1
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Aggrawal R, Halder S, Dyagala S, Saha SK. Role of Dual Nature of Ionic Liquid in Solvation Dynamics and Rotational Diffusion in Mixed Micelles: A Time‐Resolved Fluorescence and Fluorescence Anisotropy Study. ChemistrySelect 2023. [DOI: 10.1002/slct.202204360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Affiliation(s)
- Rishika Aggrawal
- Department of Chemistry Birla Institute of Technology & Science (BITS) Pilani Hyderabad Campus Telangana 500078 INDIA
| | - Sayantan Halder
- Department of Chemistry Birla Institute of Technology & Science (BITS) Pilani Hyderabad Campus Telangana 500078 INDIA
| | - Shalini Dyagala
- Department of Chemistry Birla Institute of Technology & Science (BITS) Pilani Hyderabad Campus Telangana 500078 INDIA
| | - Subit Kumar Saha
- Department of Chemistry Birla Institute of Technology & Science (BITS) Pilani Hyderabad Campus Telangana 500078 INDIA
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2
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Mondal D, Malik S, Banerjee P, Kundu N, Debnath A, Sarkar N. Modulation of Membrane Fluidity to Control Interfacial Water Structure and Dynamics in Saturated and Unsaturated Phospholipid Vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:12423-12434. [PMID: 33035065 DOI: 10.1021/acs.langmuir.0c02736] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The structure and dynamics of interfacial water in biological systems regulate the biochemical reactions. But, it is still enigmatic how the behavior of the interfacial water molecule is controlled. Here, we have investigated the effect of membrane fluidity on the structure and dynamics of interfacial water molecules in biologically relevant phopholipid vesicles. This study delineates that modulation of membrane fluidity through interlipid separation and unsaturation not only mitigate membrane rigidity but also disrupt the strong hydrogen bond (H-bond) network around the lipid bilayer interface. As a result, a disorder in H-bonding between water molecules arises several layers beyond the first hydration shell of the polar headgroup, which essentially modifies the interfacial water structure and dynamics. Furthermore, we have also provided evidence of increasing transportation through these modulated membranes, which enhance the membrane mediated isomerization reaction rate.
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Affiliation(s)
- Dipankar Mondal
- Department of Chemistry, Indian Institute of Technology Kharagpur Kharagpur 721302, West Bengal, India
| | - Sheeba Malik
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, Rajasthan, India
| | - Pavel Banerjee
- Department of Chemistry, Indian Institute of Technology Kharagpur Kharagpur 721302, West Bengal, India
| | - Niloy Kundu
- Department of Chemistry, Indian Institute of Technology Kharagpur Kharagpur 721302, West Bengal, India
- Environment Research Group, R&D and Scientific Services Department, Tata Steel Ltd., Jamshedpur 831007, India
| | - Ananya Debnath
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, Rajasthan, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology Kharagpur Kharagpur 721302, West Bengal, India
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3
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Maity A, Sarkar S, Theeyancheri L, Chakrabarti R. Choline Chloride as a Nano‐Crowder Protects HP‐36 from Urea‐Induced Denaturation: Insights from Solvent Dynamics and Protein‐Solvent Interactions. Chemphyschem 2020; 21:552-567. [DOI: 10.1002/cphc.201901078] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/22/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Atanu Maity
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Soham Sarkar
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Ligesh Theeyancheri
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Rajarshi Chakrabarti
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 India
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4
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Ngo VA, Fanning JK, Noskov SY. Comparative Analysis of Protein Hydration from MD simulations with Additive and Polarizable Force Fields. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800106] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Van A. Ngo
- Department of Biological SciencesCentre for Molecular Simulation and Biochemistry Research ClusterUniversity of Calgary Calgary Alberta T2N 1N4 Canada
| | - John Keenan Fanning
- Department of Biological SciencesCentre for Molecular Simulation and Biochemistry Research ClusterUniversity of Calgary Calgary Alberta T2N 1N4 Canada
| | - Sergei Yu Noskov
- Department of Biological SciencesCentre for Molecular Simulation and Biochemistry Research ClusterUniversity of Calgary Calgary Alberta T2N 1N4 Canada
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5
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Mohanta D, Jana M. Effects of ethanol on the secondary structure specific hydration properties of Chymotrypsin Inhibitor 2 in its folded and unfolded forms. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1496246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Dayanidhi Mohanta
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela, India
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6
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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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7
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Samanta S, Mukherjee S. Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade. J Chem Phys 2018; 148:045102. [PMID: 29390798 DOI: 10.1063/1.5004807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain. All atom molecular dynamics simulations are employed to the aqueous solutions of free SAP and SLAM-peptide bound SAP. We observed that water dynamics around different secondary structural elements became highly affected as well as nicely correlated with the SLAM-peptide induced change in structural rigidity obtained by thermodynamic quantification. A few instances of contradictory dynamic features of water to the change in structural flexibility are explained by means of occluded polar residues by the peptide. For βD, EFloop, and BGloop, both structural flexibility and solvent accessibility of the residues confirm the obvious contribution. Most importantly, we have quantified enhanced restriction in water dynamics around the second Fyn-binding site of the SAP due to SAP-SLAM complexation, even prior to the presence of Fyn. This observation leads to a novel argument that SLAM induced more restricted water molecules could offer more water entropic contribution during the subsequent Fyn binding and provide enhanced stability to the SAP-Fyn complex in the signaling cascade. Finally, SLAM induced water counteraction around the second binding site of the SAP sheds light on the allosteric property of the SAP, which becomes an integral part of the underlying signal transduction mechanism.
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Affiliation(s)
- Sudipta Samanta
- BioSystems and Micromechanics IRG (BioSyM), Singapore-MIT Alliance for Research and Technology (SMART), 1 Create Way, Republic of Singapore 138602
| | - Sanchita Mukherjee
- Indian Institute of Science Education and Research, Kolkata, Mohanpur, West Bengal 741246, India
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8
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Gavrilov Y, Leuchter JD, Levy Y. On the coupling between the dynamics of protein and water. Phys Chem Chem Phys 2017; 19:8243-8257. [DOI: 10.1039/c6cp07669f] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The solvation entropy of flexible protein regions is higher than that of rigid regions and contributes differently to the overall thermodynamic stability.
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Affiliation(s)
- Yulian Gavrilov
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Jessica D. Leuchter
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Yaakov Levy
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
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9
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Singh P, Choudhury S, Singha S, Jun Y, Chakraborty S, Sengupta J, Das R, Ahn KH, Pal SK. A sensitive fluorescent probe for the polar solvation dynamics at protein–surfactant interfaces. Phys Chem Chem Phys 2017; 19:12237-12245. [DOI: 10.1039/c6cp08804j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Relaxation dynamics at the surface of biologically important macromolecules is important taking into account their functionality in molecular recognition.
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Affiliation(s)
- Priya Singh
- Department of Chemical
- Biological & Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700 106
- India
| | - Susobhan Choudhury
- Department of Chemical
- Biological & Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700 106
- India
| | - Subhankar Singha
- Department of Chemistry
- Pohang University of Science and Technology (POSTECH)
- Pohang
- Republic of Korea
| | - Yongwoong Jun
- Department of Chemistry
- Pohang University of Science and Technology (POSTECH)
- Pohang
- Republic of Korea
| | | | - Jhimli Sengupta
- Department of Chemistry
- West Bengal State University
- Kolkata 700126
- India
| | - Ranjan Das
- Department of Chemistry
- West Bengal State University
- Kolkata 700126
- India
| | - Kyo-Han Ahn
- Department of Chemistry
- Pohang University of Science and Technology (POSTECH)
- Pohang
- Republic of Korea
| | - Samir Kumar Pal
- Department of Chemical
- Biological & Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700 106
- India
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10
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Sonu S, Kumari S, Saha SK. Solvation dynamics and rotational relaxation of coumarin 153 in mixed micelles of Triton X-100 and cationic gemini surfactants: effect of composition and spacer chain length of gemini surfactants. Phys Chem Chem Phys 2016; 18:1551-63. [DOI: 10.1039/c5cp03835a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To demonstrate simultaneously how the solvation dynamics and rotational relaxation in nonionic micelles change with the composition of a gemini surfactant and how this change depends on spacer chain length of gemini surfactants.
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Affiliation(s)
- Sonu Sonu
- Department of Chemistry
- Birla Institute of Technology & Science (BITS)
- Pilani
- India
| | - Sunita Kumari
- Department of Chemistry
- Birla Institute of Technology & Science (BITS)
- Pilani
- India
| | - Subit K. Saha
- Department of Chemistry
- Birla Institute of Technology & Science (BITS)
- Pilani
- India
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11
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Nguyen MT, Chaffee AL, Boysen RI, Nicolau DV, Hearn MT. A versatile modelling approach to determine the hydrophobicity of peptides at the atomic level. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1038533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Chowdhury R, Amin MA, Bhattacharyya K. Intermittent Fluorescence Oscillations in Lipid Droplets in a Live Normal and Lung Cancer Cell: Time-Resolved Confocal Microscopy. J Phys Chem B 2015; 119:10868-75. [DOI: 10.1021/jp5120042] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Rajdeep Chowdhury
- Department of Physical
Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Md. Asif Amin
- Department of Physical
Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Kankan Bhattacharyya
- Department of Physical
Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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13
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Spontaneous deposition of polylysine on surfaces: Role of the secondary structure to optimize noncovalent coating strategies. J Colloid Interface Sci 2015; 437:270-276. [DOI: 10.1016/j.jcis.2014.09.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 09/08/2014] [Accepted: 09/14/2014] [Indexed: 01/31/2023]
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14
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Sinha SK, Jana M, Chakraborty K, Bandyopadhyay S. In silico studies of the properties of water hydrating a small protein. J Chem Phys 2014; 141:22D502. [DOI: 10.1063/1.4895533] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Bagchi K, Roy S. Sensitivity of Water Dynamics to Biologically Significant Surfaces of Monomeric Insulin: Role of Topology and Electrostatic Interactions. J Phys Chem B 2014; 118:3805-13. [DOI: 10.1021/jp411136w] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Kushal Bagchi
- St. Joseph’s College for Arts and Science, Bangalore 560027, India
| | - Susmita Roy
- SSCU, Indian Institute of Science, Bangalore 560012, India
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16
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Lin B, Gao Y, Li Y, Zhang JZH, Mei Y. Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of myoglobin. J Mol Model 2014; 20:2189. [PMID: 24671304 DOI: 10.1007/s00894-014-2189-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 02/24/2014] [Indexed: 10/25/2022]
Abstract
Over the past few years, time-dependent ultrafast fluorescence spectroscopy method has been applied to the study of protein dynamics. However, observations from these experiments are in a controversy with other experimental studies. Participating of theoretical methods in this debate has not reconciled the contradiction, because the predicted initial relaxation from computer simulations is one-order faster than the ultrafast fluorescence spectroscopy experiment. In those simulations, pairwise force fields are employed, which have been shown to underestimate the roughness of the free energy landscape. Therefore, the relaxation rate of protein and water molecules under pairwise force fields is falsely exaggerated. In this work, we compared the relaxations of tryptophan/environment interaction under linear response approximation employing pairwise, polarized, and polarizable force fields. Results show that although the relaxation can be slowed down to a certain extent, the large gap between experiment and theory still cannot be filled.
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Affiliation(s)
- Bingbing Lin
- Center for Laser and Computational Biophysics, State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
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17
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Sen P, Pal S, Bhattacharyya K, Bagchi B. Solvation Dynamics in Biological Systems and Organized Assemblies. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200600019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Roy S, Bagchi B. Chemical Unfolding of Chicken Villin Headpiece in Aqueous Dimethyl Sulfoxide Solution: Cosolvent Concentration Dependence, Pathway, and Microscopic Mechanism. J Phys Chem B 2012; 117:4488-502. [DOI: 10.1021/jp308589b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Susmita Roy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore
560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore
560012, India
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19
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Serrano AL, Bilsel O, Gai F. Native state conformational heterogeneity of HP35 revealed by time-resolved FRET. J Phys Chem B 2012; 116:10631-8. [PMID: 22891809 DOI: 10.1021/jp211296e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The villin headpiece subdomain (HP35) has become one of the most widely used model systems in protein folding studies, due to its small size and ultrafast folding kinetics. Here, we use HP35 as a test bed to show that the fluorescence decay kinetics of an unnatural amino acid, p-cyanophenylalanine (Phe(CN)), which are modulated by a nearby quencher (e.g., tryptophan or 7-azatryptophan) through the mechanism of fluorescence resonance energy transfer (FRET), can be used to detect protein conformational heterogeneity. This method is based on the notion that protein conformations having different donor-acceptor distances and interconverting slowly compared to the fluorescence lifetime of the donor (Phe(CN)) would exhibit different donor fluorescence lifetimes. Our results provide strong evidence suggesting that the native free energy basin of HP35 is populated with conformations that differ mostly in the position and mean helicity of the C-terminal helix. This finding is consistent with several previous experimental and computational studies. Moreover, this result holds strong implications for computational investigation of the folding mechanism of HP35.
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Affiliation(s)
- Arnaldo L Serrano
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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20
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Chowdhury R, Mojumdar SS, Chattoraj S, Bhattacharyya K. Effect of ionic liquid on the native and denatured state of a protein covalently attached to a probe: Solvation dynamics study. J Chem Phys 2012; 137:055104. [DOI: 10.1063/1.4739922] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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21
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Chowdhury A, Mojumdar SS, Choudhury A, Banerjee R, Das KP, Sasmal DK, Bhattacharyya K. Deoxycholate induced tetramer of αA-crystallin and sites of phosphorylation: Fluorescence correlation spectroscopy and femtosecond solvation dynamics. J Chem Phys 2012; 136:155101. [DOI: 10.1063/1.3702810] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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22
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Xie M, Li H, Ye M, Zhang Y, Hu J. Peptide Self-Assembly on Mica under Ethanol-Containing Atmospheres: Effects of Ethanol on Epitaxial Growth of Peptide Nanofilaments. J Phys Chem B 2012; 116:2927-33. [DOI: 10.1021/jp2089438] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Muyun Xie
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences
- Graduate School of the Chinese Academy of Sciences
| | - Hai Li
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences
| | - Ming Ye
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences
| | - Yi Zhang
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences
| | - Jun Hu
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences
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23
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Roy S, Bagchi B. Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer. J Phys Chem B 2012; 116:2958-68. [DOI: 10.1021/jp209437j] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Susmita Roy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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24
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Ghatak C, Rao VG, Ghosh S, Mandal S, Sarkar N. Solvation Dynamics and Rotational Relaxation Study Inside Niosome, A Nonionic Innocuous Poly(ethylene Glycol)-Based Surfactant Assembly: An Excitation Wavelength Dependent Experiment. J Phys Chem B 2011; 115:12514-20. [DOI: 10.1021/jp204473d] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Chiranjib Ghatak
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Vishal Govind Rao
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Shirsendu Ghosh
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Sarthak Mandal
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
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25
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Bhattacharjee N, Biswas P. Local order and mobility of water molecules around ambivalent helices. J Phys Chem B 2011; 115:12257-65. [PMID: 21916474 DOI: 10.1021/jp2066106] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Water on a protein surface plays a key role in determining the structure and dynamics of proteins. Compared to the properties of bulk water, many aspects of the structure and dynamics of the water surrounding the proteins are less understood. It is interesting therefore to explore how the properties of the water within the solvation shell around the peptide molecule depend on its specific secondary structure. In this work we investigate the orientational order and residence times of the water molecules to characterize the structure, energetics, and dynamics of the hydration shell water around ambivalent peptides. Ambivalent sequences are identical sequences which display multiple secondary structures in different proteins. Molecular dynamics simulations of representative proteins containing variable helix, variable nonhelix, and conserved helix are also used to explore the local structure and mobility of water molecules in their vicinity. The results, for the first time, depict a different water distribution pattern around the conserved and variable helices. The water molecules surrounding the helical segments in variable helices are found to possess a less locally ordered structure compared to those around their corresponding nonhelical counterparts and conserved helices. The long conserved helices exhibit extremely high local residence times compared to the helical conformations of the variable helices, whereas the residence times of the nonhelical conformations of the variable helices are comparable to those of the short conserved helices. This differential pattern of the structure and dynamics of water molecules in the vicinity of conserved/variable helices may lend valuable insights for understanding the role of solvent effects in determining sequence ambivalency and help in improving the accuracy of water models used in the simulations of proteins.
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26
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Das DK, Mondal T, Mandal U, Bhattacharyya K. Probing deuterium isotope effect on structure and solvation dynamics of human serum albumin. Chemphyschem 2011; 12:814-22. [PMID: 21341353 DOI: 10.1002/cphc.201000912] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 01/18/2011] [Indexed: 12/20/2022]
Abstract
The deuterium isotopic effect on the structure and solvation dynamics of the protein, human serum albumin (HSA), has been studied by using circular dichroism (CD), femtosecond up-conversion, FRET, and single-molecule spectroscopy. The CD spectra suggest that D(2)O affects the structure of HSA, leading to a 20% decrease in the helical structure. The FRET study indicates that the distance of C153 from the lone tryptophan residue of HSA is quite similar (≈21 Å) in H(2)O and D(2)O, and hence, the location of the probe in the protein remains the same in the two solvents. The single-molecule study suggests that coumarin 153 (C153) binds almost exclusively (>96%) to one site of HSA. Solvation dynamics of C153 in HSA is found to be markedly retarded in D(2)O compared with H(2)O. In H(2)O, the solvation of C153 bound to HSA is found to be biexponential with one component of 7 ps (30%) and a long component of 350 ps (70%). In D(2)O, we detected a short component of 4 ps (41%) and a long component of 950 ps (59%). Thus, the ultraslow component of the solvation dynamics of C153 bound to HSA in D(2)O (950 ps) is 2.5-fold slower than that in H(2)O (350 ps). The marked deuterium isotope effect has been ascribed to water molecules confined in the protein environment and to a lesser extent to the structural modification of protein by D(2)O.
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Affiliation(s)
- Dibyendu Kumar Das
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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27
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Mulinacci F, Bell SE, Capelle MA, Gurny R, Arvinte T. Oxidized Recombinant Human Growth Hormone That Maintains Conformational Integrity. J Pharm Sci 2011; 100:110-22. [DOI: 10.1002/jps.22268] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 04/21/2010] [Accepted: 05/16/2010] [Indexed: 11/10/2022]
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28
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Jha A, Ishii K, Udgaonkar JB, Tahara T, Krishnamoorthy G. Exploration of the Correlation between Solvation Dynamics and Internal Dynamics of a Protein. Biochemistry 2010; 50:397-408. [DOI: 10.1021/bi101440c] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Anjali Jha
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Kunihiko Ishii
- Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Wako, Saitama 351-0198, Japan
| | - Jayant B. Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Wako, Saitama 351-0198, Japan
| | - G. Krishnamoorthy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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29
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Toptygin D, Woolf TB, Brand L. Picosecond protein dynamics: the origin of the time-dependent spectral shift in the fluorescence of the single Trp in the protein GB1. J Phys Chem B 2010; 114:11323-37. [PMID: 20701310 DOI: 10.1021/jp104425t] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
How a biological system responds to a charge shift is a challenging question directly relevant to biological function. Time-resolved fluorescence of a tryptophan residue reflects protein and solvent response to the difference in pi-electron density between the excited and the ground state. In this study we use molecular dynamics to calculate the time-dependent spectral shift (TDSS) in the fluorescence of Trp-43 in GB1 protein. A new computational method for separating solvent, protein, and fluorophore contributions to TDSS is applied to 100 nonequilibrium trajectories for GB1 in TIP3P water. The results support several nontrivial conclusions. Both longitudinal and transverse relaxation modes of bulk solvent contribute to the TDSS in proteins. All relaxation components slower than the transverse relaxation of bulk solvent have significant contributions from both protein and solvent, with a negative correlation between them. Five exponential terms in the TDSS of GB1 are well separated by their relaxation times. A 0.036 ps term is due to both solvent (60%) and protein (40%). Two exponential terms represent longitudinal (tau(L) approximately = 0.4 ps) and transverse (tau(D) approximately = 5.6 ps) relaxation modes of TIP3P water. A 131 ps term is attributable to a small change in the tertiary structure, with the alpha-helix moving 0.2 A away from the beta-strand containing Trp-43. A 2580 ps term is due to the change in the conformation of the Glu-42 side chain that brings its carboxyl group close to the positively charged end of the excited fluorophore. Interestingly, water cancels 60% of the TDSS resulting from this conformational change.
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Affiliation(s)
- Dmitri Toptygin
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA.
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30
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Agarwal M, Kushwaha HR, Chakravarty C. Local order, energy, and mobility of water molecules in the hydration shell of small peptides. J Phys Chem B 2010; 114:651-9. [PMID: 19863091 DOI: 10.1021/jp909090u] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The extent to which the presence of a biomolecular solute modifies the local energetics of water molecules, as measured by the tagged molecule potential energy (TPE), is examined using molecular dynamics simulations of the beta-hairpin of 2GB1 and the alpha-helix of deca-alanine in water. The CHARMM22 force field, in conjunction with the TIP3P solvent water model, is used for the peptides, with simulations of TIP3P and SPC/E water used as benchmarks for the behavior of bulk solvent. TIP3P water is shown to have significantly lower local tetrahedral order and higher binding energy than SPC/E at the same state point. The TIP3P and SPC/E water models show very similar dynamical correlations in the TPE fluctuations on frequency scales greater than 0.1 cm(-1). In addition, the two models show the same linear correlation between mean tetrahedral order and binding energy, suggesting that the relationship between choice of water models and simulated hydration behavior may involve a complex interplay of static and dynamic factors. The introduction of a peptide in water modifies the local TPE of water molecules as a function of distance from the biomolecular interface. There is an oscillatory variation in the TPE with distance from the peptide for water molecules lying outside a 3 A radius and extending to at least 10 A. These variations are of the order of 2-5% of the bulk TPE value and are anticorrelated with variations in local tetrahedral order in terms of locations of maxima and minima, which may be understood in terms of the relative contribution of van der Waals and Coulombic contributions to the TPE. The distance-dependent variations in local order and energetics are essentially the same for the beta-hairpin of 2GB1 as well as deca-alanine. Within a radius of 3 A, the perturbation of the solvent structure is very significant with local TPEs that are 10-15% lower than the bulk value. The chemical identity of side-chain residues and the secondary structure play an important role in determining residue-dependent variations in the TPEs. The variation in the residue-dependent tagged molecule potential energies is of the order of 3-5%, while the local residence times vary by a factor of approximately 5. The correlation of the local residence times with the local energetics within the innermost hydration layer is weak, though charged residues typically have low binding energies and large residence times.
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Affiliation(s)
- Manish Agarwal
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
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31
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Sasmal DK, Dey S, Das DK, Bhattacharyya K. Deuterium isotope effect on femtosecond solvation dynamics in methyl β-cyclodextrins. J Chem Phys 2009; 131:044509. [DOI: 10.1063/1.3176020] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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32
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Johnson ME, Malardier-Jugroot C, Murarka RK, Head-Gordon T. Hydration water dynamics near biological interfaces. J Phys Chem B 2009; 113:4082-92. [PMID: 19425247 DOI: 10.1021/jp806183v] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We performed classical molecular dynamics simulations using both fixed-charge and polarizable water and protein force fields to contrast the hydration dynamics near hydrophilic and amphiphilic peptides as a function of temperature. The high peptide concentrations we use serve as a model for the surface of folded proteins where hydration layers around each residue overlap significantly. Through simulation we determine that there are notable differences in the water dynamics analyzed from the outer and inner hydration layer regions of the amphiphilic peptide solution that explains the experimentally observed presence of two translational relaxations, while the hydrophilic peptide solution shows only a single non-Arrhenius translational process with no distinction between hydration layers. Given that water dynamics for the amphiphilic peptide system reproduces all known rotational and translational hydration dynamical anomalies exhibited by hydration water near protein surfaces, our analysis provides strong evidence that dynamical signatures near biological interfaces arises because of frustration in the hydration dynamics induced by chemical heterogeneity, as opposed to just topological roughness, of the protein surface.
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Affiliation(s)
- Margaret E Johnson
- Department of Bioengineering, University of California, Berkeley, 94720, USA
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33
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Halle B, Nilsson L. Does the Dynamic Stokes Shift Report on Slow Protein Hydration Dynamics? J Phys Chem B 2009; 113:8210-3. [DOI: 10.1021/jp9027589] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bertil Halle
- Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden, and Department of Biosciences and Nutrition, Karolinska Institutet, SE-14157 Huddinge, Sweden
| | - Lennart Nilsson
- Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden, and Department of Biosciences and Nutrition, Karolinska Institutet, SE-14157 Huddinge, Sweden
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34
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Sen S, Andreatta D, Ponomarev SY, Beveridge DL, Berg MA. Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments. J Am Chem Soc 2009; 131:1724-35. [PMID: 19191698 PMCID: PMC2750815 DOI: 10.1021/ja805405a] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Time-resolved Stokes-shift experiments measure the dynamics of biomolecules and of the perturbed solvent near them on subnanosecond time scales, but molecular dynamics simulations are needed to provide a clear interpretation of the results. Here we show that simulations using standard methods quantitatively reproduce the main features of TRSS experiments in DNA and provide a molecular assignment for the dynamics. The simulations reproduce the magnitude and unusual power-law dynamics of the Stokes shift seen in recent experiments [ Andreatta, D., et al. J. Am. Chem. Soc. 2005, 127, 7270 ]. A polarization model is introduced to eliminate cross-correlations between the different components contributing to the signal. Using this model, well-defined contributions of the DNA, water, and counterion to the experimental signal are extracted. Water is found to have the largest contribution and to be responsible for the power-law dynamics. The counterions have a smaller, but non-negligible, contribution with a time constant of 220 ps. The contribution to the signal of the DNA itself is minor and fits a 30 ps stretched exponential. Both time-averaged and dynamic distributions are calculated. They show a small subset of ions with a different coupling but no other evidence of substates or rate heterogeneity.
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Affiliation(s)
- Sobhan Sen
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067 India
| | - Daniele Andreatta
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | | | | | - Mark A. Berg
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
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35
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Kondo M, Heisler IA, Conyard J, Rivett JPH, Meech SR. Reactive Dynamics in Confined Liquids: Interfacial Charge Effects on Ultrafast Torsional Dynamics in Water Nanodroplets. J Phys Chem B 2009; 113:1632-9. [DOI: 10.1021/jp808991g] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Minako Kondo
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Ismael A. Heisler
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Jamie Conyard
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Jasmine P. H. Rivett
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Stephen R. Meech
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, U.K
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36
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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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37
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Li T, Hassanali AA, Singer SJ. Origin of slow relaxation following photoexcitation of W7 in myoglobin and the dynamics of its hydration layer. J Phys Chem B 2008; 112:16121-34. [PMID: 19368022 PMCID: PMC2818739 DOI: 10.1021/jp803042u] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular dynamics simulations are used to calculate the time-dependent Stokes shift following photoexcitation of Trp-7 (W7) in myoglobin. In agreement with experiment, a long time (approximately 60 ps) component is observed. Since the long time Stokes shift component is absent when we repeat the calculation with protein frozen at the instant of photoexcitation, we firmly establish that protein flexibility is required to observe slow Stokes shift dynamics in this case. A transition between sub-states near the middle of a 30 ns ground-state trajectory gave us an opportunity to compare solvation dynamics in two different environments. While some of the superficial features are different, we find that the underlying dynamics are shared by the two isomers. It is necessary to look beyond a decomposition of the Stokes shift into protein and water contributions and probe the underlying dynamics of protein side groups, backbone, and water dynamics to obtain a full picture of the relaxation process. We analyze water residence times, diffusion, and reorientation dynamics in the hydration layer. We find slow components in each of these quantities and critically examine their origin and how they affect the observed Stokes shift.
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Affiliation(s)
- Tanping Li
- Biophysics Program and Department of Chemistry, Ohio State University, Columbus, Ohio, USA
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38
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Praveena G, Kolandaivel P. Structural and dynamical studies of all-trans and all-cis cyclo[(1R,3S)-γ-Acc-Gly]3 peptides. J Mol Model 2008; 14:1147-57. [DOI: 10.1007/s00894-008-0357-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2007] [Accepted: 07/23/2008] [Indexed: 11/25/2022]
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39
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Mandal U, Ghosh S, Mitra G, Adhikari A, Dey S, Bhattacharyya K. A Femtosecond Study of the Interaction of Human Serum Albumin with a Surfactant (SDS). Chem Asian J 2008; 3:1430-4. [DOI: 10.1002/asia.200800114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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40
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Sinha SK, Chakraborty S, Bandyopadhyay S. Thickness of the hydration layer of a protein from molecular dynamics simulation. J Phys Chem B 2008; 112:8203-9. [PMID: 18547099 DOI: 10.1021/jp8000724] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Water molecules around a protein exhibit slow dynamics with respect to that of pure bulk water. One important issue in protein hydration is the thickness of the hydration layer (i.e., the distance from the protein surface up to which the water dynamics is influenced by the protein). Estimation of thickness is crucial to understand better the properties of "biological water" and the role that it plays in guiding the protein's function. We have performed an atomistic molecular dynamics simulation of an aqueous solution of the protein villin headpiece subdomain or HP-36 to estimate the thickness of its hydration water. In particular, several dynamical properties of water around different segments (three alpha-helices) of the protein have been calculated by varying the thickness of the hydration layers. It is found that in general the influence of the helices on water properties extends beyond the first hydration layer. However, the heterogeneous nature of water among the first hydration layers of the three helices diminishes as the thickness is increased. It indicates that, for a small protein such as HP-36, the thickness of "biological water" is uniform for different segments of the protein.
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Affiliation(s)
- Sudipta Kumar Sinha
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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41
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Distinguishing thermodynamic and kinetic views of the preferential hydration of protein surfaces. Biophys J 2008; 95:2219-25. [PMID: 18515399 DOI: 10.1529/biophysj.108.133553] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Motivated by a quasi-chemical view of protein hydration, we define specific hydration sites on the surface of globular proteins in terms of the local water density at each site relative to bulk water density. The corresponding kinetic definition invokes the average residence time for a water molecule at each site and the average time that site remains unoccupied. Bound waters are identified by high site occupancies using either definition. In agreement with previous molecular dynamics simulation studies, we find only a weak correlation between local water densities and water residence times for hydration sites on the surface of two globular proteins, lysozyme and staphylococcal nuclease. However, a strong correlation is obtained when both the average residence and vacancy times are appropriately taken into account. In addition, two distinct kinetic regimes are observed for hydration sites with high occupancies: long residence times relative to vacancy times for a single water molecule, and short residence times with high turnover involving multiple water molecules. We also correlate water dynamics, characterized by average occupancy and vacancy times, with local heterogeneities in surface charge and surface roughness, and show that both features are necessary to obtain sites corresponding to kinetically bound waters.
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42
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Chakraborty S, Bandyopadhyay S. Dynamics of water in the hydration layer of a partially unfolded structure of the protein HP-36. J Phys Chem B 2008; 112:6500-7. [PMID: 18433159 DOI: 10.1021/jp710904c] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Atomistic molecular dynamics simulations of the folded native structure and a partially unfolded molten globule structure of the protein villin headpiece subdomain or HP-36 have been carried out with explicit solvent to explore the effects of unfolding on the dynamical behavior of water present in the hydration layers of different segments (three alpha-helices) of the protein. The calculations revealed that the unfolding of helix-2 influences the translational and rotational motions of water present in the hydration layers of the three helices in a heterogeneous manner. It is observed that a correlation exists between the unfolding of helix-2 and the microscopic kinetics of protein-water hydrogen bonds formed by its residues. This in turn has an influence on the rigidity of the hydration layers of the helices in the unfolded structure versus that in the folded native structure. These results should provide a microscopic explanation to recent solvation dynamics experiments on folded native and unfolded structures of proteins.
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Affiliation(s)
- Sudip Chakraborty
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur, India
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43
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Dey S, Adhikari A, Mandal U, Ghosh S, Bhattacharyya K. A Femtosecond Study of Excitation Wavelength Dependence of a Triblock Copolymer−Surfactant Supramolecular Assembly: (PEO)20−(PPO)70−(PEO)20 and CTAC. J Phys Chem B 2008; 112:5020-6. [DOI: 10.1021/jp8002257] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Shantanu Dey
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Aniruddha Adhikari
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Ujjwal Mandal
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Subhadip Ghosh
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Kankan Bhattacharyya
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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44
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Adhikari A, Dey S, Mandal U, Das DK, Ghosh S, Bhattacharyya K. Femtosecond Solvation Dynamics in Different Regions of a Bile Salt Aggregate: Excitation Wavelength Dependence. J Phys Chem B 2008; 112:3575-80. [DOI: 10.1021/jp7106445] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Aniruddha Adhikari
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Shantanu Dey
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Ujjwal Mandal
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Dibyendu Kumar Das
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Subhadip Ghosh
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Kankan Bhattacharyya
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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45
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Gilmore J, McKenzie RH. Quantum Dynamics of Electronic Excitations in Biomolecular Chromophores: Role of the Protein Environment and Solvent. J Phys Chem A 2008; 112:2162-76. [DOI: 10.1021/jp710243t] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Joel Gilmore
- Department of Physics, University of Queensland, Brisbane 4072 Australia
| | - Ross H. McKenzie
- Department of Physics, University of Queensland, Brisbane 4072 Australia
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46
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Malardier-Jugroot C, Johnson ME, Murarka RK, Head-Gordon T. Aqueous peptides as experimental models for hydration water dynamics near protein surfaces. Phys Chem Chem Phys 2008; 10:4903-8. [DOI: 10.1039/b806995f] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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48
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Chakraborty S, Sinha SK, Bandyopadhyay S. Low-Frequency Vibrational Spectrum of Water in the Hydration Layer of a Protein: A Molecular Dynamics Simulation Study. J Phys Chem B 2007; 111:13626-31. [DOI: 10.1021/jp0746401] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sudip Chakraborty
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
| | - Sudipta Kumar Sinha
- 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
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49
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Bandyopadhyay S, Chakraborty S, Bagchi B. Coupling between hydration layer dynamics and unfolding kinetics of HP-36. J Chem Phys 2007; 125:084912. [PMID: 16965062 DOI: 10.1063/1.2335451] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We have performed atomistic molecular dynamics simulations of aqueous solutions of HP-36 at 300 K in its native state, as well as at high temperatures to explore the unfolding dynamics of the protein and its correlation with the motion of water around it. On increasing the temperature a partially unfolded molten globule state is formed where the smallest alpha helix (helix 2) unfolds into a coil. It is observed that the unfolding is initiated around the residue Phe-18 which shows a sharp displacement during unfolding. We have noticed that the unfolding of the protein affects the density of water near the protein surface. Besides, the dynamics of water in the protein hydration layer has been found to be strongly correlated with the time evolution of the unfolding process. We have introduced and calculated a displacement time correlation function to monitor the change in water motion relative to the protein backbone during unfolding. We find that the unfolding of helix 2 is associated with an increase in mobility of water around it as compared to water around the other two helices. We have also explored the microscopic aspects of secondary structure specific and site specific solvation dynamics of the protein. The calculations reveal that unfolding influences the solvation dynamics of the protein molecule in a heterogeneous manner depending on the location of the polar probe residues. This seems to be in agreement with recent experimental findings.
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Affiliation(s)
- Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India.
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50
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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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