1
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Heng S, Sutheeworapong S, Wangnai C, Champreda V, Kosugi A, Ratanakhanokchai K, Tachaapaikoon C, Ceballos RM. Hydrolysis of ionic liquid-treated substrate with an Iocasia fonsfrigidae strain SP3-1 endoglucanase. Appl Microbiol Biotechnol 2024; 108:63. [PMID: 38189956 PMCID: PMC10774164 DOI: 10.1007/s00253-023-12918-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/04/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024]
Abstract
Recently, we reported the discovery of a novel endoglucanase of the glycoside hydrolase family 12 (GH12), designated IfCelS12A, from the haloalkaliphilic anaerobic bacterium Iocasia fonsfrigidae strain SP3-1, which was isolated from a hypersaline pond in the Samut Sakhon province of Thailand (ca. 2017). IfCelS12A exhibits high substrate specificity on carboxymethyl cellulose and amorphous cellulose but low substrate specificity on b-1,3;1,4-glucan. Unlike some endoglucanases of the GH12 family, IfCelS12A does not exhibit hydrolytic activity on crystalline cellulose (i.e., Avicel™). High-Pressure Liquid Chromatography (HPLC) and Thin Layer Chromatography (TLC) analyses of products resulting from IfCelS12-mediated hydrolysis indicate mode of action for this enzyme. Notably, IfCelS12A preferentially hydrolyzes cellotetraoses, cellopentaoses, and cellohexaoses with negligible activity on cellobiose or cellotriose. Kinetic analysis with cellopentaose and barely b-D-glucan as cellulosic substrates were conducted. On cellopentaose, IfCelS12A demonstrates a 16-fold increase in activity (KM = 0.27 mM; kcat = 0.36 s-1; kcat/KM = 1.34 mM-1 s-1) compared to the enzymatic hydrolysis of barley b-D-glucan (KM: 0.04 mM, kcat: 0.51 s-1, kcat/KM = 0.08 mM-1 s-1). Moreover, IfCelS12A enzymatic efficacy is stable in hypersaline sodium chlorids (NaCl) solutions (up to 10% NaCl). Specifically, IfCel12A retains notable activity after 24 h at 2M NaCl (10% saline solution). IfCelS12A used as a cocktail component with other cellulolytic enzymes and in conjunction with mobile sequestration platform technology offers additional options for deconstruction of ionic liquid-pretreated cellulosic feedstock. KEY POINTS: • IfCelS12A from an anaerobic alkaliphile Iocasia fronsfrigidae shows salt tolerance • IfCelS12A in cocktails with other enzymes efficiently degrades cellulosic biomass • IfCelS12A used with mobile enzyme sequestration platforms enhances hydrolysis.
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Affiliation(s)
- Sobroney Heng
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
- Department of Molecular and Cell Biology, University of California, Merced, CA, 95343, USA
| | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Laboratory, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chinnapong Wangnai
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road Klong Luang, Pathumthani, 12120, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
| | - Ruben Michael Ceballos
- Department of Molecular and Cell Biology, University of California, Merced, CA, 95343, USA.
- Quantitative Systems Biology Program, University of California, Merced, CA, 95343, USA.
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2
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Zhu H, Deng X, Yakovlev VV, Zhang D. Dynamics of CH/ n hydrogen bond networks probed by time-resolved CARS spectroscopy. Chem Sci 2024:d4sc03985h. [PMID: 39156926 PMCID: PMC11323804 DOI: 10.1039/d4sc03985h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024] Open
Abstract
Hydrogen bond (HB) networks are essential for stabilizing molecular structures in solution and govern the solubility and functionality of molecules in an aqueous environment. HBs are important in biological processes such as enzyme-substrate interactions, protein folding, and DNA replication. However, the exact role of weakly polarized C-H bonds as HB proton donors in solution, such as CH/n HBs, remains mostly unknown. Here, we employ a novel approach focusing on vibrational dephasing to investigate the coherence relaxation of induced dipoles in C-H bonds within CH/n HB networks, utilizing time-resolved coherent anti-Stokes Raman scattering (T-CARS) spectroscopy. Using a representative binary system of dimethyl sulfoxide (DMSO)-water, known for its C-H backboned HB system (i.e., C-H⋯S), we observed an increase in the dephasing time of the C-H bending mode with increasing water content until a percolation threshold at a 6 : 1 water : DMSO molar ratio, where the trend is reversed. These results provide compelling evidence for the existence of C-H⋯S structures and underscore the presence of a percolation effect, suggesting a critical threshold where long-range connectivity is disputed.
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Affiliation(s)
- Hanlin Zhu
- Zhejiang Key Laboratory of Micro-nano Quantum Chips and Quantum Control, School of Physics, Zhejiang University Hangzhou Zhejiang 310027 China
- MOE Frontier Science Center for Brain Science & Brain-Machine Integration, Zhejiang University Hangzhou Zhejiang 310027 China
| | - Xinyu Deng
- Zhejiang Key Laboratory of Micro-nano Quantum Chips and Quantum Control, School of Physics, Zhejiang University Hangzhou Zhejiang 310027 China
- MOE Frontier Science Center for Brain Science & Brain-Machine Integration, Zhejiang University Hangzhou Zhejiang 310027 China
| | - Vladislav V Yakovlev
- Department of Biomedical Engineering, Texas A&M University College Station TX 77843 USA
- Department of Physics and Astronomy, Texas A&M University College Station TX 77843 USA
- Department of Electrical and Computer Engineering, Texas A&M University College Station TX 77843 USA
| | - Delong Zhang
- Zhejiang Key Laboratory of Micro-nano Quantum Chips and Quantum Control, School of Physics, Zhejiang University Hangzhou Zhejiang 310027 China
- MOE Frontier Science Center for Brain Science & Brain-Machine Integration, Zhejiang University Hangzhou Zhejiang 310027 China
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3
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Zhang L, Dai W, Rong S, Schwaneberg U, Xu G, Ni Y. Engineering diaryl alcohol dehydrogenase KpADH reveals importance of retaining hydration shell in organic solvent tolerance. Protein Sci 2024; 33:e4933. [PMID: 38501647 PMCID: PMC10949390 DOI: 10.1002/pro.4933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/27/2024] [Accepted: 02/01/2024] [Indexed: 03/20/2024]
Abstract
Alcohol dehydrogenases (ADHs) are synthetically important biocatalysts for the asymmetric synthesis of chiral alcohols. The catalytic performance of ADHs in the presence of organic solvents is often important since most prochiral ketones are highly hydrophobic. Here, the organic solvent tolerance of KpADH from Kluyveromyces polyspora was semi-rationally evolved. Using tolerant variants obtained, meticulous experiments and computational studies were conducted to explore properties including stability, activity and kinetics in the presence of various organic solvents. Compared with WT, variant V231D exhibited 1.9-fold improvement in ethanol tolerance, while S237G showed a 6-fold increase in catalytic efficiency, a higherT 50 15 $$ {\mathrm{T}}_{50}^{15} $$ , as well as 15% higher tolerance in 7.5% (v/v) ethanol. Based on 3 × 100 ns MD simulations, the increased tolerance of V231D and S237G against ethanol may be ascribed to their enhanced ability in retaining water molecules and repelling ethanol molecules. Moreover, 6.3-fold decreased KM value of V231D toward hydrophilic ketone substrate confirmed its capability of retaining hydration shell. Our results suggest that retaining hydration shell surrounding KpADH is critical for its tolerance to organic solvents, as well as catalytic performance. This study provides useful guidance for engineering organic solvent tolerance of KpADH and other ADHs.
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Affiliation(s)
- Lu Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of EducationSchool of Biotechnology, Jiangnan UniversityWuxiChina
| | - Wei Dai
- Key Laboratory of Industrial Biotechnology, Ministry of EducationSchool of Biotechnology, Jiangnan UniversityWuxiChina
| | - Shuo Rong
- Key Laboratory of Industrial Biotechnology, Ministry of EducationSchool of Biotechnology, Jiangnan UniversityWuxiChina
| | | | - Guochao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of EducationSchool of Biotechnology, Jiangnan UniversityWuxiChina
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of EducationSchool of Biotechnology, Jiangnan UniversityWuxiChina
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4
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Sahu S, Garg A, Saini R, Debnath A. Interface Water Assists in Dimethyl Sulfoxide Crossing and Poration in Model Bilayer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:5764-5775. [PMID: 38445595 DOI: 10.1021/acs.langmuir.3c03498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Understanding the mechanism of transport and pore formation by a commonly used cryoprotectant, dimethyl sulfoxide (DMSO), across cell membranes is fundamentally crucial for drug delivery and cryopreservation. To shed light on the mechanism and thermodynamics of pore formation and crossing behavior of DMSO, extensive all-atom molecular dynamics simulations of 1,2-dimyristoyl-rac-glycero-3-phosphocholine (DMPC) bilayers are performed at various concentrations of DMSO at a temperature above the physiological temperature. Our results unveil that DMSO partially depletes water from the interface and positions itself between lipid heads without full dehydration. This induces a larger area per headgroup, increased disorder, and enhanced fluidity without any disintegration even at the highest DMSO concentration studied. The enhanced disorder fosters local fluctuations at the interface that nucleate dynamic and transient pores. The potential of mean force (PMF) of DMSO crossing is derived from two types of biased simulations: a single DMSO pulling using the umbrella sampling technique and a cylindrical pore formation using the recently developed chain reaction coordinate method. In both cases, DMSO crossing encounters a barrier attributed to unfavorable polar nonpolar interactions between DMSO and lipid tails. As the DMSO concentration increases, the barrier height reduces along with the faster lateral and perpendicular diffusion of DMSO suggesting favorable permeation. Our findings suggest that the energy required for pore formation decreases when water assists in the formation of DMSO pores. Although DMSO displaces water from the interface toward the far interface region without complete dehydration, the presence of interface water diminishes pore formation free energy. The existence of interface water leads to the formation of a two-dimensional percolated water-DMSO structure at the interface, which is absent otherwise. Overall, these insights into the mechanism of DMSO crossing and pore formation in the bilayer will contribute to understanding cryoprotectant behavior under supercooled conditions in the future.
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Affiliation(s)
- Samapika Sahu
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
| | - Avinash Garg
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
| | - Renu Saini
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
| | - Ananya Debnath
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
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5
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Krishnamurthy K, Rajendran A, Nakata E, Morii T. Near Quantitative Ligation Results in Resistance of DNA Origami Against Nuclease and Cell Lysate. SMALL METHODS 2024; 8:e2300999. [PMID: 37736703 DOI: 10.1002/smtd.202300999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Indexed: 09/23/2023]
Abstract
There have been limited efforts to ligate the staple nicks in DNA origami which is crucial for their stability against thermal and mechanical treatments, and chemical and biological environments. Here, two near quantitative ligation methods are demonstrated for the native backbone linkage at the nicks in origami: i) a cosolvent dimethyl sulfoxide (DMSO)-assisted enzymatic ligation and ii) enzyme-free chemical ligation by CNBr. Both methods achieved over 90% ligation in 2D origami, only CNBr-method resulted in ≈80% ligation in 3D origami, while the enzyme-alone yielded 31-55% (2D) or 22-36% (3D) ligation. Only CNBr-method worked efficiently for 3D origami. The CNBr-mediated reaction is completed within 5 min, while DMSO-method took overnight. Ligation by these methods improved the structural stability up to 30 °C, stability during the electrophoresis and subsequent extraction, and against nuclease and cell lysate. These methods are straightforward, non-tedious, and superior in terms of cost, reaction time, and efficiency.
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Affiliation(s)
| | - Arivazhagan Rajendran
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
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6
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Hydrogen bonding structure and dynamics of cis- and trans- conformers of N-methylformamide in water, DMSO and water-DMSO mixtures at varying compositions. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Chakrabarty S, Deshmukh SH, Barman A, Bagchi S, Ghosh A. On-Off Infrared Absorption of the S═O Vibrational Probe of Dimethyl Sulfoxide. J Phys Chem B 2022; 126:4501-4508. [PMID: 35674725 DOI: 10.1021/acs.jpcb.1c10558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dimethyl sulfoxide (DMSO), a polar solvent molecule, is used in a wide range of therapeutic and pharmacological applications. Different intermolecular interactions, such as dimerization and hydrogen bonding with water, are crucial to understanding the role of DMSO in applications. Herein, we study DMSO in various solvation environments to decipher the environment-dependent dimerization and hydrogen-bonding propensity. We use a combination of infrared spectroscopy, quantum mechanical calculations, and molecular dynamics simulations to reach our conclusions. Although DMSO can exist in a dynamic equilibrium between monomers and dimers, our results show that the relative intensity of the S═O stretch and the CH3 rocking modes is a spectroscopic indicator of the extent of DMSO dimerization in solution. The dimerization (self-association) is seen to be maximum in neat DMSO. When dissolved in different solvents, the dimerization propensity decreases with increasing solvent polarity. In the presence of a protic solvent, such as water, DMSO forms a hydrogen bond with the solvent molecules, thereby reducing the extent of dimerization. Further, we estimate the hydrogen-bond occupancy of DMSO. Our results show that DMSO predominantly exists as doubly hydrogen-bonded in water.
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Affiliation(s)
- Suranjana Chakrabarty
- Department of Condensed Matter Physics and Materials Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
| | - Samadhan H Deshmukh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anjan Barman
- Department of Condensed Matter Physics and Materials Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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8
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Cheng F, Li MY, Wei DJ, Zhang XJ, Jia DX, Liu ZQ, Zheng YG. Enabling biocatalysis in high-concentration organic cosolvent by enzyme gate engineering. Biotechnol Bioeng 2021; 119:845-856. [PMID: 34928500 DOI: 10.1002/bit.28014] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 12/07/2021] [Accepted: 12/12/2021] [Indexed: 12/16/2022]
Abstract
Biocatalysis in high-concentration organic solvents (OSs) offers many advantages, but realizing this process remains a huge challenge. An R-selective ω-amine transaminase variant (AcATAM2 ) exhibited high activity toward 50 g/L pro-sitagliptin ketone 1-[1-piperidinyl]-4-[2,4,5-trifluorophenyl]-1,3-butanedione (PTfpB). However, AcATAM2 displayed unsatisfactory organic-cosolvent resistance against high-concentration dimethyl sulfoxide (DMSO), which is required to enhance the solubility of the hydrophobic substrate PTfpB. Located in the substrate-binding tunnel, enzyme gates are structural elements that undergo reversible conformational transitions, thus affecting the accessibility of the binding pocket to solvent molecules. Depending on the conformation of the enzyme gates, one can define an open or closed conformation on which the enzyme activity in OSs may depend. To enhance the DMSO resistance of AcATAM2 , we identified the beneficial residues at the "enzyme gate" region via computational analysis, alanine scanning, and site-saturation mutagenesis. Two beneficial variants, namely, AcATAM2 F56D and AcATAM2 F56V , not only displayed improved enzyme activity but also exhibited enhanced DMSO resistance (the half-life value increased from 25.71 to 42.49 h under 60% DMSO). Molecular dynamic simulations revealed that the increase in DMSO resistance was mainly caused by the decrease in the number of DMSO molecules in the substrate-binding pocket. Moreover, in the kilogram-scale experiment, the conversion of 80 g/L substrate was increased from 50% (AcATAM2 ) to 85% (M2F56D in 40% DMSO) with a high e.e. of >99% within 24 h.
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Affiliation(s)
- Feng Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Ming-You Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Dian-Ju Wei
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Xiao-Jian Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Dong-Xu Jia
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
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9
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González-Paz L, Hurtado-León ML, Lossada C, Fernández-Materán FV, Vera-Villalobos J, Loroño M, Paz JL, Jeffreys L, Alvarado YJ. Comparative study of the interaction of ivermectin with proteins of interest associated with SARS-CoV-2: A computational and biophysical approach. Biophys Chem 2021; 278:106677. [PMID: 34428682 PMCID: PMC8373590 DOI: 10.1016/j.bpc.2021.106677] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/13/2021] [Accepted: 08/15/2021] [Indexed: 01/18/2023]
Abstract
The SARS-CoV-2 pandemic has accelerated the study of existing drugs. The mixture of homologs called ivermectin (avermectin-B1a [HB1a] + avermectin-B1b [HB1b]) has shown antiviral activity against SARS-CoV-2 in vitro. However, there are few reports on the behavior of each homolog. We investigated the interaction of each homolog with promising targets of interest associated with SARS-CoV-2 infection from a biophysical and computational-chemistry perspective using docking and molecular dynamics. We observed a differential behavior for each homolog, with an affinity of HB1b for viral structures, and of HB1a for host structures considered. The induced disturbances were differential and influenced by the hydrophobicity of each homolog and of the binding pockets. We present the first comparative analysis of the potential theoretical inhibitory effect of both avermectins on biomolecules associated with COVID-19, and suggest that ivermectin through its homologs, has a multiobjective behavior.
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Affiliation(s)
- Lenin González-Paz
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), 4001 Maracaibo, Venezuela; Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Estudios Botánicos y Agroforestales (CEBA), Laboratorio de Protección Vegetal (LPV), 4001 Maracaibo, Venezuela.
| | - María Laura Hurtado-León
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), 4001 Maracaibo, Venezuela
| | - Carla Lossada
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Venezuela
| | - Francelys V Fernández-Materán
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Venezuela
| | - Joan Vera-Villalobos
- Facultad de Ciencias Naturales y Matemáticas, Departamento de Química y Ciencias Ambientales, Laboratorio de Análisis Químico Instrumental (LAQUINS), Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Marcos Loroño
- Departamento Académico de Química Analítica e Instrumental, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - J L Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Laura Jeffreys
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Ysaias J Alvarado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Venezuela.
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10
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Evaluating the activity and stability of sonochemically produced hemoglobin-copper hybrid nanoflowers against some metallic ions, organic solvents, and inhibitors. J Biosci Bioeng 2021; 132:327-336. [PMID: 34334311 DOI: 10.1016/j.jbiosc.2021.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 01/10/2023]
Abstract
The disadvantage of the conventional protein-inorganic hybrid nanoflower production method is the long incubation period of the synthesis method. This period is not suitable for practical industrial use. Herein, protein-inorganic hybrid nanoflowers were synthesized using hemoglobin and copper ion by fast sonication method for 10 min. The synthesized nanoflowers were characterized via scanning electron microscopy, energy-dispersive X-ray spectroscopy, X-ray diffraction, and Fouirer-transform infrared spectroscopy. The activity and stability of the nanoflowers in the presence of different metal ions, organic solvents, inhibitors, and storage conditions were also evaluated by comparing with free hemoglobin. According to obtained results, the optimum pH and temperatures of both hybrid nanoflower and free hemoglobin were pH 5 and 40 °C, respectively. At all pH levels, nanoflower was more stable than free protein and it was also more stable than the free hemoglobin at temperatures ranging between 50 °C and 80 °C. The free protein lost more than half of its activity in the presence of acetone, benzene, and N,N-dimethylformamide, while the hybrid nanoflower retained more than 70% of its activity for 2 h at 40 °C. The hybrid nanoflower activity was essentially increased in the presence of Ca2+, Zn2+, Fe2+, Cu2+ and Ni2+ (132%, 161%, 175%, 185% and 106%, respectively) at 5 mM concentration. The nanoflower retained more than 85% of its initial activity in the presence of all inhibitors. In addition, it retained all its activity for 3 days under different storage conditions, unlike free hemoglobin. The results demonstrated that new hybrid nanoflowers may be promising in different biotechnological applications such as catalytic biosensors and environmental or industrial catalytic processes.
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11
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Kaspar F, Neubauer P, Kurreck A. The Peculiar Case of the Hyper-thermostable Pyrimidine Nucleoside Phosphorylase from Thermus thermophilus*. Chembiochem 2021; 22:1385-1390. [PMID: 33258231 PMCID: PMC8247850 DOI: 10.1002/cbic.202000679] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/22/2020] [Indexed: 12/16/2022]
Abstract
The poor solubility of many nucleosides and nucleobases in aqueous solution demands harsh reaction conditions (base, heat, cosolvent) in nucleoside phosphorylase-catalyzed processes to facilitate substrate loading beyond the low millimolar range. This, in turn, requires enzymes that can withstand these conditions. Herein, we report that the pyrimidine nucleoside phosphorylase from Thermus thermophilus is active over an exceptionally broad pH (4-10), temperature (up to 100 °C) and cosolvent space (up to 80 % (v/v) nonaqueous medium), and displays tremendous stability under harsh reaction conditions with predicted total turnover numbers of more than 106 for various pyrimidine nucleosides. However, its use as a biocatalyst for preparative applications is critically limited due to its inhibition by nucleobases at low concentrations, which is unprecedented among nonspecific pyrimidine nucleoside phosphorylases.
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Affiliation(s)
- Felix Kaspar
- Department of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität BerlinStraße des 17. Juni 13510623BerlinGermany
- BioNukleo GmbHAckerstraße 7613355BerlinGermany
| | - Peter Neubauer
- Department of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität BerlinStraße des 17. Juni 13510623BerlinGermany
| | - Anke Kurreck
- Department of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität BerlinStraße des 17. Juni 13510623BerlinGermany
- BioNukleo GmbHAckerstraße 7613355BerlinGermany
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12
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Ghosh A, Ghosh S, Ghosh G, Patra A. Implications of relaxation dynamics of collapsed conjugated polymeric nanoparticles for light-harvesting applications. Phys Chem Chem Phys 2021; 23:14549-14563. [DOI: 10.1039/d1cp01618k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The mechanism of the formation of nanoparticles (collapsed state) from the extended state of polymers and their ultrafast excited state relaxation dynamics are illustrated.
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Affiliation(s)
- Arnab Ghosh
- School of Materials Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Srijon Ghosh
- School of Materials Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Goutam Ghosh
- School of Materials Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Amitava Patra
- School of Materials Sciences
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
- Institute of Nano Science and Technology
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13
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Markwalter CE, Uralcan B, Pelczer I, Zarzhitsky S, Hecht MH, Prud'homme RK, Debenedetti PG. Stability of Protein Structure during Nanocarrier Encapsulation: Insights on Solvent Effects from Simulations and Spectroscopic Analysis. ACS NANO 2020; 14:16962-16972. [PMID: 33211493 DOI: 10.1021/acsnano.0c06056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The dosing of peptide and protein therapeutics is complicated by rapid clearance from the blood pool and poor cellular membrane permeability. Encapsulation into nanocarriers such as liposomes or polymersomes has long been explored to overcome these limitations, but manufacturing challenges have limited clinical translation by these approaches. Recently, inverse Flash NanoPrecipitation (iFNP) has been developed to produce highly loaded polymeric nanocarriers with the peptide or protein contained within a hydrophilic core, stabilized by a hydrophobic polymer shell. Encapsulation of proteins with higher-order structure requires understanding how processing may affect their conformational state. We demonstrate a combined experimental/simulation approach to characterize protein behavior during iFNP processing steps using the Trp-cage protein TC5b as a model. Explicit-solvent fully atomistic molecular dynamics simulations with enhanced sampling techniques are coupled with two-dimensional heteronuclear multiple-quantum coherence nuclear magnetic resonance spectroscopy (2D-HMQC NMR) and circular dichroism to determine the structure of TC5b during mixed-solvent exposure encountered in iFNP processing. The simulations involve atomistic models of mixed solvents and protein to capture the complexity of the hydrogen bonding and hydrophobic interactions between water, dimethylsulfoxide (DMSO), and the protein. The combined analyses reveal structural unfolding of the protein in 11 M DMSO but confirm complete refolding after release from the polymeric nanocarrier back into an aqueous phase. These results highlight the insights that simulations and NMR provide for the formulation of proteins in nanocarriers.
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Affiliation(s)
- Chester E Markwalter
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Betul Uralcan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - István Pelczer
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Shlomo Zarzhitsky
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Michael H Hecht
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Robert K Prud'homme
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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14
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Kumari P, Kumari M, Kashyap HK. How Pure and Hydrated Reline Deep Eutectic Solvents Affect the Conformation and Stability of Lysozyme: Insights from Atomistic Molecular Dynamics Simulations. J Phys Chem B 2020; 124:11919-11927. [DOI: 10.1021/acs.jpcb.0c09873] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Pratibha Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Monika Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Hemant K. Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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15
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Halder R, Jana B. On the Correlation between Pair Hydrophobicity and Mixing Enthalpies in Water–Alcohol Binary Mixtures. J Phys Chem B 2020; 124:8023-8031. [DOI: 10.1021/acs.jpcb.0c05952] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Ritaban Halder
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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16
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Bezsudnova EY, Stekhanova TN, Ruzhitskiy AO, Popov VO. Effects of pH and temperature on (S)-amine activity of transaminase from the cold-adapted bacterium Psychrobacter cryohalolentis. Extremophiles 2020; 24:537-549. [PMID: 32418069 DOI: 10.1007/s00792-020-01174-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/27/2020] [Indexed: 10/24/2022]
Abstract
(7R,8S)-diaminopelargonic acid transaminase from the cold-adapted Gram-negative bacterium Psychrobacter cryohalolentis (Pcryo361) is able to react with unnatural substrates including (S)-( +)-1-phenylethylamine, aldehydes and α-diketones. Additionally, Pcryo361 is active at 0-50 °C and retains up to 10% of the maximum activity at 0 °C. Here, we report a detailed study on the stability and low temperature activity of Pcryo361. At the optimal pH for (S)-amine activity (pH 10.0), the enzyme was stable at 0-10 °C and no decrease in the enzyme activity was observed within 24 h in a slightly alkaline medium, pH 8.0, at 35 °C. Pcryo361 was solvent stable and was activated in 10% DMSO and DMFA at 35 °C. An analysis of the efficiency of catalysis of Pcryo361 at 35 °C and 10 °C showed that the specificity towards (S)-( +)-1-phenylethylamine dropped at 10 °C; however, the specificity towards 2,3-butanedione remained unchanged. Inhibition analysis showed that Pcryo361 activity was not inhibited by acetophenone but inhibited by amines (products of aldehyde amination). The observed pH stability and low temperature activity of Pcryo361 with activated keto substrates are attractive features in the field of development of stereoselective amination at low temperatures.
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Affiliation(s)
- Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, 119071, Russian Federation.
| | - Tatiana N Stekhanova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, 119071, Russian Federation
| | - Aleksandr O Ruzhitskiy
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, 119071, Russian Federation
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, 119071, Russian Federation.,Kurchatov Complex of NBICS-Technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova sqr 1, Moscow, 123182, Russian Federation
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17
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Zieniuk B, Fabiszewska A, Białecka-Florjańczyk E. Screening of solvents for favoring hydrolytic activity of Candida antarctica Lipase B. Bioprocess Biosyst Eng 2019; 43:605-613. [PMID: 31734716 DOI: 10.1007/s00449-019-02252-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 11/08/2019] [Indexed: 02/04/2023]
Abstract
Lipases are a group of enzymes of considerable significance in organic synthesis, among which Candida antarctica lipase B (CALB) is one of the most widely studied enzymes. The activity of the biocatalyst has been intensively characterized in many organic media, but this paper aimed to compare the effect of 20 different solvents on the activity of CALB in the hydrolysis of p-nitrophenyl laurate. Nonpolar, polar aprotic, and polar protic solvents were used for enzyme pretreatment and then entered the composition of mixed solvents reaction medium. An impact of solvents on solvation processes affecting the catalysis steps, protein denaturation, and changes of its conformation was discussed. Moreover the hydrolytic activity of CALB with partition coefficient (logP) of the solvent used was correlated. It was emphasized that the substrate solubility plays an important role in solvent selection. In the presence of hydrophobic solvents, hydration layer becomes more hydrophobic facilitating the substrate access to the enzyme surface. In turn, polar compounds are good solvents for organic substrates facilitating the penetration of the aqueous layer that surrounds the surface of the enzyme. Two variants proved to be favorable for ester hydrolysis reaction: isooctane or polar solvent such as acetone, tert -butyl methyl ether, tert-butanol or acetonitrile.
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Affiliation(s)
- Bartłomiej Zieniuk
- Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences, 159c Nowoursynowska St., 02-776, Warsaw, Poland.
| | - Agata Fabiszewska
- Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences, 159c Nowoursynowska St., 02-776, Warsaw, Poland
| | - Ewa Białecka-Florjańczyk
- Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences, 159c Nowoursynowska St., 02-776, Warsaw, Poland
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18
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Parui S, Jana B. Relative Solvent Exposure of the Alpha-Helix and Beta-Sheet in Water Determines the Initial Stages of Urea and Guanidinium Chloride-Induced Denaturation of Alpha/Beta Proteins. J Phys Chem B 2019; 123:8889-8900. [DOI: 10.1021/acs.jpcb.9b06859] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sridip Parui
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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19
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Muttathukattil AN, Singh PC, Reddy G. Role of Disulfide Bonds and Topological Frustration in the Kinetic Partitioning of Lysozyme Folding Pathways. J Phys Chem B 2019; 123:3232-3241. [PMID: 30913878 DOI: 10.1021/acs.jpcb.9b00739] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Disulfide bonds in proteins can strongly influence the folding pathways by constraining the conformational space. Lysozyme has four disulfide bonds and is widely studied for its antibacterial properties. Experiments on lysozyme infer that the protein folds through a fast and a slow pathway. However, the reasons for the kinetic partitioning in the folding pathways are not completely clear. Using a coarse-grained protein model and simulations, we show that two out of the four disulfide bonds, which are present in the α-domain of lysozyme, are responsible for the slow folding pathway. In this pathway, a kinetically trapped intermediate state, which is close to the native state, is populated. In this state, the orientations of α-helices present in the α-domain are misaligned relative to each other. The protein in this state has to partially unfold by breaking down the interhelical contacts between the misaligned helices to fold to the native state. However, the topological constraints due to the two disulfide bonds present in the α-domain make the protein less flexible, and it is trapped in this conformation for hundreds of milliseconds. On disabling these disulfide bonds, we find that the kinetically trapped intermediate state and the slow folding pathway disappear. Simulations mimicking the folding of protein without disulfide bonds under oxidative conditions show that the native disulfide bonds are formed as the protein folds, indicating that folding guides the formation of disulfide bonds. The sequence of formation of the disulfide bonds is Cys64-Cys80 → Cys76-Cys94 → Cys30-Cys115 → Cys6-Cys127. Any disulfide bond that forms before its precursor in the sequence has to break and follow the sequence for the protein to fold. These results show that lysozyme also serves as a very good model system to probe the role of disulfide bonds and topological frustration in protein folding. The predictions from the simulations can be verified by single-molecule fluorescence resonance energy transfer or single-molecule pulling experiments, which can probe heterogeneity in the folding pathways.
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Affiliation(s)
- Aswathy N Muttathukattil
- Solid State and Structural Chemistry Unit , Indian Institute of Science , Bengaluru 560012 , Karnataka , India
| | - Prashant Chandra Singh
- School of Chemical Science , Indian Association for the Cultivation of Science , 2A & 2B, Raja S.C. Mullick Road , Jadavpur, Kolkata 700032 , India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit , Indian Institute of Science , Bengaluru 560012 , Karnataka , India
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20
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Yadav NS, Choudhury D. Conformational perturbation of peptides in presence of polar organic solvents. J Mol Graph Model 2019; 89:1-12. [PMID: 30831385 DOI: 10.1016/j.jmgm.2019.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 02/08/2019] [Accepted: 02/20/2019] [Indexed: 11/17/2022]
Abstract
The critical role played by solvent environment in maintaining the conformational integrity of peptides and proteins is accepted without question. Numerous experiments have suggested that perturbing the solvent environment of peptides and proteins by the addition of polar organic solvents have important consequences for the conformation of these molecules. However, experimental studies of such perturbations often report different kinds of effects depending on the solvent used and/or the sequence/structure of the molecule under study. In this work we report a simulation based comparative study on the effects of adding two common organic solvents viz. Dimethyl sulfoxide (DMSO) and Acetonitrile (MeCN) on the dynamical conformation of a test peptide Ace-Gly-X-Gly-Nme where X is any amino acid. Our studies identify important differences in peptide solvation by these two solvents, which we attempt to correlate with the kinetic stability of the conformation, as well as the identity of the central 'X' residue in the test peptide.
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Affiliation(s)
- Neetu Singh Yadav
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Devapriya Choudhury
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
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21
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22
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Tunçer S, Gurbanov R, Sheraj I, Solel E, Esenturk O, Banerjee S. Low dose dimethyl sulfoxide driven gross molecular changes have the potential to interfere with various cellular processes. Sci Rep 2018; 8:14828. [PMID: 30287873 PMCID: PMC6172209 DOI: 10.1038/s41598-018-33234-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/25/2018] [Indexed: 12/18/2022] Open
Abstract
Dimethyl sulfoxide (DMSO) is a small molecule with polar, aprotic and amphiphilic properties. It serves as a solvent for many polar and nonpolar molecules and continues to be one of the most used solvents (vehicle) in medical applications and scientific research. To better understand the cellular effects of DMSO within the concentration range commonly used as a vehicle (0.1-1.5%, v/v) for cellular treatments, we applied Attenuated Total Reflectance (ATR) Fourier Transform Infrared (FT-IR) spectroscopy to DMSO treated and untreated epithelial colon cancer cells. Both unsupervised (Principal Component Analysis-PCA) and supervised (Linear Discriminant Analysis-LDA) pattern recognition/modelling algorithms applied to the IR data revealed total segregation and prominent differences between DMSO treated and untreated cells at whole, lipid and nucleic acid regions. Several of these data were supported by other independent techniques. Further IR data analyses of macromolecular profile indicated comprehensive alterations especially in proteins and nucleic acids. Protein secondary structure analysis showed predominance of β-sheet over α-helix in DMSO treated cells. We also observed for the first time, a reduction in nucleic acid level upon DMSO treatment accompanied by the formation of Z-DNA. Molecular docking and binding free energy studies indicated a stabilization of Z-DNA in the presence of DMSO. This alternate DNA form may be related with the specific actions of DMSO on gene expression, differentiation, and epigenetic alterations. Using analytical tools combined with molecular and cellular biology techniques, our data indicate that even at very low concentrations, DMSO induces a number of changes in all macromolecules, which may affect experimental outcomes where DMSO is used as a solvent.
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Affiliation(s)
- Sinem Tunçer
- Department of Biological Sciences, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey
- Vocational School of Health Services, Department of Medical Laboratory Techniques, Bilecik Şeyh Edebali University, Bilecik, 11230, Turkey
| | - Rafig Gurbanov
- Department of Molecular Biology and Genetics, Bilecik Şeyh Edebali University, Bilecik, 11230, Turkey
| | - Ilir Sheraj
- Department of Biological Sciences, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey
| | - Ege Solel
- Department of Biological Sciences, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey
- Department of Biomedicine, University of Bergen, Postbox 7804, Bergen, N-5020, Norway
| | - Okan Esenturk
- Department of Chemistry, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey
| | - Sreeparna Banerjee
- Department of Biological Sciences, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey.
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23
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Hazra MK, Bagchi B. Non-equilibrium solvation dynamics in water-DMSO binary mixture: Composition dependence of non-linear relaxation. J Chem Phys 2018; 149:084501. [DOI: 10.1063/1.5036689] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Milan K. Hazra
- SSCU, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- SSCU, Indian Institute of Science, Bangalore 560012, India
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24
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Sarkar S, Biswas B, Singh PC. Spectroscopic and Molecular Dynamics Simulation Study of Lysozyme in the Aqueous Mixture of Ethanol: Insights into the Nonmonotonic Change of the Structure of Lysozyme. J Phys Chem B 2018; 122:7811-7820. [DOI: 10.1021/acs.jpcb.8b03106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sunipa Sarkar
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Biswajit Biswas
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Prashant Chandra Singh
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
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25
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Daschakraborty S. How do glycerol and dimethyl sulphoxide affect local tetrahedral structure of water around a nonpolar solute at low temperature? Importance of preferential interaction. J Chem Phys 2018; 148:134501. [PMID: 29626866 DOI: 10.1063/1.5019239] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Glycerol and dimethyl sulphoxide (DMSO) have vital roles in cryoprotection of living cells, tissues, etc. The above action has been directly linked with disruption of hydrogen (H-) bond structure and dynamics of water by these cosolvents at bulk region and around various complex units, such as peptide, amino acid, protein, and lipid membrane. However, the disruption of the local structure of the water solvent around a purely hydrophobic solute is still not studied extensively. The latter is also important in the context of stabilization of protein from cold denaturation. Through all-atom molecular dynamics simulation, we have investigated the comparative effect of glycerol and DMSO on the orientational order of water around a nonpolar solute at -5 °C. A steady reduction of the tetrahedral order of water is observed at bulk (>10 Å distance from the solute) and solute interface (<5.5 Å distance from the solute) with increasing the cosolvent concentration. Contrasting roles of glycerol and DMSO have been evidenced. While DMSO affects the H-bond structure of the interfacial water more than that of the bulk water, glycerol affects the water structure almost uniformly at all regions around the solute. Furthermore, while glycerol helps to retain water molecules at the interface, DMSO significantly reduces the water content in that region. We have put forward a plausible mechanism for these contrasting roles of these cosolvents. The solute-cosolvent hydrophobic-interaction-induced orientational alignment of an interfacial cosolvent molecule determines whether the involvement of the cosolvent molecules in H-bonding with solvent water in the interface is akin to the bulk region or not.
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26
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Nandi S, Parui S, Halder R, Jana B, Bhattacharyya K. Interaction of proteins with ionic liquid, alcohol and DMSO and in situ generation of gold nano-clusters in a cell. Biophys Rev 2018; 10:757-768. [PMID: 29147940 PMCID: PMC5988615 DOI: 10.1007/s12551-017-0331-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 10/23/2017] [Indexed: 12/27/2022] Open
Abstract
In this review, we give a brief overview on how the interaction of proteins with ionic liquids, alcohols and dimethyl sulfoxide (DMSO) influences the stability, conformational dynamics and function of proteins/enzymes. We present experimental results obtained from fluorescence correlation spectroscopy on the effect of ionic liquid or alcohol or DMSO on the size (more precisely, the diffusion constant) and conformational dynamics of lysozyme, cytochrome c and human serum albumin in aqueous solution. The interaction of ionic liquid with biomolecules (e.g. protein, DNA etc.) has emerged as a current frontier. We demonstrate that ionic liquids are excellent stabilizers of protein and DNA and, in some cases, cause refolding of a protein already denatured by chemical denaturing agents. We show that in ethanol-water binary mixture, proteins undergo non-monotonic changes in size and dynamics with increasing ethanol content. We also discuss the effect of water-DMSO mixture on the stability of proteins. We demonstrate how large-scale molecular dynamics simulations have revealed the molecular origin of this observed phenomenon and provide a microscopic picture of the immediate environment of the biomolecules. Finally, we describe how favorable interactions of ionic liquids may be utilized for in situ generation of fluorescent gold nano-clusters for imaging a live cell.
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Affiliation(s)
- Somen Nandi
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Sridip Parui
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Ritaban Halder
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India.
| | - Kankan Bhattacharyya
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India.
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462 066, India.
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27
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Alavi Z, Zocchi G. Dissipation at the angstrom scale: Probing the surface and interior of an enzyme. Phys Rev E 2018; 97:052402. [PMID: 29906977 DOI: 10.1103/physreve.97.052402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Indexed: 06/08/2023]
Abstract
Pursuing a materials science approach to understanding the deformability of enzymes, we introduce measurements of the phase of the mechanical response function within the nanorheology paradigm. Driven conformational motion of the enzyme is dissipative as characterized by the phase measurements. The dissipation originates both from the surface hydration layer and the interior of the molecule, probed by examining the effect of point mutations on the mechanics. We also document changes in the mechanics of the enzyme examined, guanylate kinase, upon binding its four substrates. GMP binding stiffens the molecule, ATP and ADP binding softens it, while there is no clear mechanical signature of GDP binding. A hyperactive two-Gly mutant is found to possibly trade specificity for speed. Global deformations of enzymes are shown to be dependent on both hydration layer and polypeptide chain dynamics.
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Affiliation(s)
- Zahra Alavi
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California 90095, USA
- Department of Physics and Astronomy, Loyola Marymount University Los Angeles, Los Angeles, California 90095, USA
| | - Giovanni Zocchi
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California 90095, USA
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28
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Kumar V, Prakash A, Lynn AM. Alterations in local stability and dynamics of A4V SOD1 in the presence of trifluoroethanol. Biopolymers 2018; 109:e23102. [DOI: 10.1002/bip.23102] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/26/2017] [Accepted: 01/03/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Vijay Kumar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar; New Delhi 110025 India
| | - Amresh Prakash
- School of Computational and Integrative Sciences; Jawaharlal Nehru University; New Delhi 110067 India
| | - Andrew M. Lynn
- School of Computational and Integrative Sciences; Jawaharlal Nehru University; New Delhi 110067 India
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29
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Sedov IA, Magsumov TI. Molecular dynamics study of unfolding of lysozyme in water and its mixtures with dimethyl sulfoxide. J Mol Graph Model 2017; 76:466-474. [PMID: 28797927 DOI: 10.1016/j.jmgm.2017.07.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/28/2017] [Accepted: 07/30/2017] [Indexed: 11/17/2022]
Abstract
All-atom explicit solvent molecular dynamics was used to study the process of unfolding of hen egg white lysozyme in water and mixtures of water with dimethyl sulfoxide at different compositions. We have determined the kinetic parameters of unfolding at a constant temperature 450K. For each run, the time of disruption of the tertiary structure of lysozyme tu was defined as the moment when a certain structural criterion computed from the trajectory reaches its critical value. A good agreement is observed between the results obtained using several different criteria. The secondary structure according to DSSP calculations is found to be partially unfolded to the moment of disruption of tertiary structure, but some of its elements keep for a long time after that. The values of tu averaged over ten 30ns-long trajectories for each solvent composition are shown to decrease very rapidly with addition of dimethyl sulfoxide, and rather small amounts of dimethyl sulfoxide are found to change the pathway of unfolding. In pure water, despite the loss of tertiary contacts and disruption of secondary structure elements, the protein preserves its compact globular state at least over 130ns of simulation, while even at 5mol percents of dimethyl sulfoxide it loses its compactness within 30ns. The proposed methodology is a generally applicable tool to quantify the rate of protein unfolding in simulation studies.
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Affiliation(s)
- Igor A Sedov
- Chemical Institute, Kazan Federal University, 420008, Kremlevskaya 18, Kazan, Russia.
| | - Timur I Magsumov
- Chemical Institute, Kazan Federal University, 420008, Kremlevskaya 18, Kazan, Russia
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30
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Amin MA, Halder R, Ghosh C, Jana B, Bhattacharyya K. Effect of alcohol on the structure of cytochrome C: FCS and molecular dynamics simulations. J Chem Phys 2017; 145:235102. [PMID: 28010091 DOI: 10.1063/1.4972065] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Effect of ethanol on the size and structure of a protein cytochrome C (Cyt C) is investigated using fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulations. For FCS studies, Cyt C is covalently labeled with a fluorescent probe, alexa 488. FCS studies indicate that on addition of ethanol, the size of the protein varies non-monotonically. The size of Cyt C increases (i.e., the protein unfolds) on addition of alcohol (ethanol) up to a mole fraction of 0.2 (44.75% v/v) and decreases at higher alcohol concentration. In order to provide a molecular origin of this structural transition, we explore the conformational free energy landscape of Cyt C as a function of radius of gyration (Rg) at different compositions of water-ethanol binary mixture using MD simulations. Cyt C exhibits a minimum at Rg ∼ 13 Å in bulk water (0% alcohol). Upon increasing ethanol concentration, a second minimum appears in the free energy surface with gradually larger Rg up to χEtOH ∼ 0.2 (44.75% v/v). This suggests gradual unfolding of the protein. At a higher concentration of alcohol (χEtOH > 0.2), the minimum at large Rg vanishes, indicating compaction. Analysis of the contact map and the solvent organization around protein indicates a preferential solvation of the hydrophobic residues by ethanol up to χEtOH = 0.2 (44.75% v/v) and this causes the gradual unfolding of the protein. At high concentration (χEtOH = 0.3 (58% v/v)), due to structural organization in bulk water-ethanol binary mixture, the extent of preferential solvation by ethanol decreases. This causes a structural transition of Cyt C towards a more compact state.
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Affiliation(s)
- Md Asif Amin
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Ritaban Halder
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Catherine Ghosh
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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31
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GHOSH CATHERINE, ASIF AMIN MD, JANA BIMAN, BHATTACHARYYA KANKAN. Size and Structure of Cytochrome-c bound to Gold nano-clusters: Effect of Ethanol. J CHEM SCI 2017. [DOI: 10.1007/s12039-017-1239-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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32
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Kashid SM, Jin GY, Chakrabarty S, Kim YS, Bagchi S. Two-Dimensional Infrared Spectroscopy Reveals Cosolvent-Composition-Dependent Crossover in Intermolecular Hydrogen-Bond Dynamics. J Phys Chem Lett 2017; 8:1604-1609. [PMID: 28326785 DOI: 10.1021/acs.jpclett.7b00270] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cosolvents have versatile composition-dependent applications in chemistry and biology. The simultaneous presence of hydrophobic and hydrophilic groups in dimethyl sulfoxide (DMSO), an industrially important amphiphilic cosolvent, when combined with the unique properties of water, plays key roles in the diverse fields of pharmacology, cryoprotection, and cell biology. Moreover, molecules dissolved in aqueous DMSO exhibit an anomalous concentration-dependent nonmonotonic behavior in stability and activity near a critical DMSO mole fraction of 0.15. An experimental identification of the origin of this anomaly can lead to newer chemical and biological applications. We report a direct spectroscopic observation of the anomalous behavior using ultrafast two-dimensional infrared spectroscopy experiments. Our results demonstrate the cosolvent-concentration-dependent nonmonotonicity arises from nonidentical mechanisms in ultrafast hydrogen-bond-exchange dynamics of water above and below the critical cosolvent concentration. Comparison of experimental and theoretical results provides a molecular-level mechanistic understanding: a distinct difference in the stabilization of the solute through dynamic solute-solvent interactions is the key to the anomalous behavior.
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Affiliation(s)
- Somnath M Kashid
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Geun Young Jin
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil, Ulsan 44919, Korea
| | - Suman Chakrabarty
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
| | - Yung Sam Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil, Ulsan 44919, Korea
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, India
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33
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Olajuyigbe FM, Fatokun CO. Biochemical characterization of an extremely stable pH-versatile laccase from Sporothrix carnis CPF-05. Int J Biol Macromol 2017; 94:535-543. [DOI: 10.1016/j.ijbiomac.2016.10.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/22/2016] [Accepted: 10/14/2016] [Indexed: 10/20/2022]
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34
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Srivastava KR, Goyal B, Kumar A, Durani S. Scrutiny of electrostatic-driven conformational ordering of polypeptide chains in DMSO: a study with a model oligopeptide. RSC Adv 2017. [DOI: 10.1039/c7ra02137b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The molecular mechanism of DMSO-induced stabilisation of β-sheets is attributed to the combination of polar electrostatic interactions among side chains, and backbone desolvation through bulky side chains which promotes backbone hydrogen bonding.
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Affiliation(s)
| | - Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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35
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Muttathukattil AN, Reddy G. Osmolyte Effects on the Growth of Amyloid Fibrils. J Phys Chem B 2016; 120:10979-10989. [DOI: 10.1021/acs.jpcb.6b09215] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Aswathy N. Muttathukattil
- Solid State and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Govardhan Reddy
- Solid State and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
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36
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Preferential solvation of lysozyme in dimethyl sulfoxide/water binary mixture probed by terahertz spectroscopy. Biophys Chem 2016; 216:31-36. [DOI: 10.1016/j.bpc.2016.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/14/2016] [Accepted: 06/14/2016] [Indexed: 11/21/2022]
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37
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CHAND APRAMITA, CHOWDHURI SNEHASIS. Effects of dimethyl sulfoxide on the hydrogen bonding structure and dynamics of aqueous N-methylacetamide solution. J CHEM SCI 2016. [DOI: 10.1007/s12039-016-1092-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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38
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Indra S, Guchhait B, Biswas R. Structural anomaly and dynamic heterogeneity in cycloether/water binary mixtures: Signatures from composition dependent dynamic fluorescence measurements and computer simulations. J Chem Phys 2016; 144:124506. [DOI: 10.1063/1.4943967] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Sandipa Indra
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700098, India
| | - Biswajit Guchhait
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700098, India
| | - Ranjit Biswas
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700098, India
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39
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40
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Markiewicz BN, Mukherjee D, Troxler T, Gai F. Utility of 5-Cyanotryptophan Fluorescence as a Sensitive Probe of Protein Hydration. J Phys Chem B 2016; 120:936-44. [PMID: 26783936 DOI: 10.1021/acs.jpcb.5b12233] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tryptophan (Trp) fluorescence has been widely used to interrogate the structure, dynamics, and function of proteins. In particular, it provides a convenient and site-specific means to probe a protein's hydration status and dynamics. Herein, we show that a tryptophan analogue, 5-cyanotryptophan (TrpCN), can also be used for this purpose, but with the benefit of enhanced sensitivity to hydration. This conclusion is reached based on measurements of the static and time-resolved fluorescence properties of 5-cyanoindole, TrpCN, and TrpCN-containing peptides in different solvents, which indicate that upon dehydration the fluorescence quantum yield (QY) and lifetime (τF) of TrpCN undergo a much greater change in comparison to those of Trp. For example, in H2O the QY of TrpCN is less than 0.01, which increases to 0.11 in 1,4-dioxane. Consistently, the fluorescence decay kinetics of TrpCN in H2O are dominated by a 0.4 ns component, whereas in 1,4-dioxane the kinetics are dominated by a 6.0 ns component. The versatile utility of TrpCN as a sensitive fluorescence reporter is further demonstrated in three applications, where we used it (1) to probe the solvent property of a binary mixture consisting of dimethyl sulfoxide and H2O, (2) to monitor the binding interaction of an antimicrobial peptide with lipid membranes, and (3) to differentiate two differently hydrated environments in a folded protein.
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Affiliation(s)
- Beatrice N Markiewicz
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Debopreeti Mukherjee
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Thomas Troxler
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Feng Gai
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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41
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Koley S, Ghosh S. A deeper insight into an intriguing acetonitrile–water binary mixture: synergistic effect, dynamic Stokes shift, fluorescence correlation spectroscopy, and NMR studies. Phys Chem Chem Phys 2016; 18:32308-32318. [DOI: 10.1039/c6cp05024g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An insight study reveals the strong synergistic solvation behaviours from reporter dye molecules within the acetonitrile (ACN)–water (WT) binary mixture.
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Affiliation(s)
- Somnath Koley
- School of Chemical Sciences
- National Institute of Science Education and Research
- HBNI
- Bhubaneswar 751005
- India
| | - Subhadip Ghosh
- School of Chemical Sciences
- National Institute of Science Education and Research
- HBNI
- Bhubaneswar 751005
- India
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42
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Ghosh R, Samajdar RN, Bhattacharyya AJ, Bagchi B. Composition dependent multiple structural transformations of myoglobin in aqueous ethanol solution: a combined experimental and theoretical study. J Chem Phys 2015; 143:015103. [PMID: 26156494 DOI: 10.1063/1.4923003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Experimental studies (circular dichroism and ultra-violet (UV) absorption spectra) and large scale atomistic molecular dynamics simulations (accompanied by order parameter analyses) are combined to establish a number of remarkable (and unforeseen) structural transformations of protein myoglobin in aqueous ethanol mixture at various ethanol concentrations. The following results are particularly striking. (1) Two well-defined structural regimes, one at xEtOH ∼ 0.05 and the other at xEtOH ∼ 0.25, characterized by formation of distinct partially folded conformations and separated by a unique partially unfolded intermediate state at xEtOH ∼ 0.15, are identified. (2) Existence of non-monotonic composition dependence of (i) radius of gyration, (ii) long range contact order, (iii) residue specific solvent accessible surface area of tryptophan, and (iv) circular dichroism spectra and UV-absorption peaks are observed. Interestingly at xEtOH ∼ 0.15, time averaged value of the contact order parameter of the protein reaches a minimum, implying that this conformational state can be identified as a molten globule state. Multiple structural transformations well known in water-ethanol binary mixture appear to have considerably stronger effects on conformation and dynamics of the protein. We compare the present results with studies in water-dimethyl sulfoxide mixture where also distinct structural transformations are observed along with variation of co-solvent composition.
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Affiliation(s)
- R Ghosh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - R N Samajdar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - B Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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43
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Ghosh S, Parui S, Jana B, Bhattacharyya K. Ionic liquid induced dehydration and domain closure in lysozyme: FCS and MD simulation. J Chem Phys 2015; 143:125103. [DOI: 10.1063/1.4931974] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Shirsendu Ghosh
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Sridip Parui
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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44
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Banik D, Roy A, Kundu N, Sarkar N. Picosecond Solvation and Rotational Dynamics: An Attempt to Reinvestigate the Mystery of Alcohol–Water Binary Mixtures. J Phys Chem B 2015; 119:9905-19. [PMID: 26121323 DOI: 10.1021/acs.jpcb.5b04931] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Debasis Banik
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, West Bengal, India
| | - Arpita Roy
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, West Bengal, India
| | - Niloy Kundu
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, West Bengal, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, West Bengal, India
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45
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Solvent sorting in (mixed solvent + electrolyte) systems: Time-resolved fluorescence measurements and theory. J CHEM SCI 2015. [DOI: 10.1007/s12039-014-0750-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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46
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Banik D, Kundu N, Kuchlyan J, Roy A, Banerjee C, Ghosh S, Sarkar N. Picosecond solvation dynamics—A potential viewer of DMSO—Water binary mixtures. J Chem Phys 2015; 142:054505. [DOI: 10.1063/1.4906541] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Debasis Banik
- Department of Chemistry, Indian Institute of Technology, Kharagpur, WB 721302, India
| | - Niloy Kundu
- Department of Chemistry, Indian Institute of Technology, Kharagpur, WB 721302, India
| | - Jagannath Kuchlyan
- Department of Chemistry, Indian Institute of Technology, Kharagpur, WB 721302, India
| | - Arpita Roy
- Department of Chemistry, Indian Institute of Technology, Kharagpur, WB 721302, India
| | - Chiranjib Banerjee
- Department of Chemistry, Indian Institute of Technology, Kharagpur, WB 721302, India
| | - Surajit Ghosh
- Department of Chemistry, Indian Institute of Technology, Kharagpur, WB 721302, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur, WB 721302, India
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47
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Ghosh S, Ghosh C, Nandi S, Bhattacharyya K. Unfolding and refolding of a protein by cholesterol and cyclodextrin: a single molecule study. Phys Chem Chem Phys 2015; 17:8017-27. [DOI: 10.1039/c5cp00385g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cholesterol induced unfolding of a globular protein, human serum albumin (HSA), and β-cyclodextrin induced refolding of the unfolded protein is demonstrated in this study.
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Affiliation(s)
- Shirsendu Ghosh
- Department of Physical Chemistry
- Indian Association For The cultivation of Science
- Kolkata 700 032
- India
| | - Catherine Ghosh
- Department of Physical Chemistry
- Indian Association For The cultivation of Science
- Kolkata 700 032
- India
| | - Somen Nandi
- Department of Physical Chemistry
- Indian Association For The cultivation of Science
- Kolkata 700 032
- India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry
- Indian Association For The cultivation of Science
- Kolkata 700 032
- India
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48
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Ghosh R, Roy S, Bagchi B. Multidimensional free energy surface of unfolding of HP-36: Microscopic origin of ruggedness. J Chem Phys 2014; 141:135101. [DOI: 10.1063/1.4896762] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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49
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Koley S, Kaur H, Ghosh S. Probe dependent anomalies in the solvation dynamics of coumarin dyes in dimethyl sulfoxide–glycerol binary solvent: confirming the local environments are different for coumarin dyes. Phys Chem Chem Phys 2014; 16:22352-63. [DOI: 10.1039/c4cp03525a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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50
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Chattoraj S, Mandal AK, Bhattacharyya K. Effect of ethanol-water mixture on the structure and dynamics of lysozyme: A fluorescence correlation spectroscopy study. J Chem Phys 2014; 140:115105. [DOI: 10.1063/1.4868642] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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