1
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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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2
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Effect of hemoglobin hydration on the physical properties of erythrocyte cytoplasm and whole blood. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.141560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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3
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Poudel H, Leitner DM. Energy Transport in Class B GPCRs: Role of Protein-Water Dynamics and Activation. J Phys Chem B 2022; 126:8362-8373. [PMID: 36256609 DOI: 10.1021/acs.jpcb.2c03960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We compute energy exchange networks (EENs) through glucagon-like peptide-1 receptor (GLP-1R), a class B G-protein-coupled receptor (GPCR), in inactive and two active states, one activated by a peptide ligand and the other by a small molecule agonist, from results of molecular dynamics simulations. The reorganized network upon activation contains contributions from structural as well as from dynamic changes and corresponding entropic contributions to the free energy of activation, which are estimated in terms of the change in rates of energy transfer across non-covalent contacts. The role of water in the EENs and in activation of GLP-1R is also investigated. The dynamics of water in contact with the central polar network of the transmembrane region is found to be significantly slower for both activated states compared to the inactive state. This result is consistent with the contribution of water molecules to activation of GLP-1R previously suggested and resembles water dynamics in parts of the transmembrane region found in earlier studies of rhodopsin-like GPCRs.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada89557, United States
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada89557, United States
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4
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Biswas A, Mallik BS. Ionic Dynamics and Vibrational Spectral Diffusion of a Protic Alkylammonium Ionic Salt through Intrinsic Cationic N-H Vibrational Probe from FPMD Simulations. J Phys Chem A 2022; 126:5134-5147. [PMID: 35900106 DOI: 10.1021/acs.jpca.2c03387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We employed density functional theory (DFT)-based molecular dynamics simulations to explore the structure, dynamics, and spectral properties of the protic ionic entity trimethylammonium chloride (TMACl). Structural investigations include calculating the site-site radial distribution functions (RDFs), the distribution of constituent cations and anions in three-dimensional space, and combined distribution functions of the hydrogen-bonded pair RDF versus angle, revealing the structural characteristics of the ionic solvation and the intermolecular interactions within ions. Further, we determined the instantaneous vibrational stretching frequencies of the intrinsic N-H stretch probe modes by applying the time-series wavelet method. The associated ionic dynamics within the protic ionic compound were investigated by calculating the time-evolution of the fluctuating frequencies and the frequency-time correlation functions (FFCFs). The time scale related to the local structural relaxation process and the average hydrogen bond lifetime, ion cage dynamics, and mean squared displacement were investigated. The faster decay component of the FFCFs, depicting the intermolecular motion of intact hydrogen bonds in TMACl, is 0.07 ps for the Perdew-Burke-Ernzerhof (PBE)-based simulation and 0.06 ps for the PBE-D2 representation. The slower time scale of the longer picosecond decay time component of PBE and PBE-D2 representations are 3.13 and 2.87 ps, respectively. These picosecond time scales represent more significant fluctuations of the hydrogen-bonding partners in the ionic entity and hydrogen-bond jump events accompanied by large angular jumps. The longest picosecond time scales represent structural relaxation, including large angular jumps and ion-pair dynamics. Also, ion cage lifetimes correlate with the slowest time scale of the associated dynamics of vibrational spectral diffusion despite the type of DFT functional. This study benchmarks DFT treatments of the exchange-correlation functional with and without the van der Waals (vdW) dispersion correction scheme. The inclusion of vdW interactions to the PBE functional represents a less structured state of the ionic entity and faster dynamics of the molecular motions relative to the one predicted by the PBE system. All the results illustrate the necessity of accurately describing the Coulomb interactions, vdW dispersive interactive forces, and localized hydrogen bonds required to sustain the energetic balance in this ionic salt.
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Affiliation(s)
- Aritri Biswas
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502284, Telangana, India
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502284, Telangana, India
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5
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Gnanasekaran R, Xu Y. Understanding the Energetic Components Influencing the Thermodynamic Quantities of Carbonic Anhydrase Protein upon Ligand Binding. ChemistrySelect 2022. [DOI: 10.1002/slct.202200024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Yao Xu
- Warshel Institute for Computational Biology School of Life and Health Sciences The Chinese University of Hong Kong (Shenzhen) Shenzhen 518172 P. R. China
- School of Life Science University of Science and Technology of China Hefei 230026 P. R. China
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6
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Priyadarsini A, Mallik BS. Amphiphilicity of Intricate Layered Graphene/g-C 3N 4 Nanosheets. J Phys Chem B 2021; 125:11697-11708. [PMID: 34664957 DOI: 10.1021/acs.jpcb.1c05609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hybrid heterostructure of the tri-s-triazine form of graphitic carbon nitride (g-C3N4), a stable two-dimensional material, results from intricate layer formation with graphene. In this material, g-C3N4, an amphiphilic material, stabilizes Pickering emulsions as an emulsifier and can effectively disperse graphene. Due to the various technological applications of the hybrid nanosheets in an aqueous environment, it is essential to study the interaction of water molecules with graphene and g-C3N4 (Gr/g-C3N4)-combined heterostructure. Although few studies have been performed signifying the water orientation in the interfacial layer, we find that there is a lack of detailed studies using various dynamical and structural properties of the interfacial water molecules. The interface of the Gr/g-C3N4 hybrid structure, one of the rarely found amphiphilic interfaces (on the g-C3N3 side), is appropriate for exploring the water affinity due to the availability of heterogeneous interfacial aqueous interactions. We adopted classical molecular dynamics simulations using two models for water molecules to study the structure and dynamics of an aqueous interface. We have correlated the structural properties to dynamics and spectral properties to understand the overall behavior of the amphiphilic interface. Our results branch into two significant hydrogen bond (HB) properties in HB count and HB strength among the water molecules in the different layers. The HB counts in the different layers of water are correlated using the average distance distribution (PrO4), tetrahedral order parameters, HB donor/acceptor count, and total HBs per water molecule. A conspicuous difference is found in the HB count and related dynamics of the system. The HB lifetime and diffusion coefficient hint at the equivalent strength of HBs in the different layers. All the findings conclude that the amphiphilicity of the Gr/g-C3N4 interface can help in understanding various interfacial physical and chemical processes.
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Affiliation(s)
- Adyasa Priyadarsini
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
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7
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Poudel H, Leitner DM. Activation-Induced Reorganization of Energy Transport Networks in the β 2 Adrenergic Receptor. J Phys Chem B 2021; 125:6522-6531. [PMID: 34106712 DOI: 10.1021/acs.jpcb.1c03412] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We compute energy exchange networks (EENs) through the β2 adrenergic receptor (β2AR), a G-protein coupled receptor (GPCR), in inactive and active states, based on the results of molecular dynamics simulations of this membrane bound protein. We introduce a new definition for the reorganization of EENs upon activation that depends on the relative change in rates of energy transfer across noncovalent contacts throughout the protein. On the basis of the reorganized network that we obtain for β2AR upon activation, we identify a branched pathway between the agonist binding site and the cytoplasmic region, where a G-protein binds to the receptor when activated. The pathway includes all of the motifs containing molecular switches previously identified as contributing to the allosteric transition of β2AR upon agonist binding. EENs and their reorganization upon activation are compared with structure-based contact networks computed for the inactive and active states of β2AR.
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Affiliation(s)
- 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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8
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Biswas A, Mallik BS. Dynamics of Ionic Liquid through Intrinsic Vibrational Probes Using the Dispersion-Corrected DFT Functionals. J Phys Chem B 2021; 125:6994-7008. [PMID: 34142827 DOI: 10.1021/acs.jpcb.1c04960] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
First principles molecular dynamics simulations have been utilized to study the spectral properties of the protic ionic liquid, methylammonium formate (MAF). All simulations were performed using density functional theory (DFT) and various van der Waals-corrected exchange-correlation functionals. We calculated the vibrational stretch frequency distributions, determined the time-frequency correlations of the intrinsic vibrational probes, the N-H and C-O modes in MAF, and the frequency-structure correlations. We also estimated the average hydrogen-bond lifetimes and orientation dynamics to capture the ultrafast spectral response. The spectroscopic signature of the N-H stretching vibrations using the Becke-Lee-Yang-Parr (BLYP) and Perdew-Burke-Ernzerhof (PBE) functionals displays a spectral shift in the lower frequency side, suggesting stronger hydrogen-bonding interactions represented by the gradient approximation functionals than the van der Waals (vdW)-corrected simulations. The carboxylate frequency profiles with the dispersion-corrected representations are almost similar without a significant difference in the normalized distributions. Besides, the COO stretching frequencies at the peak maxima positions of the PBE functionals exhibit a lesser deviation from the experimental data. Spectral diffusion dynamics of the intrinsic vibrational probes on the cationic and anionic sites of the ionic liquid proceed through a short time relaxation of the intact hydrogen bonds followed by an intermediate time constant and a longer time decay indicating the switchover of hydrogen bonds. Dispersion-corrected atom-centered one-electron potential (DCACP) correction added to the BLYP system slows down the picosecond time scales of frequency correlation and the time constants of rotational motion, lengthening the overall system dynamics. The observed trends in the time-dependent decays of frequency fluctuations and the orientation autocorrelation functions correlate with the structural interactions in liquid MAF and hydrogen-bond dynamics. In this study, we examine the predictions made by different density functional treatments comparing the results of the uncorrected BLYP and PBE representations with the semiempirical vdW methods of Grimme and matching our calculated data with the experimental observations.
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Affiliation(s)
- Aritri Biswas
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
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9
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Lee Y, Kim JG, Lee SJ, Muniyappan S, Kim TW, Ki H, Kim H, Jo J, Yun SR, Lee H, Lee KW, Kim SO, Cammarata M, Ihee H. Ultrafast coherent motion and helix rearrangement of homodimeric hemoglobin visualized with femtosecond X-ray solution scattering. Nat Commun 2021; 12:3677. [PMID: 34135339 PMCID: PMC8209046 DOI: 10.1038/s41467-021-23947-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/27/2021] [Indexed: 11/17/2022] Open
Abstract
Ultrafast motion of molecules, particularly the coherent motion, has been intensively investigated as a key factor guiding the reaction pathways. Recently, X-ray free-electron lasers (XFELs) have been utilized to elucidate the ultrafast motion of molecules. However, the studies on proteins using XFELs have been typically limited to the crystalline phase, and proteins in solution have rarely been investigated. Here we applied femtosecond time-resolved X-ray solution scattering (fs-TRXSS) and a structure refinement method to visualize the ultrafast motion of a protein. We succeeded in revealing detailed ultrafast structural changes of homodimeric hemoglobin involving the coherent motion. In addition to the motion of the protein itself, the time-dependent change of electron density of the hydration shell was tracked. Besides, the analysis on the fs-TRXSS data of myoglobin allows for observing the effect of the oligomeric state on the ultrafast coherent motion. Femtosecond time-resolved X-ray solution scattering (fs-TRXSS) measurements provide information on the structural dynamics of proteins in solution. Here, the authors present a structure refinement method for the analysis of fs-TRXSS data and use it to characterise the ultrafast structural changes of homodimeric haemoglobin.
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Affiliation(s)
- Yunbeom Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Sang Jin Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Srinivasan Muniyappan
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Tae Wu Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Hosung Ki
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Hanui Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Junbeom Jo
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - So Ri Yun
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Hyosub Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Kyung Won Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Seong Ok Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | | | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea. .,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea.
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10
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Biswas A, Mallik BS. Ultrafast Aqueous Dynamics in Concentrated Electrolytic Solutions of Lithium Salt and Ionic Liquid. J Phys Chem B 2020; 124:9898-9912. [DOI: 10.1021/acs.jpcb.0c06221] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Aritri Biswas
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
| | - Bhabani S. Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
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11
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Poudel H, Reid KM, Yamato T, Leitner DM. Energy Transfer across Nonpolar and Polar Contacts in Proteins: Role of Contact Fluctuations. J Phys Chem B 2020; 124:9852-9861. [PMID: 33107736 DOI: 10.1021/acs.jpcb.0c08091] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Molecular dynamics simulations of the villin headpiece subdomain HP36 have been carried out to examine relations between rates of vibrational energy transfer across non-covalently bonded contacts and equilibrium structural fluctuations, with focus on van der Waals contacts. Rates of energy transfer across van der Waals contacts vary inversely with the variance of the contact length, with the same constant of proportionality for all nonpolar contacts of HP36. A similar relation is observed for hydrogen bonds, but the proportionality depends on contact pairs, with hydrogen bonds stabilizing the α-helices all exhibiting the same constant of proportionality, one that is distinct from those computed for other polar contacts. Rates of energy transfer across van der Waals contacts are found to be up to 2 orders of magnitude smaller than rates of energy transfer across polar contacts.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Korey M Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Takahisa Yamato
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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12
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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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13
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Biswas A, Mallik BS. Structure and stretching dynamics of water molecules around an amphiphilic amide from FPMD simulations: A case study of N,N-dimethylformamide. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112524] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Reid KM, Yamato T, Leitner DM. Variation of Energy Transfer Rates across Protein–Water Contacts with Equilibrium Structural Fluctuations of a Homodimeric Hemoglobin. J Phys Chem B 2020; 124:1148-1159. [DOI: 10.1021/acs.jpcb.9b11413] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - Takahisa Yamato
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89557, United States
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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15
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Biswas A, Mallik BS. Distinctive behavior and two-dimensional vibrational dynamics of water molecules inside glycine solvation shell. RSC Adv 2020. [DOI: 10.1039/c9ra10521b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We present a first principles molecular dynamics study of a deuterated aqueous solution of a single glycine moiety to explore the structure, dynamics, and two-dimensional infrared spectra of water molecules found in the solvation shell of glycine.
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Affiliation(s)
- Aritri Biswas
- Department of Chemistry
- Indian Institute of Technology Hyderabad
- Sangareddy
- India
| | - Bhabani S. Mallik
- Department of Chemistry
- Indian Institute of Technology Hyderabad
- Sangareddy
- India
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16
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Biswas A, Priyadarsini A, Mallik BS. Dynamics and Spectral Response of Water Molecules around Tetramethylammonium Cation. J Phys Chem B 2019; 123:8753-8766. [DOI: 10.1021/acs.jpcb.9b05466] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aritri Biswas
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285, Sangareddy, Telangana India
| | - Adyasa Priyadarsini
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285, Sangareddy, Telangana India
| | - Bhabani S. Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285, Sangareddy, Telangana India
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17
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Leitner DM, Pandey HD, Reid KM. Energy Transport across Interfaces in Biomolecular Systems. J Phys Chem B 2019; 123:9507-9524. [DOI: 10.1021/acs.jpcb.9b07086] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Hari Datt Pandey
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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18
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Low temperature dependence of protein-water interactions on barstar surface: A nano-scale modelling. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.10.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Yang C, Choi M, Kim JG, Kim H, Muniyappan S, Nozawa S, Adachi SI, Henning R, Kosheleva I, Ihee H. Protein Structural Dynamics of Wild-Type and Mutant Homodimeric Hemoglobin Studied by Time-Resolved X-Ray Solution Scattering. Int J Mol Sci 2018; 19:ijms19113633. [PMID: 30453670 PMCID: PMC6274816 DOI: 10.3390/ijms19113633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 01/30/2023] Open
Abstract
The quaternary transition between the relaxed (R) and tense (T) states of heme-binding proteins is a textbook example for the allosteric structural transition. Homodimeric hemoglobin (HbI) from Scapharca inaequivalvis is a useful model system for investigating the allosteric behavior because of the relatively simple quaternary structure. To understand the cooperative transition of HbI, wild-type and mutants of HbI have been studied by using time-resolved X-ray solution scattering (TRXSS), which is sensitive to the conformational changes. Herein, we review the structural dynamics of HbI investigated by TRXSS and compare the results of TRXSS with those of other techniques.
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Affiliation(s)
- Cheolhee Yang
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
| | - Minseo Choi
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
| | - Hanui Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
| | - Srinivasan Muniyappan
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
| | - Shunsuke Nozawa
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
| | - Shin-Ichi Adachi
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA.
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA.
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
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20
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Leitner DM, Yamato T. MAPPING ENERGY TRANSPORT NETWORKS IN PROTEINS. REVIEWS IN COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1002/9781119518068.ch2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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21
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Reid KM, Yamato T, Leitner DM. Scaling of Rates of Vibrational Energy Transfer in Proteins with Equilibrium Dynamics and Entropy. J Phys Chem B 2018; 122:9331-9339. [DOI: 10.1021/acs.jpcb.8b07552] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Takahisa Yamato
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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22
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Leitner DM. Molecules and the Eigenstate Thermalization Hypothesis. ENTROPY 2018; 20:e20090673. [PMID: 33265762 PMCID: PMC7513195 DOI: 10.3390/e20090673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/02/2018] [Accepted: 09/03/2018] [Indexed: 11/18/2022]
Abstract
We review a theory that predicts the onset of thermalization in a quantum mechanical coupled non-linear oscillator system, which models the vibrational degrees of freedom of a molecule. A system of N non-linear oscillators perturbed by cubic anharmonic interactions exhibits a many-body localization (MBL) transition in the vibrational state space (VSS) of the molecule. This transition can occur at rather high energy in a sizable molecule because the density of states coupled by cubic anharmonic terms scales as N3, in marked contrast to the total density of states, which scales as exp(aN), where a is a constant. The emergence of a MBL transition in the VSS is seen by analysis of a random matrix ensemble that captures the locality of coupling in the VSS, referred to as local random matrix theory (LRMT). Upon introducing higher order anharmonicity, the location of the MBL transition of even a sizable molecule, such as an organic molecule with tens of atoms, still lies at an energy that may exceed the energy to surmount a barrier to reaction, such as a barrier to conformational change. Illustrative calculations are provided, and some recent work on the influence of thermalization on thermal conduction in molecular junctions is also discussed.
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Affiliation(s)
- David M Leitner
- Department of Chemistry, University of Nevada, Reno, NV 89557, USA
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23
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Khatua P, Bandyopadhyay S. Dynamical crossover of water confined within the amphiphilic nanocores of aggregated amyloid β peptides. Phys Chem Chem Phys 2018; 20:14835-14845. [PMID: 29781021 DOI: 10.1039/c8cp01942h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
It is believed that the self-assembly of amyloid beta (Aβ) peptides in the brain is the cause of Alzheimer's disease. Atomistic molecular dynamics simulations of aqueous solutions of Aβ protofilaments of different sizes at room temperature have been carried out to explore the dynamic properties of water confined within the core and at the exterior surface of the protofilaments. Attempts have been made to understand how the non-uniform distortion of the protofilaments associated with their structural crossover influences the diffusivity and the hydrogen bonding environment of the confined water molecules. In contrast to the homogeneous solvent dynamical environment at the exterior surface, the calculations revealed heterogeneously restricted motions of water confined within the distorted cores of the protofilaments. Importantly, it is demonstrated that the structural crossover of the aggregates observed for the decamer is associated with a dynamical transition of water confined within its core. A direct one-to-one correlation between the heterogeneously restricted core water motions and the kinetics of the breaking and formation of hydrogen bonds quantitatively demonstrated that a modified hydrogen bond arrangement within the cores of higher order Aβ protofilaments is the origin behind the crossover in core water mobility. A fraction of the water molecules forming short-lived water-water hydrogen bonds within the core of the crossover protofilament decamer are believed to diffuse away easily from the core and thus play a crucial role in further growth of the protofilament by facilitating the binding of new peptide monomers.
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Affiliation(s)
- Prabir Khatua
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India.
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24
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Abdizadeh H, Atilgan AR, Atilgan C, Dedeoglu B. Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins. Metallomics 2018; 9:1513-1533. [PMID: 28967944 DOI: 10.1039/c7mt00216e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
With the advances in three-dimensional structure determination techniques, high quality structures of the iron transport proteins transferrin and the bacterial ferric binding protein (FbpA) have been deposited in the past decade. These are proteins of relatively large size, and developments in hardware and software have only recently made it possible to study their dynamics using standard computational resources. We review computational techniques towards understanding the equilibrium and kinetic properties of iron transport proteins under different environmental conditions. At the level of detail that requires quantum chemical treatments, the octahedral geometry around iron has been scrutinized and it has been established that the iron coordinating tyrosines are in an unusual deprotonated state. At the atomistic level, both the N-lobe and the full bilobal structure of transferrin have been studied under varying conditions of pH, ionic strength and binding of other metal ions by molecular dynamics (MD) simulations. These studies have allowed questions to be answered, among others, on the function of second shell residues in iron release, the role of synergistic anions in preparing the active site for iron binding, and the differences between the kinetics of the N- and the C-lobe. MD simulations on FbpA have led to the detailed observation of the binding kinetics of phosphate to the apo form, and to the conformational preferences of the holo form under conditions mimicking the environmental niches provided by the periplasmic space. To study the dynamics of these proteins with their receptors, one must resort to coarse-grained methodologies, since these systems are prohibitively large for atomistic simulations. A study of the complex of human transferrin (hTf) with its pathogenic receptor by such methods has revealed a potential mechanistic explanation for the defense mechanism that arises in evolutionary warfare. Meanwhile, the motions in the transferrin receptor bound hTf have been shown to disfavor apo hTf dissociation, explaining why the two proteins remain in complex during the recycling process from the endosome to the cell surface. Open problems and possible technological applications related to metal ion binding-release in iron transport proteins that may be handled by hybrid use of quantum mechanical, MD and coarse-grained approaches are discussed.
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Affiliation(s)
- H Abdizadeh
- Faculty of Engineering and Natural Sciences, Sabancı University, Orhanlı 34956, Tuzla, Istanbul, Turkey.
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25
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Elola MD, Rodriguez J. Influence of Cholesterol on the Dynamics of Hydration in Phospholipid Bilayers. J Phys Chem B 2018; 122:5897-5907. [PMID: 29742895 DOI: 10.1021/acs.jpcb.8b00360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the dynamics of interfacial waters in dipalmitoylphosphatidylcholine (DPPC) bilayers upon the addition of cholesterol, by molecular dynamics simulations. Our data reveal that the inclusion of cholesterol modifies the membrane aqueous interfacial dynamics: waters diffuse faster, their rotational decay time is shorter, and the DPPC/water hydrogen bond dynamics relaxes faster than in the pure DPPC membrane. The observed acceleration of the translational water dynamics agrees with recent experimental results, in which, by means of NMR techniques, an increment of the surface water diffusivity is measured upon the addition of cholesterol. A microscopic analysis of the lipid/water hydrogen bond network at the interfacial region suggests that the mechanism underlying the observed water mobility enhancement is given by the rupture of a fraction of interlipid water bridge hydrogen bonds connecting two different DPPC molecules, concomitant to the formation of new lipid/solvent bonds, whose dynamics is faster than that of the former. The consideration of a simple two-state model for the decay of the hydrogen bond correlation function yielded excellent results, obtaining two well-separated characteristic time scales: a slow one (∼250 ps) associated with bonds linking two DPPC molecules, and a fast one (∼15 ps), related to DPPC/solvent bonds.
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Affiliation(s)
- M Dolores Elola
- Departamento de Física , Comisión Nacional de Energía Atómica , Av Libertador 8250, 1429 Buenos Aires , Argentina
| | - Javier Rodriguez
- Departamento de Física , Comisión Nacional de Energía Atómica , Av Libertador 8250, 1429 Buenos Aires , Argentina.,ECyT , UNSAM , Martín de Irigoyen 3100, 1650 San Martín, Provincia de Buenos Aires , Argentina
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26
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Gupta M, Khatua P, Chakravarty C, Bandyopadhyay S. Hydration Behavior along the Folding Pathways of Trpzip4, Trpzip5 and Trpzip6. J Phys Chem B 2018; 122:1560-1572. [DOI: 10.1021/acs.jpcb.7b10135] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Madhulika Gupta
- Department
of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
| | - Prabir Khatua
- Molecular
Modeling Laboratory, Department of Chemistry, Indian Institute of Technology-Kharagpur, Kharagpur 721302, India
| | - Charusita Chakravarty
- Department
of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
| | - Sanjoy Bandyopadhyay
- Molecular
Modeling Laboratory, Department of Chemistry, Indian Institute of Technology-Kharagpur, Kharagpur 721302, India
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27
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Alrayyani M, Wang X, Miljanić OŠ. Confinement of Water Pentamers within the Crystals of a Reduced Cyclotribenzoin. Chemistry 2017; 23:16476-16478. [DOI: 10.1002/chem.201704883] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Maymounah Alrayyani
- Department of Chemistry University of Houston 3585 Cullen Blvd. Room 112 Houston TX 77204-5003 USA
- Chemistry Department Faculty of Science King Abdulaziz University Jeddah 23218 Saudi Arabia
| | - Xiqu Wang
- Department of Chemistry University of Houston 3585 Cullen Blvd. Room 112 Houston TX 77204-5003 USA
| | - Ognjen Š. Miljanić
- Department of Chemistry University of Houston 3585 Cullen Blvd. Room 112 Houston TX 77204-5003 USA
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28
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Gnanasekaran R. Computational study to understand the energy transfer pathways within amicyanin. J Mol Graph Model 2017; 78:88-95. [PMID: 29054098 DOI: 10.1016/j.jmgm.2017.09.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/28/2017] [Accepted: 09/30/2017] [Indexed: 11/27/2022]
Abstract
Vibrational energy diffusivities between the residues present in Amicyanin copper protein are calculated and presented in form of communication map. From those results energy flow pathways from the copper metal ion to the inter protein residue Glu31 are identified. Our finding suggests many different pathways are possible and copper metal ion in oxidized and reduced state switches the pathways. Our finding also suggests the cooperative nature of surrounding residues and water molecules towards selecting the pathways. The major transport channels in the oxidised state are, Cu2+---> MET28---> LYS29---> TYR30---> GLU31 and Cu2+---> MET98---> TYR30--- > GLU31. And in the reduced state Cu+---> CYS9---> TYR30---> GLU31 and Cu+---> MET28---> LYS2---> TYR30---> GLU31. We studied further the interaction energies between the copper ion and neighbouring residues using B3LYP/QZVP method. Both the methods complement each other in predicting the energy flow pathways and the cooperative nature of residues.
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29
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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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30
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Foroutan M, Fatemi SM, Esmaeilian F. A review of the structure and dynamics of nanoconfined water and ionic liquids via molecular dynamics simulation. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2017; 40:19. [PMID: 28229319 DOI: 10.1140/epje/i2017-11507-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 01/30/2017] [Indexed: 05/04/2023]
Abstract
During the past decade, the research on fluids in nanoconfined geometries has received considerable attention as a consequence of their wide applications in different fields. Several nanoconfined systems such as water and ionic liquids, together with an equally impressive array of nanoconfining media such as carbon nanotube, graphene and graphene oxide have received increasingly growing interest in the past years. Water is the first system that has been reviewed in this article, due to its important role in transport phenomena in environmental sciences. Water is often considered as a highly nanoconfined system, due to its reduction to a few layers of water molecules between the extended surface of large macromolecules. The second system discussed here is ionic liquids, which have been widely studied in the modern green chemistry movement. Considering the great importance of ionic liquids in industry, and also their oil/water counterpart, nanoconfined ionic liquid system has become an important area of research with many fascinating applications. Furthermore, the method of molecular dynamics simulation is one of the major tools in the theoretical study of water and ionic liquids in nanoconfinement, which increasingly has been joined with experimental procedures. In this way, the choice of water and ionic liquids in nanoconfinement is justified by applying molecular dynamics simulation approaches in this review article.
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Affiliation(s)
- Masumeh Foroutan
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran.
| | - S Mahmood Fatemi
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Farshad Esmaeilian
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
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31
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Pandey HD, Leitner DM. Vibrational energy transport in molecules and the statistical properties of vibrational modes. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2016.07.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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32
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Sheu SY, Liu YC, Yang DY. Interfacial water effect on cooperativity and signal communication in Scapharca dimeric hemoglobin. Phys Chem Chem Phys 2017; 19:7380-7389. [DOI: 10.1039/c7cp00280g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cooperativity is important in controlling the biological functions of allosteric proteins.
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Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences and Institute of Genome Sciences
- National Yang-Ming University
- Taipei 112
- Taiwan
- Institute of Biomedical Informatics
| | - Yu-Cheng Liu
- Institute of Biomedical Informatics
- National Yang-Ming University
- Taipei 112
- Taiwan
| | - Dah-Yen Yang
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 106
- Taiwan
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33
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Gnanasekaran R. Probing the communication of deoxythymidine triphosphate in HIV-1 reverse transcriptase by communication maps and interaction energy studies. Phys Chem Chem Phys 2017; 19:29608-29616. [DOI: 10.1039/c7cp06386e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We calculate communication maps for HIV-1 Reverse Transcriptase (RT) to elucidate energy transfer pathways between deoxythymidine triphosphate (dTTP) and other parts of the protein.
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34
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Abstract
We examine energy dynamics in the unliganded and liganded states of the homodimeric hemoglobin from Scapharca inaequivalvis (HbI), which exhibits cooperativity mediated by the cluster of water molecules at the interface upon ligand binding and dissociation. We construct and analyze a dynamic network in which nodes representing the residues, hemes, and water cluster are connected by edges that represent energy transport times, as well as a nonbonded network (NBN) indicating regions that respond rapidly to local strain within the protein via nonbonded interactions. One of the two largest NBNs includes the Lys30-Asp89 salt bridge critical for stabilizing the dimer. The other includes the hemes and surrounding residues, as well as, in the unliganded state, the cluster of water molecules between the globules. Energy transport in the protein appears to be controlled by the Lys30-Asp89 salt bridge critical for stabilizing the dimer, as well as the interface water cluster in the unliganded state. Possible connections between energy transport dynamics in response to local strain identified here and allosteric transitions in HbI are discussed.
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Affiliation(s)
- David M Leitner
- Department of Chemistry and Chemical Physics Program, University of Nevada , Reno, Nevada 89557, United States
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35
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Chakraborty K, Bandyopadhyay S. Effects of protein-DNA complex formation on the intermolecular vibrational density of states of interfacial water. Phys Chem Chem Phys 2016; 18:7780-8. [PMID: 26912116 DOI: 10.1039/c5cp07562a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single-stranded DNAs (ss-DNAs) are formed as intermediates during DNA metabolic processes. ss-DNA binding (SSB) proteins specifically bind to the single-stranded segments of the DNA and protect it from being degraded. We have performed room temperature molecular dynamics simulations of the aqueous solution of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element (FUSE) binding protein (FBP) complexed with two ss-DNA oligomers. Efforts have been made to explore the influence of complex formation on low-frequency vibrational density of states of the surface water molecules. It is revealed that increased back scattering of water confined around the complexed structures leads to significant blue shifts of the band corresponding to the O···O···O bending or restricted transverse motions of water, the effect being more for the bridged water molecules. Importantly, it is demonstrated that the formation of such complexed structures of a similar type may often influence the transverse and longitudinal degrees of freedom of the surrounding water molecules in a nonuniform manner.
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Affiliation(s)
- Kaushik Chakraborty
- 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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36
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Kim JG, Muniyappan S, Oang KY, Kim TW, Yang C, Kim KH, Kim J, Ihee H. Cooperative protein structural dynamics of homodimeric hemoglobin linked to water cluster at subunit interface revealed by time-resolved X-ray solution scattering. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:023610. [PMID: 27158635 PMCID: PMC4833754 DOI: 10.1063/1.4947071] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 04/06/2016] [Indexed: 05/30/2023]
Abstract
Homodimeric hemoglobin (HbI) consisting of two subunits is a good model system for investigating the allosteric structural transition as it exhibits cooperativity in ligand binding. In this work, as an effort to extend our previous study on wild-type and F97Y mutant HbI, we investigate structural dynamics of a mutant HbI in solution to examine the role of well-organized interfacial water cluster, which has been known to mediate intersubunit communication in HbI. In the T72V mutant of HbI, the interfacial water cluster in the T state is perturbed due to the lack of Thr72, resulting in two less interfacial water molecules than in wild-type HbI. By performing picosecond time-resolved X-ray solution scattering experiment and kinetic analysis on the T72V mutant, we identify three structurally distinct intermediates (I1, I2, and I3) and show that the kinetics of the T72V mutant are well described by the same kinetic model used for wild-type and F97Y HbI, which involves biphasic kinetics, geminate recombination, and bimolecular CO recombination. The optimized kinetic model shows that the R-T transition and bimolecular CO recombination are faster in the T72V mutant than in the wild type. From structural analysis using species-associated difference scattering curves for the intermediates, we find that the T-like deoxy I3 intermediate in solution has a different structure from deoxy HbI in crystal. In addition, we extract detailed structural parameters of the intermediates such as E-F distance, intersubunit rotation angle, and heme-heme distance. By comparing the structures of protein intermediates in wild-type HbI and the T72V mutant, we reveal how the perturbation in the interfacial water cluster affects the kinetics and structures of reaction intermediates of HbI.
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Affiliation(s)
| | | | | | | | | | | | - Jeongho Kim
- Department of Chemistry, Inha University , Incheon 402-751, South Korea
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37
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Morón MC, Prada-Gracia D, Falo F. Macro and nano scale modelling of water–water interactions at ambient and low temperature: relaxation and residence times. Phys Chem Chem Phys 2016; 18:9377-87. [DOI: 10.1039/c5cp06791j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A method to predict magnitudes in quantitative agreement with experimental data has been devised and applied to model water–water interactions at low temperature.
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Affiliation(s)
- María Carmen Morón
- Instituto de Ciencia de Materiales de Aragón (ICMA)
- Consejo Superior de Investigaciones Científicas-Universidad de Zaragoza
- E-50009 Zaragoza
- Spain
- Departamento de Física de la Materia Condensada
| | - Diego Prada-Gracia
- Freiburg Institute for Advanced Studies
- School of Soft Matter Research
- 79104 Freiburg im Breisgau
- Germany
| | - Fernando Falo
- Departamento de Física de la Materia Condensada
- Facultad de Ciencias
- Universidad de Zaragoza
- Zaragoza
- Spain
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38
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Cheng S, Shi T, Wang XL, Liang J, Wu H, Xie L, Li Y, Zhao YL. Features of S-nitrosylation based on statistical analysis and molecular dynamics simulation: cysteine acidity, surrounding basicity, steric hindrance and local flexibility. MOLECULAR BIOSYSTEMS 2015; 10:2597-606. [PMID: 25030274 DOI: 10.1039/c4mb00322e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
S-Nitrosylation is involved in protein functional regulation and cellular signal transduction. Although intensive efforts have been made, the molecular mechanisms of S-nitrosylation have not yet been fully understood. In this work, we carried out a survey on 213 protein structures with S-nitrosylated cysteine sites and molecular dynamic simulations of hemoglobin as a case study. It was observed that the S-nitrosylated cysteines showed a lower pKa, a higher population of basic residues, a lower population of big-volume residues in the neighborhood, and relatively higher flexibility. The case study of hemoglobin showed that, compared to that in the T-state, Cysβ93 in the R-state hemoglobin possessed the above structural features, in agreement with the previous report that the R-state was more reactive in S-nitrosylation. Moreover, basic residues moved closer to the Cysβ93 in the dep-R-state hemoglobin, while big-volume residues approached the Cysβ93 in the dep-T-state. Using the four characteristics, i.e. cysteine acidity, surrounding basicity, steric hindrance, and local flexibility, a 3-dimensional model of S-nitrosylation was constructed to explain 61.9% of the S-nitrosylated and 58.1% of the non-S-nitrosylated cysteines. Our study suggests that cysteine deprotonation is a prerequisite for protein S-nitrosylation, and these characteristics might be useful in identifying specificity of protein S-nitrosylation.
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Affiliation(s)
- Shangli Cheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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39
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Lee SS, Park S, Kim JY, Kim HR, Lee S, Oh HB. Infrared multiple photon dissociation spectroscopy and density functional theory (DFT) studies of protonated permethylated β-cyclodextrin-water non-covalent complexes. Phys Chem Chem Phys 2015; 16:8376-83. [PMID: 24658048 DOI: 10.1039/c3cp54841d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present infrared multiple photon dissociation (IRMPD) spectroscopy and quantum chemical calculation results for the protonated permethylated β-cyclodextrin (CD)-water non-covalent complex, the simplest β-CD non-covalent complex, in the gas-phase. The IRMPD spectrum in the region 2700-3750 cm(-1) consisted of three strong peaks at 3096, 3315, and 3490 cm(-1). These spectral features in the experimental IRMPD spectrum were compared with a large set of infrared absorption spectra predicted using density functional theory (DFT) calculations for the protonated β-CD-water complex. Complex III (see ), in which the water molecule (at the primary rim) and the proton (at the secondary rim) were separated, was found to suitably reflect the main spectral characteristics found in the experimental IRMPD spectrum. The absence of the homodromic hydrogen bond ring, due to replacement of hydroxyl groups with methoxy groups in permethylated β-CD, rendered the primary rim open compared with the unmodified β-CD 'one-gate-closed' lowest energy conformer. This study demonstrates that IRMPD studies combined with DFT theoretical calculations can be a good method for studying molecular interactions of large host-guest pairs.
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Affiliation(s)
- Sung-Sik Lee
- Department of Applied Chemistry, Kyung Hee University, Gyeonggi 446-701, Korea.
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40
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Leitner DM, Buchenberg S, Brettel P, Stock G. Vibrational energy flow in the villin headpiece subdomain: Master equation simulations. J Chem Phys 2015; 142:075101. [DOI: 10.1063/1.4907881] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- David M. Leitner
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, USA
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - Sebastian Buchenberg
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Paul Brettel
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Gerhard Stock
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany
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Narayanan Krishnamoorthy A, Holm C, Smiatek J. Local Water Dynamics around Antifreeze Protein Residues in the Presence of Osmolytes: The Importance of Hydroxyl and Disaccharide Groups. J Phys Chem B 2014; 118:11613-21. [DOI: 10.1021/jp507062r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Christian Holm
- Institut für Computerphysik, Universität Stuttgart, D-70569 Stuttgart, Germany
| | - Jens Smiatek
- Institut für Computerphysik, Universität Stuttgart, D-70569 Stuttgart, Germany
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42
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Agbo JK, Xu Y, Zhang P, Straub JE, Leitner DM. Vibrational energy flow across heme–cytochrome c and cytochrome c–water interfaces. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1504-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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43
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Takayanagi M, Kurisaki I, Nagaoka M. Non-site-specific allosteric effect of oxygen on human hemoglobin under high oxygen partial pressure. Sci Rep 2014; 4:4601. [PMID: 24710521 PMCID: PMC3978498 DOI: 10.1038/srep04601] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 03/12/2014] [Indexed: 12/11/2022] Open
Abstract
Protein allostery is essential for vital activities. Allosteric regulation of human hemoglobin (HbA) with two quaternary states T and R has been a paradigm of allosteric structural regulation of proteins. It is widely accepted that oxygen molecules (O2) act as a “site-specific” homotropic effector, or the successive O2 binding to the heme brings about the quaternary regulation. However, here we show that the site-specific allosteric effect is not necessarily only a unique mechanism of O2 allostery. Our simulation results revealed that the solution environment of high O2 partial pressure enhances the quaternary change from T to R without binding to the heme, suggesting an additional “non-site-specific” allosteric effect of O2. The latter effect should play a complementary role in the quaternary change by affecting the intersubunit contacts. This analysis must become a milestone in comprehensive understanding of the allosteric regulation of HbA from the molecular point of view.
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Affiliation(s)
- Masayoshi Takayanagi
- 1] Venture Business Laboratory, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan [2] Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan [3] Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Honmachi, Kawaguchi 332-0012, Japan
| | - Ikuo Kurisaki
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Masataka Nagaoka
- 1] Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan [2] Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Honmachi, Kawaguchi 332-0012, Japan
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44
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Agbo JK, Gnanasekaran R, Leitner DM. Communication Maps: Exploring Energy Transport through Proteins and Water. Isr J Chem 2014. [DOI: 10.1002/ijch.201300139] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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45
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Rao JS, Smith MD, Cruz L. The Stability of a β-Hairpin Is Altered by Surface–Water Interactions under Confinement. J Phys Chem B 2014; 118:3517-23. [DOI: 10.1021/jp411122h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- J. Srinivasa Rao
- Department of Physics, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania, 19104, United States
| | - Micholas Dean Smith
- Department of Physics, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania, 19104, United States
| | - Luis Cruz
- Department of Physics, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania, 19104, United States
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46
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Xu Y, Leitner DM. Communication maps of vibrational energy transport through Photoactive Yellow Protein. J Phys Chem A 2014; 118:7280-7. [PMID: 24552496 DOI: 10.1021/jp411281y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We calculate communication maps for Photoactive Yellow Protein (PYP) from the purple phototropic eubacterium Halorhodospira halophile and use them to elucidate energy transfer pathways from the chromophore through the rest of the protein in the ground and excited state. The calculations reveal that in PYP excess energy from the chromophore flows mainly to regions of the surrounding residues that hydrogen bond to the chromophore. In addition, quantum mechanics/molecular mechanics and molecular dynamics (MD) simulations of the dielectric response of the protein and solvent environment due to charge rearrangement on the chromophore following photoexcitation are also presented, with both approaches yielding similar time constants for the response. Results of MD simulations indicate that the residues hydrogen bonding to the chromophore make the largest contribution to the response.
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Affiliation(s)
- Yao Xu
- Department of Chemistry and Chemical Physics Program, University of Nevada , Reno, Nevada 89557, United States
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47
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Xu Y, Leitner DM. Vibrational Energy Flow through the Green Fluorescent Protein–Water Interface: Communication Maps and Thermal Boundary Conductance. J Phys Chem B 2014; 118:7818-26. [DOI: 10.1021/jp412141z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yao Xu
- Department
of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
- Physikalische
Chemie II, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - David M. Leitner
- Department
of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
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48
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Xu Y, Gnanasekaran R, Leitner DM. The dielectric response to photoexcitation of GFP: A molecular dynamics study. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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49
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Yu D, Hennig M, Mole RA, Li JC, Wheeler C, Strässle T, Kearley GJ. Proline induced disruption of the structure and dynamics of water. Phys Chem Chem Phys 2013; 15:20555-64. [DOI: 10.1039/c3cp51874d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Kastritis PL, Bonvin AMJJ. On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface 2012; 10:20120835. [PMID: 23235262 PMCID: PMC3565702 DOI: 10.1098/rsif.2012.0835] [Citation(s) in RCA: 276] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Interactions between proteins are orchestrated in a precise and time-dependent manner, underlying cellular function. The binding affinity, defined as the strength of these interactions, is translated into physico-chemical terms in the dissociation constant (Kd), the latter being an experimental measure that determines whether an interaction will be formed in solution or not. Predicting binding affinity from structural models has been a matter of active research for more than 40 years because of its fundamental role in drug development. However, all available approaches are incapable of predicting the binding affinity of protein–protein complexes from coordinates alone. Here, we examine both theoretical and experimental limitations that complicate the derivation of structure–affinity relationships. Most work so far has concentrated on binary interactions. Systems of increased complexity are far from being understood. The main physico-chemical measure that relates to binding affinity is the buried surface area, but it does not hold for flexible complexes. For the latter, there must be a significant entropic contribution that will have to be approximated in the future. We foresee that any theoretical modelling of these interactions will have to follow an integrative approach considering the biology, chemistry and physics that underlie protein–protein recognition.
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Affiliation(s)
- Panagiotis L Kastritis
- Bijvoet Center for Biomolecular Research, Faculty of Science, Chemistry, Utrecht University, , Padualaan 8, Utrecht, The Netherlands
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