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Salehi SM, Pezzella M, Willard A, Meuwly M, Karplus M. Water dynamics around T 0 vs R 4 of hemoglobin from local hydrophobicity analysis. J Chem Phys 2023; 158:025101. [PMID: 36641390 DOI: 10.1063/5.0129990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The local hydration around tetrameric hemoglobin (Hb) in its T0 and R4 conformational substates is analyzed based on molecular dynamics simulations. Analysis of the local hydrophobicity (LH) for all residues at the α1β2 and α2β1 interfaces, responsible for the quaternary T → R transition, which is encoded in the Monod-Wyman-Changeux model, as well as comparison with earlier computations of the solvent accessible surface area, makes clear that the two quantities measure different aspects of hydration. Local hydrophobicity quantifies the presence and structure of water molecules at the interface, whereas "buried surface" reports on the available space for solvent. For simulations with Hb frozen in its T0 and R4 states, the correlation coefficient between LH and buried surface is 0.36 and 0.44, respectively, but it increases considerably if the 95% confidence interval is used. The LH with Hb frozen and flexible changes little for most residues at the interfaces but is significantly altered for a few select ones: Thr41α, Tyr42α, Tyr140α, Trp37β, Glu101β (for T0) and Thr38α, Tyr42α, Tyr140α (for R4). The number of water molecules at the interface is found to increase by ∼25% for T0 → R4, which is consistent with earlier measurements. Since hydration is found to be essential to protein function, it is clear that hydration also plays an essential role in allostery.
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Affiliation(s)
- Seyedeh Maryam Salehi
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Marco Pezzella
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Adam Willard
- Department of Chemistry MIT, Cambridge, Massachusetts 02139, USA
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Martin Karplus
- Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138, USA
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Samajdar RN, Asampille G, Atreya HS, Bhattacharyya AJ. Hemoglobin Dynamics in Solution vis-à-vis Under Confinement: An Electrochemical Perspective. J Phys Chem B 2020; 124:5771-5779. [PMID: 32551673 DOI: 10.1021/acs.jpcb.0c02372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Confining heme protein in silico often leads to beneficial functionalities such as an enhanced electrochemical response from the heme center. This can be harnessed to design effective biosensors for medical diagnostics. Proteins under confinement, surface confinement on the electrode to be precise, have more ordered and monodisperse structure compared to the protein in bulk solution. As the electrochemical response of a protein comes from those protein molecules that are confined within the electrical double layer across the electrode-electrolyte interface, it is expected that restriction of conformational fluctuations of the polymeric protein will help in enhancement of the electrochemical response. This is probably the prima facie reason for electrochemical response enhancement under confinement. We examine the dynamic features of hemoglobin under confinement vis-à-vis that in bulk solution. We use a variety of spectroscopic techniques across a wide time-space window to establish the following facts: (a) hardening of the protein polypeptide backbone, (b) slowing down of protein diffusion, (c) increase in relaxation times in NMR, and (d) slowing down of dielectric relaxation times under confinement. This indicates an overall quenching of protein dynamics when the protein is confined inside silica matrix. Thus, we hypothesize that along with retention of secondary structure, this quenching of dynamics contributes to the enhancement of electrochemical response observed.
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Affiliation(s)
- Rudra N Samajdar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Hanudatta S Atreya
- NMR Research Center, Indian Institute of Science, Bangalore 560012, India
| | - Aninda J Bhattacharyya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
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Fujiwara S, Chatake T, Matsuo T, Kono F, Tominaga T, Shibata K, Sato-Tomita A, Shibayama N. Ligation-Dependent Picosecond Dynamics in Human Hemoglobin As Revealed by Quasielastic Neutron Scattering. J Phys Chem B 2017; 121:8069-8077. [DOI: 10.1021/acs.jpcb.7b05182] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Satoru Fujiwara
- Quantum
Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Toshiyuki Chatake
- Research
Reactor Institute, Kyoto University, 2 Asashiro-Nishi, Kumatori, Osaka 590-0494, Japan
| | - Tatsuhito Matsuo
- Quantum
Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Fumiaki Kono
- Quantum
Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Taiki Tominaga
- Neutron
Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Kaoru Shibata
- Neutron
Science Section, J-PARC Center, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Ayana Sato-Tomita
- Division
of Biophysics, Department of Physiology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
| | - Naoya Shibayama
- Division
of Biophysics, Department of Physiology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
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Fujiwara S, Araki K, Matsuo T, Yagi H, Yamada T, Shibata K, Mochizuki H. Dynamical Behavior of Human α-Synuclein Studied by Quasielastic Neutron Scattering. PLoS One 2016; 11:e0151447. [PMID: 27097022 PMCID: PMC4838215 DOI: 10.1371/journal.pone.0151447] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/29/2016] [Indexed: 12/02/2022] Open
Abstract
α-synuclein (αSyn) is a protein consisting of 140 amino acid residues and is abundant in the presynaptic nerve terminals in the brain. Although its precise function is unknown, the filamentous aggregates (amyloid fibrils) of αSyn have been shown to be involved in the pathogenesis of Parkinson's disease, which is a progressive neurodegenerative disorder. To understand the pathogenesis mechanism of this disease, the mechanism of the amyloid fibril formation of αSyn must be elucidated. Purified αSyn from bacterial expression is monomeric but intrinsically disordered in solution and forms amyloid fibrils under various conditions. As a first step toward elucidating the mechanism of the fibril formation of αSyn, we investigated dynamical behavior of the purified αSyn in the monomeric state and the fibril state using quasielastic neutron scattering (QENS). We prepared the solution sample of 9.5 mg/ml purified αSyn, and that of 46 mg/ml αSyn in the fibril state, both at pD 7.4 in D2O. The QENS experiments on these samples were performed using the near-backscattering spectrometer, BL02 (DNA), at the Materials and Life Science Facility at the Japan Accelerator Research Complex, Japan. Analysis of the QENS spectra obtained shows that diffusive global motions are observed in the monomeric state but largely suppressed in the fibril state. However, the amplitude of the side chain motion is shown to be larger in the fibril state than in the monomeric state. This implies that significant solvent space exists within the fibrils, which is attributed to the αSyn molecules within the fibrils having a distribution of conformations. The larger amplitude of the side chain motion in the fibril state than in the monomeric state implies that the fibril state is entropically favorable.
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Affiliation(s)
- Satoru Fujiwara
- Quantum Beam Science Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan
- * E-mail:
| | - Katsuya Araki
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Tatsuhito Matsuo
- Quantum Beam Science Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan
| | - Hisashi Yagi
- Center for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan
| | - Takeshi Yamada
- Research Center for Neutron Science and Technology, CROSS-Tokai, Tokai, Ibaraki, Japan
| | - Kaoru Shibata
- Neutron Science Section, J-PARC Center, Tokai, Ibaraki, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
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Choudhury S, Mondal PK, Sharma VK, Mitra S, Sakai VG, Mukhopadhyay R, Pal SK. Direct Observation of Coupling between Structural Fluctuation and Ultrafast Hydration Dynamics of Fluorescent Probes in Anionic Micelles. J Phys Chem B 2015; 119:10849-57. [PMID: 25874585 DOI: 10.1021/jp511899q] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The coupling of structural fluctuation and the dynamics of associated water molecules of biological macromolecules is vital for various biological activities. Although a number of molecular dynamics (MD) studies on proteins/DNA predicted the importance of such coupling, experimental evidence of variation of hydration dynamics with controlled structural fluctuation even in model macromolecule is sparse and raised controversies in the contemporary literature. Here, we have investigated dynamics of hydration at the surfaces of two similar anionic micelles sodium dodecyl sulfate (SDS) and sodium dodecylbenzenesulfonate (SDBS) as model macromolecules using coumarin 500 (C500) as spectroscopic probe with femtosecond to picosecond time resolution up to 20 ns time window. The constituting surfactants SDS and SDBS are structurally similar except one benzene moiety in the SDBS may offer additional rigidity to the SDBS micelles through π-stacking and added bulkiness. The structural integrity of the micelles in the aqueous medium is confirmed in dynamic light scattering (DLS) studies. A variety of studies including polarization gated fluorescence spectroscopy and quasielastic neutron scattering (QENS) have been used to confirm differential structural fluctuation of SDS and SDBS micelles. We have also employed femtosecond-resolved Förster resonance energy transfer (FRET) in order to study binding of a cationic organic ligand ethidium bromide (EtBr) salt at the micellar surfaces. The distance distribution of the donor (C500)-acceptor (EtBr) in the micellar media reveals the manifestation of the structural flexibility of the micelles. Our studies on dynamical coupling of the structural flexibility with surface hydration in the nanoscopic micellar media may find the relevance in the "master-slave" type water dynamics in biologically relevant macromolecules.
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Affiliation(s)
- Susobhan Choudhury
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Prasanna Kumar Mondal
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - V K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre , Mumbai 400085, India
| | - S Mitra
- Solid State Physics Division, Bhabha Atomic Research Centre , Mumbai 400085, India
| | - V Garcia Sakai
- Science and Technology Facilities Council, Rutherford Appleton Laboratory , Didcot, OX11 0QX, U.K
| | - R Mukhopadhyay
- Solid State Physics Division, Bhabha Atomic Research Centre , Mumbai 400085, India
| | - Samir Kumar Pal
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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Internal motions of actin characterized by quasielastic neutron scattering. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:661-71. [DOI: 10.1007/s00249-011-0669-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 12/28/2010] [Accepted: 01/03/2011] [Indexed: 10/18/2022]
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From powder to solution: hydration dependence of human hemoglobin dynamics correlated to body temperature. Biophys J 2009; 96:5073-81. [PMID: 19527667 DOI: 10.1016/j.bpj.2009.03.043] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 02/25/2009] [Accepted: 03/30/2009] [Indexed: 11/23/2022] Open
Abstract
A transition in hemoglobin (Hb), involving partial unfolding and aggregation, has been shown previously by various biophysical methods. The correlation between the transition temperature and body temperature for Hb from different species, suggested that it might be significant for biological function. To focus on such biologically relevant human Hb dynamics, we studied the protein internal picosecond motions as a response to hydration, by elastic and quasielastic neutron scattering. Rates of fast diffusive motions were found to be significantly enhanced with increasing hydration from fully hydrated powder to concentrated Hb solution. In concentrated protein solution, the data showed that amino acid side chains can explore larger volumes above body temperature than expected from normal temperature dependence. The body temperature transition in protein dynamics was absent in fully hydrated powder, indicating that picosecond protein dynamics responsible for the transition is activated only at a sufficient level of hydration. A collateral result from the study is that fully hydrated protein powder samples do not accurately describe all aspects of protein picosecond dynamics that might be necessary for biological function.
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Jansson H, Kargl F, Fernandez-Alonso F, Swenson J. Dynamics of a protein and its surrounding environment: A quasielastic neutron scattering study of myoglobin in water and glycerol mixtures. J Chem Phys 2009; 130:205101. [DOI: 10.1063/1.3138765] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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Mondal SK, Sahu K, Bhattacharyya K. Study of Biological Assemblies by Ultrafast Fluorescence Spectroscopy. REVIEWS IN FLUORESCENCE 2009. [DOI: 10.1007/978-0-387-88722-7_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Tatke SS, Loong CK, D'Souza N, Schoephoerster RT, Prabhakaran M. Large scale motions in a biosensor protein glucose oxidase: a combined approach by QENS, normal mode analysis, and molecular dynamics studies. Biopolymers 2008; 89:582-94. [PMID: 18273893 DOI: 10.1002/bip.20956] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The characteristics of the glucose oxidase were studied using a combination of experimental and theoretical techniques. Quasi elastic neutron scattering experiments were used to obtain the vibrational frequencies of the protein. These were compared to theoretical results obtained by normal mode analysis. Results indicate a good match between the experimental and theoretical values. Molecular dynamic simulation with covariant analysis was used to study the structure and dynamics of glucose oxidase. Various parameters like the radius of gyration, root mean square fluctuations, solvent accessibility were studied for evaluating the structural stability of the protein. The frequency of vibration calculated from the three methods is used to derive the large scale motions. Theses studies were used to predict the suitable lysine residues for linkage with carbon nanotubes.
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Affiliation(s)
- Sujit S Tatke
- Biomedical Engineering Department, FL International University, Miami, FL, USA
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Schirò G, Sclafani M, Caronna C, Natali F, Plazanet M, Cupane A. Dynamics of myoglobin in confinement: An elastic and quasi-elastic neutron scattering study. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.07.045] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Hydration dependent dynamics in sol–gel encapsulated myoglobin. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:543-9. [DOI: 10.1007/s00249-007-0249-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 11/15/2007] [Accepted: 11/20/2007] [Indexed: 10/22/2022]
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14
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Ghosh S, Mandal U, Adhikari A, Dey S, Bhattacharyya K. Study of organized and biological systems using an ultrafast laser. INT REV PHYS CHEM 2007. [DOI: 10.1080/01442350701416888] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Sahu K, Mondal SK, Ghosh S, Bhattacharyya K. Ultrafast Dynamics in Biological Systems and in Nano-Confined Environments. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.1033] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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