and Modeling of the Cell, Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, Lyon 69367, France
| | - Elisa Frezza
- Université Paris Cité, CiTCoM, CNRS, Paris F-75006, France
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2
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Reid KM, Poudel H, Leitner DM. Dynamics of Hydrogen Bonds between Water and Intrinsically Disordered and Structured Regions of Proteins. J Phys Chem B 2023; 127:7839-7847. [PMID: 37672685 DOI: 10.1021/acs.jpcb.3c03102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Recent studies indicate more restricted dynamics of water around intrinsically disordered proteins (IDPs) than structured proteins. We examine here the dynamics of hydrogen bonds between water molecules and two proteins, small ubiquitin-related modifier-1 (SUMO-1) and ubiquitin-conjugating enzyme E2I (UBC9), which we compare around intrinsically disordered regions (IDRs) and structured regions of these proteins. It has been recognized since some time that excluded volume effects, which influence access of water molecules to hydrogen-bonding sites, and the strength of hydrogen bonds between water and protein affect hydrogen bond lifetimes. While we find those two properties to mediate lifetimes of hydrogen bonds between water and protein residues in this study, we also find that the lifetimes are affected by the concentration of charged groups on other nearby residues. These factors are more important in determining the hydrogen bond lifetimes than whether a residue hydrogen bonding with water belongs to an IDR or to a structured region.
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Affiliation(s)
- Korey M Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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3
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Shikata K, Kikutsuji T, Yasoshima N, Kim K, Matubayasi N. Revealing the hidden dynamics of confined water in acrylate polymers: Insights from hydrogen-bond lifetime analysis. J Chem Phys 2023; 158:2887576. [PMID: 37125720 DOI: 10.1063/5.0148753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/13/2023] [Indexed: 05/02/2023] Open
Abstract
Polymers contain functional groups that participate in hydrogen bond (H-bond) with water molecules, establishing a robust H-bond network that influences bulk properties. This study utilized molecular dynamics (MD) simulations to examine the H-bonding dynamics of water molecules confined within three poly(meth)acrylates: poly(2-methoxyethyl acrylate) (PMEA), poly(2-hydroxyethyl methacrylate) (PHEMA), and poly(1-methoxymethyl acrylate) (PMC1A). Results showed that H-bonding dynamics significantly slowed as the water content decreased. Additionally, the diffusion of water molecules and its correlation with H-bond breakage were analyzed. Our findings suggest that when the H-bonds between water molecules and the methoxy oxygen of PMEA are disrupted, those water molecules persist in close proximity and do not diffuse on a picosecond time scale. In contrast, the water molecules H-bonded with the hydroxy oxygen of PHEMA and the methoxy oxygen of PMC1A diffuse concomitantly with the breakage of H-bonds. These results provide an in-depth understanding of the impact of polymer functional groups on H-bonding dynamics.
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Affiliation(s)
- Kokoro Shikata
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Takuma Kikutsuji
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuhiro Yasoshima
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Department of Information and Computer Engineering, National Institute of Technology, Toyota College, 2-1 Eiseicho, Toyota, Aichi 471-8525, Japan
| | - Kang Kim
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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4
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Ghoshdastidar D, Bansal M. Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif. Biophys J 2022; 121:3987-4000. [PMID: 35978548 PMCID: PMC9674967 DOI: 10.1016/j.bpj.2022.08.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/28/2022] [Accepted: 08/15/2022] [Indexed: 11/02/2022] Open
Abstract
Selective gene regulation is mediated by recognition of specific DNA sequences by transcription factors (TFs). The extremely challenging task of searching out specific cognate DNA binding sites among several million putative sites within the eukaryotic genome is achieved by complex molecular recognition mechanisms. Elements of this recognition code include the core binding sequence, the flanking sequence context, and the shape and conformational flexibility of the composite binding site. To unravel the extent to which DNA flexibility modulates TF binding, in this study, we employed experimentally guided molecular dynamics simulations of ternary complex of closely related Hox heterodimers Exd-Ubx and Exd-Scr with DNA. Results demonstrate that flexibility signatures embedded in the flanking sequences impact TF binding at the cognate binding site. A DNA sequence has intrinsic shape and flexibility features. While shape features are localized, our analyses reveal that flexibility features of the flanking sequences percolate several basepairs and allosterically modulate TF binding at the core. We also show that lack of flexibility in the motif context can render the cognate site resistant to protein-induced shape changes and subsequently lower TF binding affinity. Overall, this study suggests that flexibility-guided DNA shape, and not merely the static shape, is a key unexplored component of the complex DNA-TF recognition code.
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Affiliation(s)
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India.
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5
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Martin J, Frezza E. A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations. Front Mol Biosci 2022; 9:970109. [PMID: 36275619 PMCID: PMC9583002 DOI: 10.3389/fmolb.2022.970109] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Protein-protein interactions are at the basis of many protein functions, and the knowledge of 3D structures of protein-protein complexes provides structural, mechanical and dynamical pieces of information essential to understand these functions. Protein-protein interfaces can be seen as stable, organized regions where residues from different partners form non-covalent interactions that are responsible for interaction specificity and strength. They are commonly described as a peripheral region, whose role is to protect the core region that concentrates the most contributing interactions, from the solvent. To get insights into the dynamics of protein-protein complexes, we carried out all-atom molecular dynamics simulations in explicit solvent on eight different protein-protein complexes of different functional class and interface size by taking into account the bound and unbound forms. On the one hand, we characterized structural changes upon binding of the proteins, and on the other hand we extensively analyzed the interfaces and the structural waters involved in the binding. Based on our analysis, in 6 cases out of 8, the interfaces rearranged during the simulation time, in stable and long-lived substates with alternative residue-residue contacts. These rearrangements are not restricted to side-chain fluctuations in the periphery but also affect the core interface. Finally, the analysis of the waters at the interface and involved in the binding pointed out the importance to take into account their role in the estimation of the interaction strength.
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Affiliation(s)
- Juliette Martin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5086 MMSB, Lyon, France
- *Correspondence: Juliette Martin, ; Elisa Frezza,
| | - Elisa Frezza
- Université Paris Cité, CiTCoM, Paris, France
- *Correspondence: Juliette Martin, ; Elisa Frezza,
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6
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Reuhl M, Vogel M. Temperature-Dependent Dynamics at Protein-Solvent Interfaces. J Chem Phys 2022; 157:074705. [DOI: 10.1063/5.0105062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We perform differential scanning calorimetry, broadband dielectric spectroscopy (BDS), and nuclear magnetic resonance (NMR) studies to ascertain the molecular dynamics in mixtures of ethylene glycol with elastin or lysozyme over broad temperature ranges. To focus on the protein-solvent interface, we use mixtures with about equal numbers of amino acids and solvent molecules. The elastin and lysozyme mixtures show similar glass transition steps, which extend over a broad temperature range of 157-185K. The BDS and NMR studies yield fully consistent results for the fastest process P1, which is caused by the structural relaxation of ethylene glycol between the protein molecules and follows an Arrhenius law with an activation energy of Ea=0.63eV. It involves quasi-isotropic reorientation and is very similar in the elastin and lysozyme matrices but different from the alpha and beta relaxations of bulk ethylene glycol. Two slower BDS processes P2 and P3 have protein-dependent time scales, but exhibit a similar Arrhenius-like temperature dependence with an activation energy of Ea~0.81eV. However, P2 and P3 do not have a clear NMR signature. In particular, the NMR results for the lysozyme mixture reveal that the protein backbone does not show isotropic alpha-like motion on the P2 and P3 time scales but only restricted beta-like reorientation. The different activation energies of the P1 and P2/P3 processes do not support an intimate coupling of protein and ethylene glycol dynamics. The present results are compared with previous findings for mixtures of proteins with water or glycerol, implying qualitatively different dynamical couplings at various protein-solvent interfaces.
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Affiliation(s)
| | - Michael Vogel
- Institute of Condensed Matter Physics, TU Darmstadt, Germany
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7
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Singh AV, Kayal A, Malik A, Maharjan RS, Dietrich P, Thissen A, Siewert K, Curato C, Pande K, Prahlad D, Kulkarni N, Laux P, Luch A. Interfacial Water in the SARS Spike Protein: Investigating the Interaction with Human ACE2 Receptor and In Vitro Uptake in A549 Cells. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7976-7988. [PMID: 35736838 PMCID: PMC9260741 DOI: 10.1021/acs.langmuir.2c00671] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/02/2022] [Indexed: 05/09/2023]
Abstract
The severity of global pandemic due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has engaged the researchers and clinicians to find the key features triggering the viral infection to lung cells. By utilizing such crucial information, researchers and scientists try to combat the spread of the virus. Here, in this work, we performed in silico analysis of the protein-protein interactions between the receptor-binding domain (RBD) of the viral spike protein and the human angiotensin-converting enzyme 2 (hACE2) receptor to highlight the key alteration that happened from SARS-CoV to SARS-CoV-2. We analyzed and compared the molecular differences between spike proteins of the two viruses using various computational approaches such as binding affinity calculations, computational alanine, and molecular dynamics simulations. The binding affinity calculations showed that SARS-CoV-2 binds a little more firmly to the hACE2 receptor than SARS-CoV. The major finding obtained from molecular dynamics simulations was that the RBD-ACE2 interface is populated with water molecules and interacts strongly with both RBD and ACE2 interfacial residues during the simulation periods. The water-mediated hydrogen bond by the bridge water molecules is crucial for stabilizing the RBD and ACE2 domains. Near-ambient pressure X-ray photoelectron spectroscopy (NAP-XPS) confirmed the presence of vapor and molecular water phases in the protein-protein interfacial domain, further validating the computationally predicted interfacial water molecules. In addition, we examined the role of interfacial water molecules in virus uptake by lung cell A549 by binding and maintaining the RBD/hACE2 complex at varying temperatures using nanourchins coated with spike proteins as pseudoviruses and fluorescence-activated cell sorting (FACS) as a quantitative approach. The structural and dynamical features presented here may serve as a guide for developing new drug molecules, vaccines, or antibodies to combat the COVID-19 pandemic.
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Affiliation(s)
- Ajay Vikram Singh
- Department
of Chemical and Product Safety, German Federal
Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | | | | | - Romi Singh Maharjan
- Department
of Chemical and Product Safety, German Federal
Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Paul Dietrich
- SPECS
Surface Nano Analysis GmbH, Voltastrasse 5, 13355 Berlin, Germany
| | - Andreas Thissen
- SPECS
Surface Nano Analysis GmbH, Voltastrasse 5, 13355 Berlin, Germany
| | - Katherina Siewert
- Department
of Chemical and Product Safety, German Federal
Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Caterina Curato
- Department
of Chemical and Product Safety, German Federal
Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | | | | | | | - Peter Laux
- Department
of Chemical and Product Safety, German Federal
Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Andreas Luch
- Department
of Chemical and Product Safety, German Federal
Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
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8
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Zhang R, Cross TA, Peng X, Fu R. Surprising Rigidity of Functionally Important Water Molecules Buried in the Lipid Headgroup Region. J Am Chem Soc 2022; 144:7881-7888. [PMID: 35439409 PMCID: PMC9165019 DOI: 10.1021/jacs.2c02145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Understanding water dynamics and structure is an important topic in biological systems. It is generally held in the literature that the interfacial water of hydrated phospholipids is highly mobile, in fast exchange with the bulk water ranging from the nano- to femtosecond timescale. Although nuclear magnetic resonance (NMR) is a powerful tool for structural and dynamic studies, direct probing of interfacial water in hydrated phospholipids is formidably challenging due to the extreme population difference between bulk and interfacial water. We developed a novel 17O solid-state NMR technique in combination with an ultra-high-field magnet (35.2 T) to directly probe the functionally important interfacial water. By selectively suppressing the dominant bulk water signal, we observed two distinct water species in the headgroup region of hydrated dimyristoylphosphatidylcholine (DMPC) lipid bilayers for the first time. One water species denoted as "confined water" is chemically and dynamically different from the bulk water (∼0.17 ppm downfield and a slightly shorter spin-lattice relaxation time). Another water species denoted as "bound water" has severely restricted motion and a distinct chemical shift (∼12 ppm upfield). Additionally, the bulk water is not as "free" as pure water, resulting from the fast exchange with the water molecules that weakly and transiently interact with the lipid choline groups. These new discoveries clearly indicate the existence of the interfacial water molecules that are relatively stable over the NMR timescale (on the order of milliseconds), providing an opportunity to characterize water dynamics on the millisecond or slower timescale in biomacromolecules.
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Affiliation(s)
- Rongfu Zhang
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32301, United States
| | - Timothy A Cross
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32301, United States
| | - Xinhua Peng
- CAS Key Laboratory of Microscale Magnetic Resonance and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Riqiang Fu
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
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9
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Yamazoe K, Higaki Y, Inutsuka Y, Miyawaki J, Takahara A, Harada Y. Critical In-Plane Density of Polyelectrolyte Brush for the Ordered Hydrogen-Bonded Structure of Incorporated Water. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:3076-3081. [PMID: 35230121 DOI: 10.1021/acs.langmuir.1c02895] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A polymer electrolyte brush is a reasonable platform to confine water molecules within a nanoscopic area to study their role in the function of interacting media because of their adjustable nanospace and charge by changing the in-plane density and side chains of the brush. Here, we demonstrate how the in-plane spacing of cationic polymer brush chains, poly[2-(methacryloyloxy)ethyltrimethylammonium chloride] (PMTAC), affects the hydrogen bond configuration of incorporated water using soft X-ray emission spectroscopy. At the critical in-plane density σ = 0.30 chains/nm2 of PMTAC, tetrahedrally coordinated water molecules started to melt into distorted or broken hydrogen-bonded configurations. Considering the charge on the quaternary ammonium cations, the electric field required to form a tetrahedrally coordinated hydrogen-bonded configuration was estimated as ∼500 kV cm-1 and is effective up to ∼1 nm from the surface of the polymer chain. These findings are useful for designing specific interface properties and the resultant surface function of polyelectrolyte-based materials.
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Affiliation(s)
- Kosuke Yamazoe
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Yuji Higaki
- Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshihiro Inutsuka
- Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Jun Miyawaki
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
- Synchrotron Radiation Research Organization, The University of Tokyo, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Atsushi Takahara
- Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshihisa Harada
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
- Synchrotron Radiation Research Organization, The University of Tokyo, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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10
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Kalwarczyk T, Bielec K, Burdzy K, Holyst R. Influence of molecular rebinding on the reaction rate of complex formation. Phys Chem Chem Phys 2021; 23:19343-19351. [PMID: 34524310 DOI: 10.1039/d1cp02820k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We simulated Brownian diffusion and reaction-diffusion processes to study the influence of molecular rebinding on the reaction rates of bimolecular reactions. We found that the number of rebinding events, Nreb, is proportional to the target's size and inversely proportional to the diffusion coefficient D and simulation time-step Δt. We found the proportionality constant close to π-1/2. We confirmed that Nreb is defined as a ratio of the activation-limited rate constant ka to the diffusion-limited rate constant, kD. We provide the formula describing the reactivity coefficient κ, modelling the transient-native complex transition for the activation-controlled reaction rates. We show that κ is proportional to (D/Δt)1/2. Finally, we apply our rebinding-including reaction rate model to the real reactions of photoacid dissociation and protein association. Based on literature data for both types of reactions, we found the Δt time-scale. We show that for the photodissociation of a proton, the Δt is equal to 171 ± 18 fs and the average number of rebinding events is approximately equal to 40. For proteins, Δt is of the order of 100 ps with around 20 rebinding events. In both cases the timescale is similar to the timescale of fluctuation of the solvent molecules surrounding the reactants; vibrations and bending in the case of photoacid dissociation and diffusional motion for proteins.
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Affiliation(s)
- Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Krzysztof Bielec
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Krzysztof Burdzy
- Department of Mathematics, Box 354350, University of Washington, Seattle, WA 98195, USA
| | - Robert Holyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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11
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Camisasca G, De Marzio M, Gallo P. Effect of trehalose on protein cryoprotection: Insights into the mechanism of slowing down of hydration water. J Chem Phys 2021; 153:224503. [PMID: 33317300 DOI: 10.1063/5.0033526] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study, with molecular dynamics simulations, a lysozyme protein immersed in a water-trehalose solution upon cooling. The aim is to understand the cryoprotectant role played by this disaccharide through the modifications that it induces on the slow dynamics of protein hydration water with its presence. The α-relaxation shows a fragile to strong crossover about 20° higher than that in the bulk water phase and 15° higher than that in lysozyme hydration water without trehalose. The protein hydration water without trehalose was found to show a second slower relaxation exhibiting a strong to strong crossover coupled with the protein dynamical transition. This slower relaxation time importantly appears enormously slowed down in our cryoprotectant solution. On the other hand, this long-relaxation in the presence of trehalose is also connected with a stronger damping of the protein structural fluctuations than that found when the protein is in contact with the pure hydration water. Therefore, this appears to be the mechanism through which trehalose manifests its cryoprotecting function.
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Affiliation(s)
- Gaia Camisasca
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
| | - Margherita De Marzio
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
| | - Paola Gallo
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
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12
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Competition between chiral solvents and chiral monomers in the helical bias of supramolecular polymers. Nat Chem 2021; 13:200-207. [PMID: 33257888 DOI: 10.1038/s41557-020-00583-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/19/2020] [Indexed: 01/30/2023]
Abstract
Solute-solvent interactions are key for the assembly and proper functioning of biomacromolecules and play important roles in many fields of organic and polymer chemistry. Despite numerous reports describing the effects of (chiral) solvents on helical conformations of (supramolecular) polymers, the combination of chiral solvents and chiral monomers is unexplored. Here we report diastereomeric differences in the supramolecular polymerization of enantiomers of chiral triphenylene-2,6,10-tricarboxamides in chiral chlorinated solvents. Competition between the preferences induced by the stereocentres of the assembled monomers and those present in the solvent molecules results in unforeseen temperature-dependent solvation effects. By combining experiments and mathematical modelling, we show that the observed differences between enantiomers originate from the combined additive entropic effects of stereocentres present in the monomer and in the solvent. Remarkably, copolymerizations show that the chiral solvent can bias the copolymer helicity and thereby overrule the helical preference of the monomers. Our results highlight the importance of cumulative solvation effects in supramolecular polymerizations.
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13
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Revisiting the Rate-Limiting Step of the ANS-Protein Binding at the Protein Surface and Inside the Hydrophobic Cavity. Molecules 2021; 26:molecules26020420. [PMID: 33466888 PMCID: PMC7830758 DOI: 10.3390/molecules26020420] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 11/17/2022] Open
Abstract
8-Anilino-1-naphthalenesulfonic acid (ANS) is used as a hydrophobic fluorescence probe due to its high intensity in hydrophobic environments, and also as a microenvironment probe because of its unique ability to exhibit peak shift and intensity change depending on the surrounding solvent environment. The difference in fluorescence can not only be caused by the microenvironment but can also be affected by the binding affinity, which is represented by the binding constant (K). However, the overall binding process considering the binding constant is not fully understood, which requires the ANS fluorescence binding mechanism to be examined. In this study, to reveal the rate-limiting step of the ANS-protein binding process, protein concentration-dependent measurements of the ANS fluorescence of lysozyme and bovine serum albumin were performed, and the binding constants were analyzed. The results suggest that the main factor of the binding process is the microenvironment at the binding site, which restricts the attached ANS molecule, rather than the attractive diffusion-limited association. The molecular mechanism of ANS-protein binding will help us to interpret the molecular motions of ANS molecules at the binding site in detail, especially with respect to an equilibrium perspective.
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14
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Donati G, Petrone A, Rega N. Multiresolution continuous wavelet transform for studying coupled solute-solvent vibrations via ab initio molecular dynamics. Phys Chem Chem Phys 2020; 22:22645-22661. [PMID: 33015693 DOI: 10.1039/d0cp02495c] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Vibrational analysis in solution and the theoretical determination of infrared and Raman spectra are of key importance in many fields of chemical interest. Vibrational band dynamics of molecules and their sensitivity to the environment can also be captured by these spectroscopies in their time dependent version. However, it is often difficult to provide an interpretation of the experimental data at the molecular scale, such as molecular mechanisms or the processes hidden behind them. In this work, we present a theoretical-computational protocol based on ab initio molecular dynamics simulations and a combination of normal-like (generalized) mode analysis of solute-solvent clusters with a wavelet transform, for the first time. The case study is the vibrational dynamics of N-methyl-acetamide (NMA) in water solution, a well-known model of hydration of peptides and proteins. Amide modes are typical bands of peptide and protein backbone, and their couplings with the environment are very challenging in terms of the accurate prediction of solvent induced intensity and frequency shifts. The contribution of water molecules surrounding NMA to the composition of generalized and time resolved modes is introduced in our vibrational analysis, showing unequivocally its influence on the amide mode spectra. It is also shown that such mode compositions need the inclusion of the first shell solvent molecules to be accurately described. The wavelet analysis is proven to be strongly recommended to follow the time evolution of the spectra, and to capture vibrational band couplings and frequency shifts over time, preserving at the same time a well-balanced time-frequency resolution. This peculiar feature also allows one to perform a combined structural-vibrational analysis, where the different strengths of hydrogen bond interactions can quantitatively affect the amide bands over time at finite temperature. The proposed method allows for the direct connection between vibrational modes and local structural changes, providing a link from the spectroscopic observable to the structure, in this case the peptide backbone, and its hydration layouts.
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Affiliation(s)
- Greta Donati
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M. S. Angelo, Via Cintia, I-80126 Napoli, Italy.
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15
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Leitner DM, Hyeon C, Reid KM. Water-mediated biomolecular dynamics and allostery. J Chem Phys 2020; 152:240901. [DOI: 10.1063/5.0011392] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
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16
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Mondal S, Bandyopadhyay S. Heterogeneous Dynamical Environment at the Interface of a Protein-DNA Complex. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4567-4581. [PMID: 32267701 DOI: 10.1021/acs.langmuir.9b03175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Binding between protein and DNA is an essential process to regulate different biological activities. Two puzzling questions in protein-DNA recognition are (i) how the protein's binding domain identifies the DNA sequence in an aqueous solution and (ii) how the formation of the complex alters the dynamical environment around it. In this work, we present results obtained from molecular dynamics simulations of the N-terminal α-helical domain of the λ-repressor protein (in dimeric form) bound to the corresponding operator DNA. Effects of formation of the complex in modifying the microscopic dynamics of water as well as the kinetics of hydrogen bonds at the interface have been explored. Locally heterogeneous restricted water motions at the complex interface have been observed, the extent of restriction being more significant around the directly bound residues of the protein and the DNA. In particular, the calculation revealed the existence of significantly constrained motionally restricted water layer that can form either bridges around the directly bound residues of the protein and DNA or are engaged in forming water-mediated contacts between a fraction of the unbound residues. More importantly, it is observed that the restricted water motion around the complex is correlated with the hydrogen bond relaxation time scale at the interface. It is further demonstrated that the kinetics of water-water hydrogen bonds involving the bridged water are influenced more due to complex formation.
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Affiliation(s)
- Sandip Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
- Centre for Computational and Data Sciences, Indian Institute of Technology, Kharagpur 721302, India
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17
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Dutta S, Ghosh M, Karmakar R, Chakrabarti J. Dynamic signature of ligand binding over a protein surface. Phys Rev E 2019; 100:062411. [PMID: 31962438 DOI: 10.1103/physreve.100.062411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Indexed: 06/10/2023]
Abstract
We study the motion of Zn^{2+} in the presence of ubiquitin by all-atom molecular-dynamics simulations. We observe that unlike normal diffusive liquid, metal ions show an exponential tail in the self-van Hove function (self-vHf). Moreover, the metal ions are trapped strongly by acidic residues which form a binding pocket over the protein surface. The exponential tail disappears by mutation of trapping residues, suggesting that the tail appears due to trapped motion of the ions. The mean-squared displacements, however, in all the cases show linear dependence on time. Our model establishes that ligand binding generically results in an exponential tail of self-vHf. The self-vHf may give an approach to find binding pockets over a protein surface.
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Affiliation(s)
- Sutapa Dutta
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
| | - Mahua Ghosh
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
| | - Rahul Karmakar
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
| | - J Chakrabarti
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
- Thematic Unit of Excellence on Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
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18
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Bizimana LA, Epstein J, Turner DB. Inertial water response dominates protein solvation dynamics. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.04.069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Wohlfromm T, Vogel M. On the coupling of protein and water dynamics in confinement: Spatially resolved molecular dynamics simulation studies. J Chem Phys 2019; 150:245101. [DOI: 10.1063/1.5097777] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Timothy Wohlfromm
- Institut für Festkörperphysik, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Michael Vogel
- Institut für Festkörperphysik, Technische Universität Darmstadt, 64289 Darmstadt, Germany
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20
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Ota C, Takano K. Spectroscopic Analysis of Protein-Crowded Environments Using the Charge-Transfer Fluorescence Probe 8-Anilino-1-Naphthalenesulfonic Acid. Chemphyschem 2019; 20:1456-1466. [PMID: 30945450 DOI: 10.1002/cphc.201900226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/01/2019] [Indexed: 12/11/2022]
Abstract
The molecular behaviors of proteins under crowding conditions are crucial for understanding the protein actions in intracellular environments. Under a crowded environment, the distance between protein molecules is almost the same size as the molecular level, thus, both the excluded volume effect and short ranged soft chemical interaction on protein surface could induce the complicated influence on the protein behavior cooperatively. Recently, various kinds of analytical approaches from macroscopic to microscopic aspects have been made to evaluate the crowding effect. The method, however, has not been established to evaluate the surface specific interactions on protein surface. In this study, the analytical method to evaluate the crowding effect has been suggested by using a charge-transfer fluorescence probe, ANS. By employing the unique property of ANS attaching to charged residues on the surface of lysozyme, the crowding effect was focused, while the case was compared as a reference, in which ANS is confined in hydrophobic pockets of BSA. Consequently, the surface specific changes of fluorescence spectra were readily observed under the crowded environment, whereas the fluorescence spectra of ANS in protein inside did not change. This result suggests the fluorescence spectra of ANS binding to protein surface have the capability to estimate the crowding effect of proteins.
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Affiliation(s)
- Chikashi Ota
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Sakyo-ku, Kyoto, 606-8522, Japan
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21
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Sahu P, Musharaf Ali S, Shenoy KT, Mohan S. Nanoscopic insights of saline water in carbon nanotube appended filters using molecular dynamics simulations. Phys Chem Chem Phys 2019; 21:8529-8542. [PMID: 30957831 DOI: 10.1039/c9cp00648f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nanotube appended membranes are shown to be very promising due to their ultrafast water transport and very high salt rejection ability. Using classical molecular dynamics, the present study reports the nanoscopic assessment of various molecular events for nanotube-based desalination, which might be useful for nanoscale devices during process operation at the macroscopic scale. The characteristics of water and ion flow are discussed with varied strength of pressure gradient and salt concentration for different scales of confinement. The results revealed that the membranes comprising nanotubes of 1.0-1.1 nm diameter can be optimized for efficient water desalination with more than >95% salt rejection. Furthermore, the anomalies in water flux through nanotubes are linked with the hydration characteristics of ions inside CNTs. The results show the maximum hydration of confined ions inside the nanotubes, which indicated the minimum permeability of water due to freezing effects. Furthermore, the MD results revealed that akin to bulk phases, the mass transport through nanotubes can be linked with the component diffusivity in the medium. It has been demonstrated that not only the diffusivities of water and ions, but even the gradient of water to ion diffusivity might be utilized to predict and explore the experimental observations, which might be helpful in optimizing the operational regime in nanotube-based filtrations. Moreover, the thermodynamic characteristics of the flow are discussed in terms of the entropy of water and ions using the robust two-phase thermodynamic (2PT) method. The results reflect that the entropy of water is linked to the distortion of the hydrogen bond network inside the nanotube confinement, at the nanotube-water interface and at the bulk solution, whereas the entropy of ions seems to be majorly dominated by their oscillation. Also, the interconnection of hydration structure, mass flux and the diffusivity of water and ions along with their thermodynamic origin are discussed.
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Affiliation(s)
- Pooja Sahu
- Chemical Engineering Division, Bhabha Atomic Research Center, Mumbai, Maharashtra 400085, India.
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22
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Cai X, Xie WJ, Yang Y, Long Z, Zhang J, Qiao Z, Yang L, Gao YQ. Structure of water confined between two parallel graphene plates. J Chem Phys 2019; 150:124703. [DOI: 10.1063/1.5080788] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Xiaoxia Cai
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Wen Jun Xie
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Ying Yang
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Zhuoran Long
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Jun Zhang
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Zhuoran Qiao
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Lijiang Yang
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Yi Qin Gao
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
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23
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Ultrafast energy relaxation dynamics of amide I vibrations coupled with protein-bound water molecules. Nat Commun 2019; 10:1010. [PMID: 30824834 PMCID: PMC6397197 DOI: 10.1038/s41467-019-08899-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 02/06/2019] [Indexed: 12/11/2022] Open
Abstract
The influence of hydration water on the vibrational energy relaxation in a protein holds the key to understand ultrafast protein dynamics, but its detection is a major challenge. Here, we report measurements on the ultrafast vibrational dynamics of amide I vibrations of proteins at the lipid membrane/H2O interface using femtosecond time-resolved sum frequency generation vibrational spectroscopy. We find that the relaxation time of the amide I mode shows a very strong dependence on the H2O exposure, but not on the D2O exposure. This observation indicates that the exposure of amide I bond to H2O opens up a resonant relaxation channel and facilitates direct resonant vibrational energy transfer from the amide I mode to the H2O bending mode. The protein backbone motions can thus be energetically coupled with protein-bound water molecules. Our findings highlight the influence of H2O on the ultrafast structure dynamics of proteins.
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24
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Franck JM, Han S. Overhauser Dynamic Nuclear Polarization for the Study of Hydration Dynamics, Explained. Methods Enzymol 2018; 615:131-175. [PMID: 30638529 DOI: 10.1016/bs.mie.2018.09.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We outline the physical properties of hydration water that are captured by Overhauser Dynamic Nuclear Polarization (ODNP) relaxometry and explore the insights that ODNP yields about the water and the surface that this water is coupled to. As ODNP relies on the pairwise cross-relaxation between the electron spin of a spin probe and a proton nuclear spin of water, it captures the dynamics of single-particle diffusion of an ensemble of water molecules moving near the spin probe. ODNP principally utilizes the same physics as other nuclear magnetic resonance (NMR) relaxometry (i.e., relaxation measurement) techniques. However, in ODNP, electron paramagnetic resonance (EPR) excites the electron spins probes and their high net polarization acts as a signal amplifier. Furthermore, it renders ODNP parameters highly sensitive to water moving at rates commensurate with the EPR frequency of the spin probe (typically 10GHz). Also, ODNP selectively enhances the NMR signal contributions of water moving within close proximity to the spin label. As a result, ODNP can capture ps-ns movements of hydration waters with high sensitivity and locality, even in samples with protein concentrations as dilute as 10 µM. To date, the utility of the ODNP technique has been demonstrated for two major applications: the characterization of the spatial variation in the properties of the hydration layer of proteins or other surfaces displaying topological diversity, and the identification of structural properties emerging from highly disordered proteins and protein domains. The former has been shown to correlate well with the properties of hydration water predicted by MD simulations and has been shown capable of evaluating the hydrophilicity or hydrophobicity of a surface. The latter has been demonstrated for studies of an interhelical loop of proteorhodopsin, the partial structure of α-synuclein embedded at the lipid membrane surface, incipient structures adopted by tau proteins en route to fibrils, and the structure and hydration profile of a transmembrane peptide. This chapter focuses on offering a mechanistic understanding of the ODNP measurement and the molecular dynamics encoded in the ODNP parameters. In particular, it clarifies how the electron-nuclear dipolar coupling encodes information about the molecular dynamics in the nuclear spin self-relaxation and, more importantly, the electron-nuclear spin cross-relaxation rates. The clarification of the molecular dynamics underlying ODNP should assist in establishing a connection to theory and computer simulation that will offer far richer interpretations of ODNP results in future studies.
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Affiliation(s)
- John M Franck
- Department of Chemistry, Syracuse University, Syracuse, NY, United States.
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, United States; Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, United States
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25
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Oh Y, Sung BJ. Facilitated and Non-Gaussian Diffusion of Cholesterol in Liquid Ordered Phase Bilayers Depends on the Flip-Flop and Spatial Arrangement of Cholesterol. J Phys Chem Lett 2018; 9:6529-6535. [PMID: 30346769 DOI: 10.1021/acs.jpclett.8b02982] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The diffusion of cholesterol in biological membranes is critical to cellular processes such as the formation of cholesterol-enriched domains. The cholesterol diffusion may be complicated especially when cholesterol flip-flops and/or stays at the membrane center. Understanding the diffusion mechanism of cholesterol at a molecular level should be, therefore, a topic of interest. We perform molecular dynamics simulations up to 100 μs for lipid bilayers with various concentrations of cholesterol. We find that cholesterol diffusion in the liquid ordered phase depends on whether it is within leaflets or at the bilayer center, is non-Gaussian for several microseconds, and is enhanced significantly compared to that of lipids. Cholesterol at the bilayer center diffuses fast, while cholesterol in the hydrocarbon region with upright orientation diffuses relatively slowly. Such position-dependent dynamics of cholesterol leads to facilitated and non-Gaussian diffusion.
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Affiliation(s)
- Younghoon Oh
- Department of Chemistry and Research Institute for Basic Science , Sogang University , Seoul 04107 , Republic of Korea
| | - Bong June Sung
- Department of Chemistry and Research Institute for Basic Science , Sogang University , Seoul 04107 , Republic of Korea
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26
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Maestre-Reyna M, Yamamoto J, Huang WC, Tsai MD, Essen LO, Bessho Y. Twist and turn: a revised structural view on the unpaired bubble of class II CPD photolyase in complex with damaged DNA. IUCRJ 2018; 5:608-618. [PMID: 30224964 PMCID: PMC6126647 DOI: 10.1107/s205225251800996x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/11/2018] [Indexed: 06/08/2023]
Abstract
Cyclobutane pyrimidine dimer (CPD) photolyases harness the energy of blue light to repair UV-induced DNA CPDs. Upon binding, CPD photolyases cause the photodamage to flip out of the duplex DNA and into the catalytic site of the enzyme. This process, called base-flipping, induces a kink in the DNA, as well as an unpaired bubble, which are stabilized by a network of protein-nucleic acid interactions. Previously, several co-crystal structures have been reported in which the binding mode of CPD photolyases has been studied in detail. However, in all cases the internucleoside linkage of the photodamage site was a chemically synthesized formacetal analogue and not the natural phosphodiester. Here, the first crystal structure and conformational analysis via molecular-dynamics simulations of a class II CPD photolyase in complex with photodamaged DNA that contains a natural cyclobutane pyrimidine dimer with an intra-lesion phosphodiester linkage are presented. It is concluded that a highly conserved bubble-intruding region (BIR) mediates stabilization of the open form of CPD DNA when complexed with class II CPD photolyases.
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Affiliation(s)
- Manuel Maestre-Reyna
- Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Wei-Cheng Huang
- Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, Hans-Meerwein Strasse 6, Marburg 35032, Germany
| | - Yoshitaka Bessho
- Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan
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27
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Correlating interfacial water dynamics with protein-protein interaction in complex of GDF-5 and BMPRI receptors. Biophys Chem 2018; 240:50-62. [PMID: 29890403 DOI: 10.1016/j.bpc.2018.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 04/03/2018] [Accepted: 05/22/2018] [Indexed: 11/21/2022]
Abstract
GDF-5 mediated signal transduction regulating chondrogenesis and skeletogenesis involves three different type-I receptors viz. Act-RI, BMPRIA and BMPRIB. BMPRIA and BMPRIB generally shows temporal and spatial co-expression but some spatially different expression pattern has also been observed. BMPRIA receptor is the key receptor implicated in BMP signalling during osteogenesis and is expressed in osteoblasts during the course of bone formation. However, BMPRIB appears to be primarily expressed in mesenchymal pre-cartilage condensations and also found in differentiated osteoblast and chondrocytes. The extracellular pH affects bone cell function and it is experimentally known that mineralization of bone is affected by shift of pH in cultured osteoblast. Here we report the effect of pH on dynamics of water present at the interface of GDF-5:BMPRIA and GDF-5:BMPRIB and binding interaction energy of these complexes. Water dynamics at different pH was analysed using residence time and hydrogen bond relaxation kinetics. pH influences the interaction energy between GDF-5 and BMPRIA and BMPRIB receptors indicating the electrostatic environment modulating the activity of two receptors. This pH dependence of interaction energy is further supported by similar behaviour of hydrogen bond existence of buried water molecules at the interface. In contrast to this the slow and fast exchanging water molecules do not show similar pH dependence of hydrogen bonding relaxation kinetics. Hence; we conclude that only buried water molecule at the interface influences the protein-protein interaction and the electrostatic environment of the extracellular fluid might decide the specificity of the two receptors.
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28
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Pandey HD, Leitner DM. Thermodynamics of Hydration Water around an Antifreeze Protein: A Molecular Simulation Study. J Phys Chem B 2017; 121:9498-9507. [DOI: 10.1021/acs.jpcb.7b05892] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hari Datt Pandey
- Department of Chemistry and
Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
| | - David M. Leitner
- Department of Chemistry and
Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
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29
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Abstract
The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.
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Affiliation(s)
- Damien Laage
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut
für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - James T. Hynes
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
- Department
of Chemistry and Biochemistry, University
of Colorado, Boulder, Colorado 80309, United
States
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