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Moral R, Paul S. Exploring Cyclic Peptide Nanotube Stability Across Diverse Lipid Bilayers and Unveiling Water Transport Dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:882-895. [PMID: 38134046 DOI: 10.1021/acs.langmuir.3c03030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Cyclic Peptide Nanotubes (CPNTs) have emerged as compelling candidates for various applications, particularly as nanochannels within lipid bilayers. In this study, the stability of two CPNTs, namely 8 × [(Cys-Gly-Met-Gly)2] and 8 × [(Gly-Leu)4], are comprehensively investigated across different lipid bilayers, including 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), a mixed model membrane (POPE/POPG), and a realistic yeast model membrane. The results demonstrate that both CPNTs maintain their tubular structures in all lipid bilayers, with [(Cys-Gly-Met-Gly)2] showing increased stability over an extended period in these lipid membranes. The insertion of CPNTs shows negligible impact on lipid bilayer properties, including area per lipid, volume per lipid, and bilayer thickness. The study demonstrates that the CPNT preserves its two-line water movement pattern within all the lipid membranes, reaffirming their potential as water channels. The MSD curves further reveal that the dynamics of water molecules inside the nanotube are similar for all the bilayer systems with minor differences that arise due to different lipid environments.
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Affiliation(s)
- Rimjhim Moral
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
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2
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Estejab A, García Cárcamo RA, Getman RB. Influence of an electrified interface on the entropy and energy of solvation of methanol oxidation intermediates on platinum(111) under explicit solvation. Phys Chem Chem Phys 2022; 24:4251-4261. [PMID: 35107094 DOI: 10.1039/d1cp05358b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Liquid water and electric fields play significant roles in phenomena occurring at catalytic and electrocatalytic interfaces; however, how their interplay influences interfacial energetics remains uncertain. Electric fields control the orientations of water molecules, which we hypothesized would influence the solvation thermodynamics of surface species. To explore this hypothesis, we used multiscale simulations involving density functional theory and classical molecular dynamics. We computed the energies and entropies of solvation of surface species on Pt(111), specifically, adsorbed CH3OH, COH, and CO, which are intermediates in the pathway of methanol oxidation, in the presence of electric fields spanning -0.5 to +0.5 V Å-1. We found that both the energy and entropy of solvation depend on the strength and direction of the field, with the entropy of solvation being significantly impacted. Both the energy and entropy dependence on the field can be ascribed to water molecule orientations. Specifically, more positive fields orient water molecules so that they can more effectively hydrogen bond with surface species, which strengthens the energies of solvation. However, at more negative fields, competition with the surface species causes interfacial water molecules to reorient, which leads to disorder in the water structure and hence increased entropy.
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Affiliation(s)
- Ali Estejab
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC 29634-0909, USA.
| | - Ricardo A García Cárcamo
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC 29634-0909, USA.
| | - Rachel B Getman
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC 29634-0909, USA.
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3
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Paul R, Mitra A, Paul S. A computational approach on the stereoselective binding of peptides from aqueous medium with endo-functionalized molecular tubes. Phys Chem Chem Phys 2021; 23:22703-22717. [PMID: 34605508 DOI: 10.1039/d1cp02288a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The need to obtain enantiomerically pure isomers of amino acids and peptides is often realized in the field of biology and in the pharmaceutical industry. Research is underway to devise simple methods for the chiral resolution of amino acids from their racemic mixtures. Inspired by this objective, in our present work, we have computationally shown the possibility of chiral separation of the enantiomeric pairs of two model peptides, namely, (D,L)-aspargine and (D,L)-phenylalanine, in the presence of water. For this purpose, we have used two synthetic supramolecular receptors named host-1a and host-1b, respectively. Molecular dynamics simulations and quantum chemical methods are employed to analyze the structural features and the energy aspects involved in the separation process. The information obtained at the molecular level helps us gain better insights into the key interactions that operate to produce such enantioselectivity. We have also investigated the dynamics and changes in the water structure in the vicinity of the host molecules, both in the presence and absence of the model peptides. The D- and L-isomers of the same peptide undergo complexation with a particular host molecule registering a difference of more than 1.5 kcal mol-1 (obtained from PMF and MM-PBSA analyses) in their respective energies. This indicates that the chiral separation of the peptides with the help of these endo-fuctionalized molecular tube receptors may be energetically feasible. The connection between the peptide stereochemistry and its interaction with the endo-functionalized hosts would be instrumental in designing novel segregation techniques that can be further extended to separate larger model peptides or proteins.
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Affiliation(s)
- Rabindranath Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India.
| | - Aritra Mitra
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India.
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India.
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Shiraga K, Urabe M, Matsui T, Kikuchi S, Ogawa Y. Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor. Phys Chem Chem Phys 2020; 22:19468-19479. [PMID: 32761010 DOI: 10.1039/d0cp02265a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The biological functions of proteins depend on harmonization with hydration water surrounding them. Indeed, the dynamical transition of proteins, such as thermal denaturation, is dependent on the changes in the mobility of hydration water. However, the role of hydration water during dynamical transition is yet to be fully understood due to technical limitations in precisely characterizing the amount of hydration water. A state-of-the-art CMOS dielectric sensor consisting of 65 GHz LC resonators addressed this issue by utilizing the feature that oscillation frequency sensitively shifts in response to the complex dielectric constant at 65 GHz with extremely high precision. This study aimed to establish an analytical algorithm to derive the hydration number from the measured frequency shift and to demonstrate the transition of hydration number upon the thermal denaturation of human serum albumin. The determined hydration number in the native state drew a "global" hydration picture beyond the first solvation shell, with substantially reduced uncertainty of the hydration number (about ±1%). This allowed the detection of a rapid increase in the hydration number at about 55 °C during the heating process, which was in excellent phase with the irreversible rupture of the α-helical structure into solvent-exposed extended chains, whereas the hydration number did not trace the forward path in the subsequent cooling process. Our result indicates that the weakening of water hydrogen bonds trigger the unfolding of the protein structure first, followed by the changes in the number of hydration water as a consequence of thermal denaturation.
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Affiliation(s)
- Keiichiro Shiraga
- RIKEN Center for Integrative Medical Sciences (IMS), Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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Pal S, Roy R, Paul S. Potential of a Natural Deep Eutectic Solvent, Glyceline, in the Thermal Stability of the Trp-Cage Mini-protein. J Phys Chem B 2020; 124:7598-7610. [DOI: 10.1021/acs.jpcb.0c03501] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Rituparna Roy
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
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Szekely O, Olsen GL, Novakovic M, Rosenzweig R, Frydman L. Assessing Site-Specific Enhancements Imparted by Hyperpolarized Water in Folded and Unfolded Proteins by 2D HMQC NMR. J Am Chem Soc 2020; 142:9267-9284. [PMID: 32338002 PMCID: PMC7304870 DOI: 10.1021/jacs.0c00807] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Hyperpolarized water
can be a valuable aid in protein NMR, leading
to amide group 1H polarizations that are orders of magnitude
larger than their thermal counterparts. Suitable procedures can exploit
this to deliver 2D 1H–15N correlations
with good resolution and enhanced sensitivity. These enhancements
depend on the exchange rates between the amides and the water, thereby
yielding diagnostic information about solvent accessibility. This
study applied this “HyperW” method to four proteins
exhibiting a gamut of exchange behaviors: PhoA(350–471), an unfolded 122-residue fragment; barstar, a fully folded ribonuclease
inhibitor; R17, a 13.3 kDa system possessing folded and unfolded forms
under slow interconversion; and drkN SH3, a protein domain whose folded
and unfolded forms interchange rapidly and with temperature-dependent
population ratios. For PhoA4(350–471) HyperW sensitivity
enhancements were ≥300×, as expected for an unfolded protein
sequence. Though fully folded, barstar also exhibited substantial
enhancements; these, however, were not uniform and, according to CLEANEX
experiments, reflected the solvent-exposed residues. R17 showed the
expected superposition of ≥100-fold enhancements for its unfolded
form, coexisting with more modest enhancements for their folded counterparts.
Unexpected, however, was the behavior of drkN SH3, for which HyperW
enhanced the unfolded but, surprisingly, enhanced even more certain folded protein sites. These preferential enhancements were
repeatedly and reproducibly observed. A number of explanations—including
three-site exchange magnetization transfers between water and the
unfolded and folded states; cross-correlated relaxation processes
from hyperpolarized “structural” waters and labile side-chain
protons; and the possibility that faster solvent exchange rates characterize
certain folded sites over their unfolded counterparts—are considered
to account for them.
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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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Zhang X, DeFever RS, Sarupria S, Getman RB. Free Energies of Catalytic Species Adsorbed to Pt(111) Surfaces under Liquid Solvent Calculated Using Classical and Quantum Approaches. J Chem Inf Model 2019; 59:2190-2198. [PMID: 30821458 DOI: 10.1021/acs.jcim.9b00089] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solvent plays an important role in liquid phase heterogeneous catalysis; however, methods for calculating the free energies of catalytic phenomena at the solid-liquid interface are not well-established. For example, solvent molecules alter the energies of catalytic species and participate in catalytic reactions and can thus significantly influence catalytic performance. In this work, we begin to establish methods for calculating the free energies of such phenomena, specifically, by employing an explicit solvation method using a multiscale sampling (MSS) approach. This MSS approach combines classical molecular dynamics with density functional theory. We use it to calculate the free energies of solvation of catalytic species, specifically adsorbed NH*, NH2*, CO*, COH*, CH2OH*, and C3H7O3* on Pt(111) surfaces under aqueous phase and under a mixed H2O/CH3OH solvent. We compare our calculated values with analogous values from implicit solvation for validation and to identify situations where implicit solvation is sufficient versus where explicit solvent is needed to compute adsorbate free energies. Our results indicate that explicit quantum-based methods are needed when adsorbates form chemical bonds and/or strong hydrogen bonds with H2O solvent. Using MSS, we further separate the calculated free energies into energetic and entropic contributions in order to understand how each influences the free energy. We find that adsorbates that exhibit strong energies also exhibit strong and negative entropies, and we attribute this relationship to hydrogen bonding between the adsorbates and the solvent molecules, which provides a large energetic contribution but reduces the overall mobility of the solvent.
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Affiliation(s)
- Xiaohong Zhang
- Department of Chemical and Biomolecular Engineering , Clemson University , Clemson , South Carolina 29634-0909 , United States
| | - Ryan S DeFever
- Department of Chemical and Biomolecular Engineering , Clemson University , Clemson , South Carolina 29634-0909 , United States
| | - Sapna Sarupria
- Department of Chemical and Biomolecular Engineering , Clemson University , Clemson , South Carolina 29634-0909 , United States
| | - Rachel B Getman
- Department of Chemical and Biomolecular Engineering , Clemson University , Clemson , South Carolina 29634-0909 , United States
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9
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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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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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11
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On the water structure at hydrophobic interfaces and the roles of water on transition-metal catalyzed reactions: A short review. Catal Today 2017. [DOI: 10.1016/j.cattod.2017.02.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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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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On the ability of molecular dynamics simulation and continuum electrostatics to treat interfacial water molecules in protein-protein complexes. Sci Rep 2016; 6:38259. [PMID: 27905545 PMCID: PMC5131287 DOI: 10.1038/srep38259] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 10/28/2016] [Indexed: 01/23/2023] Open
Abstract
Interfacial waters are increasingly appreciated as playing a key role in protein-protein interactions. We report on a study of the prediction of interfacial water positions by both Molecular Dynamics and explicit solvent-continuum electrostatics based on the Dipolar Poisson-Boltzmann Langevin (DPBL) model, for three test cases: (i) the barnase/barstar complex (ii) the complex between the DNase domain of colicin E2 and its cognate Im2 immunity protein and (iii) the highly unusual anti-freeze protein Maxi which contains a large number of waters in its interior. We characterize the waters at the interface and in the core of the Maxi protein by the statistics of correctly predicted positions with respect to crystallographic water positions in the PDB files as well as the dynamic measures of diffusion constants and position lifetimes. Our approach provides a methodology for the evaluation of predicted interfacial water positions through an investigation of water-mediated inter-chain contacts. While our results show satisfactory behaviour for molecular dynamics simulation, they also highlight the need for improvement of continuum methods.
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Chakraborty K, Bandyopadhyay S. Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules. J Chem Phys 2015; 143:045106. [DOI: 10.1063/1.4927568] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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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