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Chatterjee H, Mahapatra AJ, Zacharias M, Sengupta N. Helical reorganization in the context of membrane protein folding: Insights from simulations with bacteriorhodopsin (BR) fragments. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184333. [PMID: 38740122 DOI: 10.1016/j.bbamem.2024.184333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/20/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
Membrane protein folding is distinct from folding of soluble proteins. Conformational acquisition in major membrane protein subclasses can be delineated into insertion and folding processes. An exception to the "two stage" folding, later developed to "three stage" folding, is observed within the last two helices in bacteriorhodopsin (BR), a system that serves as a model membrane protein. We employ a reductionist approach to understand interplay of molecular factors underlying the apparent defiance. Leveraging available solution NMR structures, we construct, sample in silico, and analyze partially (PIn) and fully inserted (FIn) BR membrane states. The membrane lateral C-terminal helix (CH) in PIn is markedly prone to transient structural distortions over microsecond timescales; a disorder prone region (DPR) is thereby identified. While clear transmembrane propensities are not acquired, the distortions induce alterations in local membrane curvature and area per lipid. Importantly, energetic decompositions reveal that overall, the N-terminal helix (NH) is thermodynamically more stable in the PIn. Higher overall stability of the FIn arises from favorable interactions between the NH and the CH. Our results establish lack of spontaneous transition of the PIn to the FIn, and attributes their partitioning to barriers that exceed those accessible with thermal fluctuations. This work paves the way for further detailed studies aimed at determining the thermo-kinetic roles of the initial five helices, or complementary external factors, in complete helical folding and insertion in BR. We comment that complementing such efforts with the growing field of machine learning assisted energy landscape searches may offer unprecedented insights.
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Affiliation(s)
- Hindol Chatterjee
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Anshuman J Mahapatra
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Martin Zacharias
- Center for Functional Protein Assemblies, TUM School of Natural Sciences Technical University Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany.
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India.
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2
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Zhao R, Lu S, Li S, Shen H, Wang Y, Gao Y, Shen X, Wang F, Wu J, Liu W, Chen K, Yao X, Li J. Enzymatic Preparation and Processing Properties of DPP-IV Inhibitory Peptides Derived from Wheat Gluten: Effects of Pretreatment Methods and Protease Types. Foods 2024; 13:216. [PMID: 38254517 PMCID: PMC10814021 DOI: 10.3390/foods13020216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/25/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
The choice of appropriate proteases and pretreatment methods significantly influences the preparation of bioactive peptides. This study aimed to investigate the effects of different pretreatment methods on the hydrolytic performance of diverse proteases during the production of dipeptidyl peptidase-IV (DPP-IV) inhibitory peptides derived from wheat and their foaming and emulsion properties. Dry heating, aqueous heating, and ultrasound treatment were employed as pretreatments for the protein prior to the enzymatic hydrolysis of wheat gluten. FTIR analysis results indicated that all pretreatment methods altered the secondary structure of the protein; however, the effects of dry heating treatment on the secondary structure content were opposite to those of aqueous heating and ultrasound treatment. Nevertheless, all three methods enhanced the protein solubility and surface hydrophobicity. By using pretreated proteins as substrates, five different types of proteases were employed for DPP-IV inhibitory peptide production. The analysis of the DPP-IV inhibitory activity, degree of hydrolysis, and TCA-soluble peptide content revealed that the specific pretreatments had a promoting or inhibiting effect on DPP-IV inhibitory peptide production depending on the protease used. Furthermore, the pretreatment method and the selected type of protease collectively influenced the foaming and emulsifying properties of the prepared peptides.
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Affiliation(s)
- Rui Zhao
- Key Laboratory of Green and Low-Carbon Processing Technology for Plant-Based Food of China National Light Industry Council, Beijing Technology and Business University, No. 33 Fucheng Road, Beijing 100048, China;
- Food Processing Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (S.L.); (H.S.); (Y.W.); (Y.G.); (X.S.); (F.W.); (J.W.); (K.C.)
- Beijing Huiyuan Food & Beverage Co., Ltd., Beijing 101305, China; (S.L.); (W.L.)
- Heilongjiang Province Key Laboratory of Food Processing, Harbin 150086, China
- Heilongjiang Province Engineering Research Center of Whole Grain Nutritious Food, Harbin 150086, China
| | - Shuwen Lu
- Food Processing Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (S.L.); (H.S.); (Y.W.); (Y.G.); (X.S.); (F.W.); (J.W.); (K.C.)
- Heilongjiang Province Key Laboratory of Food Processing, Harbin 150086, China
- Heilongjiang Province Engineering Research Center of Whole Grain Nutritious Food, Harbin 150086, China
| | - Shaozhen Li
- Beijing Huiyuan Food & Beverage Co., Ltd., Beijing 101305, China; (S.L.); (W.L.)
| | - Huifang Shen
- Food Processing Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (S.L.); (H.S.); (Y.W.); (Y.G.); (X.S.); (F.W.); (J.W.); (K.C.)
- Heilongjiang Province Key Laboratory of Food Processing, Harbin 150086, China
- Heilongjiang Province Engineering Research Center of Whole Grain Nutritious Food, Harbin 150086, China
| | - Yao Wang
- Food Processing Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (S.L.); (H.S.); (Y.W.); (Y.G.); (X.S.); (F.W.); (J.W.); (K.C.)
- Heilongjiang Province Key Laboratory of Food Processing, Harbin 150086, China
- Heilongjiang Province Engineering Research Center of Whole Grain Nutritious Food, Harbin 150086, China
| | - Yang Gao
- Food Processing Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (S.L.); (H.S.); (Y.W.); (Y.G.); (X.S.); (F.W.); (J.W.); (K.C.)
- Heilongjiang Province Key Laboratory of Food Processing, Harbin 150086, China
- Heilongjiang Province Engineering Research Center of Whole Grain Nutritious Food, Harbin 150086, China
| | - Xinting Shen
- Food Processing Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (S.L.); (H.S.); (Y.W.); (Y.G.); (X.S.); (F.W.); (J.W.); (K.C.)
- Heilongjiang Province Key Laboratory of Food Processing, Harbin 150086, China
- Heilongjiang Province Engineering Research Center of Whole Grain Nutritious Food, Harbin 150086, China
| | - Fei Wang
- Food Processing Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (S.L.); (H.S.); (Y.W.); (Y.G.); (X.S.); (F.W.); (J.W.); (K.C.)
- Heilongjiang Province Key Laboratory of Food Processing, Harbin 150086, China
- Heilongjiang Province Engineering Research Center of Whole Grain Nutritious Food, Harbin 150086, China
| | - Jiawu Wu
- Food Processing Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (S.L.); (H.S.); (Y.W.); (Y.G.); (X.S.); (F.W.); (J.W.); (K.C.)
- Heilongjiang Province Key Laboratory of Food Processing, Harbin 150086, China
- Heilongjiang Province Engineering Research Center of Whole Grain Nutritious Food, Harbin 150086, China
| | - Wenhui Liu
- Beijing Huiyuan Food & Beverage Co., Ltd., Beijing 101305, China; (S.L.); (W.L.)
| | - Kaixin Chen
- Food Processing Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (S.L.); (H.S.); (Y.W.); (Y.G.); (X.S.); (F.W.); (J.W.); (K.C.)
- Heilongjiang Province Key Laboratory of Food Processing, Harbin 150086, China
- Heilongjiang Province Engineering Research Center of Whole Grain Nutritious Food, Harbin 150086, China
| | - Xinmiao Yao
- Food Processing Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (S.L.); (H.S.); (Y.W.); (Y.G.); (X.S.); (F.W.); (J.W.); (K.C.)
- Heilongjiang Province Key Laboratory of Food Processing, Harbin 150086, China
- Heilongjiang Province Engineering Research Center of Whole Grain Nutritious Food, Harbin 150086, China
| | - Jian Li
- Key Laboratory of Green and Low-Carbon Processing Technology for Plant-Based Food of China National Light Industry Council, Beijing Technology and Business University, No. 33 Fucheng Road, Beijing 100048, China;
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Sahu S, Ghosh S, Sinha SK, Datta S, Sengupta N. Thermal Sensitivity of the Enzymatic Activity of β-Glucosidase: Simulations Lend Mechanistic Insights into Experimental Observations. Biochemistry 2023; 62:3440-3452. [PMID: 37997958 DOI: 10.1021/acs.biochem.3c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
A crucial prerequisite for industrial applications of enzymes is the maintenance of specific activity across wide thermal ranges. β-Glucosidase (EC 3.2.1.21) is an essential enzyme for converting cellulose in biomass to glucose. While the reaction mechanisms of β-glucosidases from various thermal ranges (hyperthermophilic, thermophilic, and mesophilic) are similar, the factors underlying their thermal sensitivity remain obscure. The work presented here aims to unravel the molecular mechanisms underlying the thermal sensitivity of the enzymatic activity of the β-glucosidase BglB from the bacterium Paenibacillus polymyxa. Experiments reveal a maximum enzymatic activity at 315 K, with a marked decrease in the activity below and above this temperature. Employing in silico simulations, we identified the crucial role of the active site tunnel residues in the thermal sensitivity. Specific tunnel residues were identified via energetic decomposition and protein-substrate hydrogen bond analyses. The experimentally observed trends in specific activity with temperature coincide with variations in overall binding free energy changes, showcasing a predominantly electrostatic effect that is consistent with enhanced catalytic pocket-substrate hydrogen bonding (HB) at Topt. The entropic advantage owing to the HB substate reorganization was found to facilitate better substrate binding at 315 K. This study elicits molecular-level insights into the associative mechanisms between thermally enabled fluctuations and enzymatic activity. Crucial differences emerge between molecular mechanisms involving the actual substrate (cellobiose) and a commonly employed chemical analogue. We posit that leveraging the role of fluctuations may reveal unexpected insights into enzyme behavior and offer novel paradigms for enzyme engineering.
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Affiliation(s)
- Sneha Sahu
- Protein Engineering Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Sayani Ghosh
- Protein Engineering Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Sushant K Sinha
- Protein Engineering Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Supratim Datta
- Protein Engineering Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
- Center for the Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
- Center for the Climate and Environmental Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
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Ma Z, Mu K, Zhu J, Xiao M, Wang L, Jiang X. Molecular dynamics simulations identify the topological weak spots of a protease CN2S8A. J Mol Graph Model 2023; 124:108571. [PMID: 37487372 DOI: 10.1016/j.jmgm.2023.108571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/06/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023]
Abstract
Thermophilic enzymes are highly desired in industrial applications due to their efficient catalytic activity at high temperature. However, most enzymes exhibit inferior thermostability and it remains challenging to identify the optimal sites for designing mutations to improve protein stability. To tackle this issue, we integrated topological analysis and all-atom molecular dynamics simulations to efficiently pinpoint the thermally-unstable regions in protein structures. Using a protease CN2S8A as the model, we analyzed the intramolecular hydrogen bonding interactions between adjacent secondary structure elements, and then identified the topological weak spots of CN2S8A where weak hydrogen bonding interactions were formed. To examine the role of these sites in protein structural stability, we designed three virtual mutations at different weak spots and characterized the effects of these mutations on the structural properties of CN2S8A. The results showed that all three mutations increased the protein structural stability. In conclusion, these findings provide a novel method to identify the topological weak spots of proteins, with implications in the rational design of biocatalysts with superior thermostability.
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Affiliation(s)
- Zhenyu Ma
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Kaijie Mu
- Biomedicine Discovery Institute, Monash University, Melbourne, 3500, Australia
| | - Jingyi Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Min Xiao
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China.
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5
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Puglisi R, Karunanithy G, Hansen DF, Pastore A, Temussi PA. The anatomy of unfolding of Yfh1 is revealed by site-specific fold stability analysis measured by 2D NMR spectroscopy. Commun Chem 2021; 4:127. [PMID: 35243007 PMCID: PMC7612453 DOI: 10.1038/s42004-021-00566-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Most techniques allow detection of protein unfolding either by following the behaviour of single reporters or as an averaged all-or-none process. We recently added 2D NMR spectroscopy to the well-established techniques able to obtain information on the process of unfolding using resonances of residues in the hydrophobic core of a protein. Here, we questioned whether an analysis of the individual stability curves from each resonance could provide additional site-specific information. We used the Yfh1 protein that has the unique feature to undergo both cold and heat denaturation at temperatures above water freezing at low ionic strength. We show that stability curves inconsistent with the average NMR curve from hydrophobic core residues mainly comprise exposed outliers that do nevertheless provide precious information. By monitoring both cold and heat denaturation of individual residues we gain knowledge on the process of cold denaturation and convincingly demonstrate that the two unfolding processes are intrinsically different.
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Affiliation(s)
- Rita Puglisi
- grid.511435.7UK-DRI at King’s College London, The Wohl Institute, London, UK
| | - Gogulan Karunanithy
- grid.83440.3b0000000121901201Department of Structural Biology, Division of Biosciences, University College London, London, UK
| | - D. Flemming Hansen
- grid.83440.3b0000000121901201Department of Structural Biology, Division of Biosciences, University College London, London, UK
| | - Annalisa Pastore
- grid.511435.7UK-DRI at King’s College London, The Wohl Institute, London, UK ,grid.5398.70000 0004 0641 6373European Synchrotron Radiation Facility, Grenoble, France
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6
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Roy P, Sengupta N. Hydration of a small protein under carbon nanotube confinement: Adsorbed substates induce selective separation of the dynamical response. J Chem Phys 2021; 154:204702. [PMID: 34241160 DOI: 10.1063/5.0047078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The co-involvement of biological molecules and nanomaterials has increasingly come to the fore in modern-day applications. While the "bio-nano" (BN) interface presents physico-chemical characteristics that are manifestly different from those observed in isotropic bulk conditions, the underlying molecular reasons remain little understood; this is especially true of anomalies in interfacial hydration. In this paper, we leverage atomistic simulations to study differential adsorption characteristics of a small protein on the inner (concave) surface of a single-walled carbon nanotube whose diameter exceeds dimensions conducive to single-file water movement. Our findings indicate that the extent of adsorption is decided by the degree of foldedness of the protein conformational substate. Importantly, we find that partially folded substates, but not the natively folded one, induce reorganization of the protein hydration layer into an inner layer water closer to the nanotube axis and an outer layer water in the interstitial space near the nanotube walls. Further analyses reveal sharp dynamical differences between water molecules in the two layers as observed in the onset of increased heterogeneity in rotational relaxation and the enhanced deviation from Fickian behavior. The vibrational density of states reveals that the dynamical distinctions are correlated with differences in crucial bands in the power spectra. The current results set the stage for further systematic studies of various BN interfaces vis-à-vis control of hydration properties.
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Affiliation(s)
- Priti Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
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7
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Chatterjee P, Le T, Bui HTD, Cho MK, Ham S. Atomic Level Investigations of Early Aggregation of Tau43 in Water I. Conformational Propensity of Monomeric Tau43. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Prathit Chatterjee
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
| | - Thi‐Diem Le
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
| | - Huong T. D. Bui
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
| | - Myung Keun Cho
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
- Department of Chemistry College of Natural Sciences, Seoul National University, Gwanak‐ro 1, Gwanak‐ku Seoul 08826 Korea
| | - Sihyun Ham
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
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Naidu KT, Rao DK, Prabhu NP. Cryo vs Thermo: Duality of Ethylene Glycol on the Stability of Proteins. J Phys Chem B 2020; 124:10077-10088. [PMID: 33143422 DOI: 10.1021/acs.jpcb.0c06247] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Osmolytes are known to stabilize proteins under stress conditions. Thermal denaturation studies on globular proteins (β-lactoglobulin, cytochrome c, myoglobin, α-chymotrypsin) in the presence of ethylene glycol (EG), a polyol class of osmolyte, demonstrate a unique property of EG. EG stabilizes proteins against cold denaturation and destabilizes them during heat-induced denaturation. Further, chemical denaturation experiments performed at room temperature and at a sub-zero temperature (-10 °C) show that EG stabilizes the proteins at subzero temperature but destabilizes them at room temperature. The experiments carried out in the presence of glycerol, however, showed that glycerol stabilizes proteins against all of the denaturing conditions. This differential effect has not been reported for any other polyol class of osmolyte and might be specific to EG. Moreover, molecular dynamics simulations of all of the four proteins were carried out at three different temperatures, 240, 300, and 340 K, in the absence and presence of EG (20 and 40%). The results suggest that EG preferably accumulates around the hydrophobic residues and reduces the hydrophobic hydration of the proteins at a low temperature leading to stabilization of the proteins. At 340 K, the preferential hydration of the proteins is significantly reduced and the preferential binding of EG destabilizes the proteins like common denaturants.
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Affiliation(s)
- K Tejaswi Naidu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - D Krishna Rao
- Tata Institute of Fundamental Research (TIFR) Centre for Interdisciplinary Sciences, Hyderabad 500107, India
| | - N Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
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Roy P, Roy S, Sengupta N. Disulfide Reduction Allosterically Destabilizes the β-Ladder Subdomain Assembly within the NS1 Dimer of ZIKV. Biophys J 2020; 119:1525-1537. [PMID: 32946768 DOI: 10.1016/j.bpj.2020.08.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/13/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
The Zika virus (ZIKV) was responsible for a recent debilitating epidemic that till date has no cure. A potential way to reduce ZIKV virulence is to limit the action of the nonstructural proteins involved in its viral replication. One such protein, NS1, encoded as a monomer by the viral genome, plays a major role via symmetric oligomerization. We examine the homodimeric structure of the dominant β-ladder segment of NS1 with extensive all atom molecular dynamics. We find it stably bounded by two spatially separated interaction clusters (C1 and C2) with significant differences in the nature of their interactions. Four pairs of distal, intramonomeric disulfide bonds are found to be coupled to the stability, local structure, and wettability of the interfacial region. Symmetric reduction of the intramonomeric disulfides triggers marked dynamical heterogeneity, interfacial wettability, and asymmetric salt-bridging propensity. Harnessing the model-free Lipari-Szabo based formalism for estimation of conformational entropy (Sconf), we find clear signatures of heterogeneity in the monomeric conformational entropies. The observed asymmetry, very small in the unperturbed state, expands significantly in the reduced states. This allosteric effect is most noticeable in the electrostatically bound C2 cluster that underlies the greatest stability in the unperturbed state. Allosteric induction of conformational and thermodynamic asymmetry is expected to affect the pathways leading to symmetric higher-ordered oligomerization, and thereby affect crucial replication pathways.
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Affiliation(s)
- Priti Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Subhajit Roy
- Centre for Excellence in Basic Sciences (CBS), University of Mumbai, Vidyanagari, Mumbai, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India.
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10
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Soeratri W, Hidayah R, Rosita N. Effect of Combination Soy Bean Oil and Oleic Acid to Characteristic, Penetration, Physical Stability of Nanostructure Lipid Carrier Resveratrol. FOLIA MEDICA INDONESIANA 2019. [DOI: 10.20473/fmi.v55i3.15505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Resveratrol is an antioxidant that can be used as anti-aging. Topical use has several problems because solubility in water is low and unstable to light. This study aimed to evaluate the effect of the combination of soy bean oil and oleic acid liquid lipids on the characteristics, penetration, and stability of resveratrol nanostructured lipid carriers (NLC). Nanostructured lipid carriers (NLC) were made with high shear homogeneous technique. To determine the characterization of NLC, diffraction scanning calorimetry, X-ray diffraction, and Fourier transforms infrared spectrophotometry were used. Examination of the morphological form was carried out with a transmission electron microscope. The particle size and polydispersity index examination were measured by the Delsa Nano™ particle size analyzer, while the efficiency of trapping resveratrol in the NLC system was measured by the dialysis membrane method. Furthermore, the penetration depth test on the skin of mice was done by fluorescence microscope method using rhodamine B markers. Physical stability test was performed by examination of particle size and index polydispersity for 30 days. The formula with liquid soy bean oil and oleic acid liquid lipids improved the characteristics including the effectiveness of entrapment and colloidal stability. However, the formula with soy bean oil and oleic acid combination liquid lipids did not provide better penetration into the skin than the use of single liquid lipids. While the formula with soy bean oil and oleic acid liquid lipids proved to improve the physical stability for 30 days.
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11
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Menon S, Sengupta N. The Cold Thermal Response of an Amyloid Oligomer Differs from Typical Globular Protein Cold Denaturation. J Phys Chem Lett 2019; 10:2453-2457. [PMID: 31002516 DOI: 10.1021/acs.jpclett.9b00709] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In contrast with the general behavior of folded proteins, the cold thermal response of amyloid assemblies is difficult to elicit with simple models. We exploit exhaustive simulations to evaluate the thermal response of a barrel-shaped model amyloid oligomer, with a distinct hydrophobic core akin to that of folded proteins. Cumulative thermal data over the range of 210-483 K indicate a sharp inflection and rise in structural stability as the temperature is decreased below the melting temperature of the water model. This is not commensurate with the equilibrium free energy profile obtained with core packing as the order parameter. However, energetic analyses and the size of their fluctuations indicate the crucial role of hydration in mediating structural transitions, beyond the expected temperature-dependent hydrophobic effect. Structural ordering of the hydration layer over bulk water is maximized at the transition and vanishes at high temperatures. This is a first direct demonstration of the microscopic influence of hydration water on the low-temperature response of an amyloid assembly close to the cryo-regime.
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Affiliation(s)
- Sneha Menon
- Physical Chemistry Division , CSIR-National Chemical Laboratory , Pune 411008 , India
- Academy of Scientific and Innovative Research (AcSIR) , Ghaziabad 201002 , India
| | - Neelanjana Sengupta
- Department of Biological Sciences , Indian Institute of Science Education and Research Kolkata , Mohanpur 741246 , India
- Centre for Advanced Functional Materials (CAFM) , Indian Institute of Science Education and Research Kolkata , Mohanpur 741246 , India
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12
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Roy P, Ghosh B, Chatterjee P, Sengupta N. Cosolvent Impurities in SWCNT Nanochannel Confinement: Length Dependence of Water Dynamics Investigated with Atomistic Simulations. J Chem Inf Model 2019; 59:2026-2034. [PMID: 30908024 DOI: 10.1021/acs.jcim.8b00889] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The advent of nanotechnology has seen a growing interest in the nature of fluid flow and transport under nanoconfinement. The present study leverages fully atomistic molecular dynamics (MD) simulations to study the effect of nanochannel length and intrusion of molecules of the organic solvent, hexafluoro-2-propanol (HFIP), on the dynamical characteristics of water within it. Favorable interactions of HFIP with the nanochannels comprised of single-walled carbon nanotubes traps them over time scales greater than 100 ns, and confinement confers small but distinguishable spatial redistribution between neighboring HFIP pairs. Water molecules within the nanochannels show clear signatures of dynamical slowdown relative to bulk water even for pure systems. The presence of HFIP causes further rotational and translational slowdown in waters when the nanochannel dimension falls below a critical length of 30 Å. The enhanced slowdown in the presence of HFIP is quantified from characteristic relaxation parameters and diffusion coefficients in the absence and presence of HFIP. It is finally seen that the net flow of water between the ends of the nanochannel shows a decreasing dependence with nanochannel length only when the number of HFIP molecules is small. These results lend insights into devising ways of modulating solvent properties within nanochannels with cosolvent impurities.
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Affiliation(s)
- Priti Roy
- Department of Biological Sciences , Indian Institute of Science Education and Research Kolkata , Mohanpur 741 246 , India
| | - Brataraj Ghosh
- Department of Biological Sciences , Indian Institute of Science Education and Research Kolkata , Mohanpur 741 246 , India
| | - Prathit Chatterjee
- Advanced Polymer Lab in association with Polymer Research Centre , IISER Kolkata, ADO ADDITIVES MFG PVT. LTD. , 201/A, Nadibhag 2nd Lane , Madhyamgram, Kolkata 700 128 , India
| | - Neelanjana Sengupta
- Department of Biological Sciences , Indian Institute of Science Education and Research Kolkata , Mohanpur 741 246 , India.,Centre for Advanced Functional Materials (CAFM) , Indian Institute of Science Education and Research Kolkata , Mohanpur 741 246 , India
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13
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Custer GS, Xu H, Matysiak S, Das P. How Hydrophobic Hydration Destabilizes Surfactant Micelles at Low Temperature: A Coarse-Grained Simulation Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:12590-12599. [PMID: 30247911 DOI: 10.1021/acs.langmuir.8b01994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Micelles are self-assembled aggregates of amphiphilic surfactant molecules that are important in a variety of applications, including drug delivery, detergency, and catalysis. It is known that the micellization process is driven by the same physiochemical forces that drive protein folding, aggregation, and biological membrane self-assembly. Nevertheless, the molecular details of how micelle stability changes in water at low temperature are not fully clear. We develop and use a coarse-grained model to investigate how the interplay between nonionic surfactants and the surrounding water at the nanoscale affects the stability of micelles at high and low temperatures. Simulations of preformed C12E5 micelles in explicit water at a range of temperatures reveal the existence of two distinct surfactant conformations within the micelle, a bent structure and an extended structure, the latter being more prevalent at low temperature. Favorable interactions of the surfactant with more ordered solvation water stabilizes the extended configuration, allowing nanoscale wetting of the dry, hydrophobic core of the micelle, leading to the micelle breaking. Taken together, our coarse-grained simulations unravel how energetic and structural changes of the surfactant and the surrounding water destabilize micelles at low temperature, which is a direct consequence of the weakened hydrophobicity. Our approach thus provides an effective mean for extracting the molecular-level changes during hydrophobicity-driven destabilization of molecular self-assembly, which is important in a wide range of fields, including biology, polymer science, and nanotechnology.
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Affiliation(s)
| | | | | | - Payel Das
- IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598 , United States
- Department of Applied Physics and Applied Mathematics , Columbia University , New York 10027 , United States
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14
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15
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Sočan J, Kazemi M, Isaksen GV, Brandsdal BO, Åqvist J. Catalytic Adaptation of Psychrophilic Elastase. Biochemistry 2018; 57:2984-2993. [PMID: 29726678 DOI: 10.1021/acs.biochem.8b00078] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The class I pancreatic elastase from Atlantic salmon is considered to be a cold-adapted enzyme in view of the cold habitat, the reduced thermostability of the enzyme, and the fact that it is faster than its mesophilic porcine counterpart at room temperature. However, no experimental characterization of its catalytic properties at lower temperatures has actually been reported. Here we use extensive computer simulations of its catalytic reaction, at different temperatures and with different peptide substrates, to compare its characteristics with those of porcine pancreatic elastase, with which it shares 67% sequence identity. We find that both enzymes have a preference for smaller aliphatic residues at the P1 position, while the reaction rate with phenylalanine at P1 is predicted to be substantially lower. With the former class of substrates, the calculated reaction rates for salmon enzyme are consistently higher than those of the porcine ortholog at all temperatures examined, and the difference is most pronounced at the lowest temperature. As observed for other cold-adapted enzymes, this is caused by redistribution of the activation free energy in terms of enthalpy and entropy and can be linked to differences in the mobility of surface-exposed loops in the two enzymes. Such mobility changes are found to be reflected by characteristic sequence conservation patterns in psychrophilic and mesophilic species. Hence, calculations of mutations in a single surface loop show that the temperature dependence of the catalytic reaction is altered in a predictable way.
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Affiliation(s)
- Jaka Sočan
- Department of Cell and Molecular Biology , Uppsala University, Biomedical Center , Box 596 , SE-751 24 Uppsala , Sweden
| | - Masoud Kazemi
- Department of Cell and Molecular Biology , Uppsala University, Biomedical Center , Box 596 , SE-751 24 Uppsala , Sweden
| | - Geir Villy Isaksen
- Department of Cell and Molecular Biology , Uppsala University, Biomedical Center , Box 596 , SE-751 24 Uppsala , Sweden.,Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry , University of Tromsø , N9037 Tromsø , Norway
| | - Bjørn Olav Brandsdal
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry , University of Tromsø , N9037 Tromsø , Norway
| | - Johan Åqvist
- Department of Cell and Molecular Biology , Uppsala University, Biomedical Center , Box 596 , SE-751 24 Uppsala , Sweden
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16
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Jiang X, Li W, Chen G, Wang L. Dynamic Perturbation of the Active Site Determines Reversible Thermal Inactivation in Glycoside Hydrolase Family 12. J Chem Inf Model 2017; 57:288-297. [DOI: 10.1021/acs.jcim.6b00692] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xukai Jiang
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
| | - Wen Li
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
| | - Guanjun Chen
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
| | - Lushan Wang
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
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17
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Chatterjee P, Sengupta N. Signatures of protein thermal denaturation and local hydrophobicity in domain specific hydration behavior: a comparative molecular dynamics study. MOLECULAR BIOSYSTEMS 2016; 12:1139-50. [PMID: 26876051 DOI: 10.1039/c6mb00017g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We investigate, using atomistic molecular dynamics simulations, the association of surface hydration accompanying local unfolding in the mesophilic protein Yfh1 under a series of thermal conditions spanning its cold and heat denaturation temperatures. The results are benchmarked against the thermally stable protein, Ubq, and behavior at the maximum stability temperature. Local unfolding in Yfh1, predominantly in the beta sheet regions, is in qualitative agreement with recent solution NMR studies; the corresponding Ubq unfolding is not observed. Interestingly, all domains, except for the beta sheet domains of Yfh1, show increased effective surface hydrophobicity with increase in temperature, as reflected by the density fluctuations of the hydration layer. Velocity autocorrelation functions (VACF) of oxygen atoms of water within the hydration layers and the corresponding vibrational density of states (VDOS) are used to characterize alteration in dynamical behavior accompanying the temperature dependent local unfolding. Enhanced caging effects accompanying transverse oscillations of the water molecules are found to occur with the increase in temperature preferentially for the beta sheet domains of Yfh1. Helical domains of both proteins exhibit similar trends in VDOS with changes in temperature. This work demonstrates the existence of key signatures of the local onset of protein thermal denaturation in solvent dynamical behavior.
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Affiliation(s)
- Prathit Chatterjee
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India.
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18
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Jiang X, Chen G, Wang L. Structural and dynamic evolution of the amphipathic N-terminus diversifies enzyme thermostability in the glycoside hydrolase family 12. Phys Chem Chem Phys 2016; 18:21340-50. [DOI: 10.1039/c6cp02998a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The N-terminus diversifies enzyme thermostability in the GH12 family, which was investigated by MD simulations, and provides potential applications in protein engineering.
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Affiliation(s)
- Xukai Jiang
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan 250100
- China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan 250100
- China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan 250100
- China
- State Key Laboratory of Biochemical Engineering
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19
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Nayar D, Chakravarty C. Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models. J Phys Chem B 2015; 119:11106-20. [PMID: 26132437 DOI: 10.1021/acs.jpcb.5b02937] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replica exchange molecular dynamics is used to study the effect of different rigid-body (mTIP3P, TIP4P, SPC/E) and hybrid (H1.56, H3.00) water models on the conformational free energy landscape of the alanine oligopeptides (acAnme and acA5nme), in conjunction with the CHARMM22 force field. The free energy landscape is mapped out as a function of the Ramachandran angles. In addition, various secondary structure metrics, solvation shell properties, and the number of peptide-solvent hydrogen bonds are monitored. Alanine dipeptide is found to have similar free energy landscapes in different solvent models, an insensitivity which may be due to the absence of possibilities for forming i-(i + 4) or i-(i + 3) intrapeptide hydrogen bonds. The pentapeptide, acA5nme, where there are three intrapeptide backbone hydrogen bonds, shows a conformational free energy landscape with a much greater degree of sensitivity to the choice of solvent model, though the three rigid-body water models differ only quantitatively. The pentapeptide prefers nonhelical, non-native PPII and β-sheet populations as the solvent is changed from SPC/E to the less tetrahedral liquid (H1.56) to an LJ-like liquid (H3.00). The pentapeptide conformational order metrics indicate a preference for open, solvent-exposed, non-native structures in hybrid solvent models at all temperatures of study. The possible correlations between the properties of solvent models and secondary structure preferences of alanine oligopeptides are discussed, and the competition between intrapeptide, peptide-solvent, and solvent-solvent hydrogen bonding is shown to be crucial in the relative free energies of different conformers.
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Affiliation(s)
- Divya Nayar
- Department of Chemistry, Indian Institute of Technology-Delhi , New Delhi 110016, India
| | - Charusita Chakravarty
- Department of Chemistry, Indian Institute of Technology-Delhi , New Delhi 110016, India
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