1
|
Reiser PJ, Belevych N, Shope L, Hanaoka B. Methanol gel electrophoresis: Separation of human fast and slow myosin light chain 1 and other myofibrillar protein isoforms on a single gel format. Electrophoresis 2024. [PMID: 38785173 DOI: 10.1002/elps.202400004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
This report describes a novel sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) resolving gel format that consistently yields the electrophoretic separation of the fast and slow isoforms of human sarcomeric myosin light chain 1 (MLC1). The inclusion of methanol as a constituent of the resolving gel impacted the electrophoretic mobility of proteins across a broad range of molecular masses. There was greater separation of the fast and slow isoforms of human MLC1, as well as separation and high resolution of fast and slow isoforms of the three myosin heavy chain isoforms that are expressed in human skeletal muscle on the same gel format. Furthermore, the same resolving gel format substantially altered the electrophoretic mobility of at least one isoform of tropomyosin in human striated muscle. It is possible that the inclusion of methanol in SDS-PAGE resolving gels could improve the separation of other proteins that are expressed in muscle and in other tissues and cell types.
Collapse
Affiliation(s)
- Peter J Reiser
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, Ohio, USA
| | - Natalya Belevych
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, Ohio, USA
| | - Logan Shope
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, Ohio, USA
| | - Beatriz Hanaoka
- Division of Rheumatology and Immunology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
2
|
Ghanta KP, Mondal S, Hajari T, Bandyopadhyay S. Impact of an Ionic Liquid on Amino Acid Side Chains: A Perspective from Molecular Simulation Studies. J Chem Inf Model 2023; 63:959-972. [PMID: 36721873 DOI: 10.1021/acs.jcim.2c01310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ionic liquids (ILs) are known to modify the structural stability of proteins. The modification of the protein conformation is associated with the accumulation of ILs around the amino acid (AA) side chains and the nature of interactions between them. To understand the microscopic picture of the structural arrangements of ILs around the AA side chains, room temperature molecular dynamics (MD) simulations have been carried out in this work with a series of hydrophobic, polar and charged AAs in aqueous solutions containing the IL 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) at 2 M concentration. The calculations revealed distinctly nonuniform distribution of the IL components around different AAs. In particular, it is demonstrated that the BMIM+ cations preferentially interact with the aromatic AAs through favorable stacking interactions between the cation imidazolium head groups and the aromatic AA side chains. This results in preferential parallel alignments and enhanced population of the cations around the aromatic AAs. The potential of mean force (PMF) calculations revealed that such favorable stacking interactions provide greater stability to the contact pairs (CPs) formed between the aromatic AAs and the IL cations as compared to the other AAs. It is further quantified that for most of the AAs (except the cationic ones), a favorable enthalpy contribution more than compensates for the entropy cost to form stable CPs with the IL cations. These findings are likely to provide valuable fundamental information toward understanding the effects of ILs on protein conformational stability.
Collapse
Affiliation(s)
- Krishna Prasad Ghanta
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur721302, India
| | - Souvik Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur721302, India
| | - Timir Hajari
- Department of Chemistry, City College, Kolkata700009, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur721302, India
| |
Collapse
|
3
|
Wakayama K, Kimura S, Kobatake Y, Kamishina H, Nishii N, Takashima S, Honda R, Kamatari YO. Molecular Mechanisms of Aggregation of Canine SOD1 E40K Amyloidogenic Mutant Protein. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010156. [PMID: 36615350 PMCID: PMC9822309 DOI: 10.3390/molecules28010156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022]
Abstract
Canine degenerative myelopathy (DM) is a human amyotrophic lateral sclerosis (ALS)-like neurodegenerative disease. It is a unique, naturally occurring animal model of human ALS. Canine DM is associated with the aggregation of canine superoxide dismutase 1 (cSOD1), which is similar to human ALS. Almost 100% of cases in dogs are familial, and the E40K mutation in cSOD1 is a major causative mutation of DM. Therefore, it is important to understand the molecular mechanisms underlying cSOD1(E40K) aggregation. To address this, we first analyzed the structural model of wild type cSOD1. Interactions were evident between amino acid E40 and K91. Therefore, the mutation at residue E40 causes loss of the interaction and may destabilize the native structure of cSOD1. Differential scanning fluorimetry revealed that the E40K mutant was less stable than the wild type. Moreover, stability could be recovered by the E40K and K91E double mutation. Acceleration of amyloid fibril formation in vitro and aggregate formation in cells of cSOD1(E40K) was also suppressed by the introduction of this double mutation in thioflavin T fluorescence assay results and in transfectant cells, respectively. These results clearly show the importance of the interaction between amino acid residues E40 and K91 in cSOD1 for the stability of the native structure and aggregation.
Collapse
Affiliation(s)
- Kento Wakayama
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Shintaro Kimura
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Yui Kobatake
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Hiroaki Kamishina
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Kyoto AR, 33 Sayama-Nakamichi, Kumiyama, Kuze, Kyoto 613-0036, Japan
| | - Naohito Nishii
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Satoshi Takashima
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Ryo Honda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yuji O. Kamatari
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Institute for Glyco-Core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Correspondence: ; Tel.: +81-58-293-3900
| |
Collapse
|
4
|
Borotto NB, Richards TK. Rapid Online Oxidation of Proteins and Peptides via Electrospray-Accelerated Ozonation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2078-2086. [PMID: 36194498 DOI: 10.1021/jasms.2c00182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Mass spectrometry-based analyses of protein conformation continue to grow in utilization due their speed, low sample requirements, and applicability to most protein systems. These techniques typically rely on chemical derivatization of proteins and as with all label-based analyses must ensure the integrity of the protein conformation throughout the duration of the labeling reaction. Hydroxyl radical footprinting of proteins and the recently developed fast fluoroalkylation of proteins attempt to bypass this consideration via rapid reactions that occur on time scales faster than protein folding, but they often require microfluidic setups or electromagnetic radiation sources. In this work, we demonstrate that ozonation of proteins and peptides, which normally occurs in the second to minute time scales, can be accelerated to the submillisecond to millisecond time scale with an electrospray ionization source. This rapid ozonation results in selective labeling of tryptophan and methionine residues. When applied to cytochrome C and carbonic anhydrase, this labeling technique is sensitive to solution conditions and correlates with solution-phase analyses of conformation. While significant work is still needed to characterize this fast chemical labeling strategy, it requires no complicated sample handling, electromagnetic radiation sources, or microfluidic systems outside of the electrospray source and may represent a facile alternative to other rapid labeling technologies that are utilized today.
Collapse
Affiliation(s)
- Nicholas B Borotto
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | | |
Collapse
|
5
|
Olawale F, Ogunyemi O, Folorunso IM. Repurposing clinically approved drugs as Wee1 checkpoint kinase inhibitors: an in silico investigation integrating molecular docking, ensemble QSAR modelling and molecular dynamics simulation. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2101673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Femi Olawale
- Nano-Gene and Drug Delivery Group, Department of Biochemistry, School of life science, University of KwaZulu Natal, Durban, South Africa
| | - Oludare Ogunyemi
- Human Nutraceuticals and Bioinformatics Research Unit, Department of Biochemistry, Salem University, Lokoja, Nigeria
| | - Ibukun Mary Folorunso
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology Akure, Akure, Nigeria
| |
Collapse
|
6
|
Denda M, Otaka A. Advances in Preparation of Peptide and Protein Thioesters Aiming to Use in Medicinal Sciences. Chem Pharm Bull (Tokyo) 2022; 70:316-323. [DOI: 10.1248/cpb.c21-01019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Masaya Denda
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Akira Otaka
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| |
Collapse
|
7
|
Korotkova PD, Yurchenko AA, Timofeev VI, Gusel’nikova AR, Vladimirov GK, Shumm AB, Vladimirov YA. Early Stage of Structural Changes and Molecular Dynamics of Cytochrome C in an Aqueous Solution Caused by the Addition of Methanol. CRYSTALLOGR REP+ 2022. [DOI: 10.1134/s1063774522020079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
8
|
Li J, Yang Z, Lin X, Wu S, Li G, Li N, Otter D, Zhu F, Hartinger C, Corke H, Hemar Y. In-flow SAXS investigation of whey protein isolate hydrolyzed by bromelain. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2021.127662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
9
|
Quanten T, De Mayaer T, Shestakova P, Parac-Vogt TN. Selectivity and Reactivity of Zr IV and Ce IV Substituted Keggin Type Polyoxometalates Toward Cytochrome c in Surfactant Solutions. Front Chem 2018; 6:372. [PMID: 30211153 PMCID: PMC6121075 DOI: 10.3389/fchem.2018.00372] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/02/2018] [Indexed: 12/15/2022] Open
Abstract
In this paper we investigate the effect of three different types of surfactants, on the hydrolysis of Cytochrome c (Cyt c), a predominantly α helical protein containing a heme group, promoted by [Ce(α PW11O39)2]10- (CeK) and [Zr(α PW11O39)2]10- (ZrK) polyoxometalates. In the presence of SDS, Zw3 12, or CHAPS surfactants, which are commonly used for solubilizing hydrophobic proteins, the specificity of CeK or ZrK toward hydrolysis of Cyt c does not change. However, the hydrolysis rate of Cyt c by CeK was increased in the presence of SDS, but decreased in the presence of CHAPS, and was nearly inhibited in the presence of Zw3 12. The Circular dichroism and Tryptophan fluorescence spectroscopy have shown that the structural changes in Cyt c caused by surfactants are similar to those caused by POMs, hence the same specificity in the absence or presence of surfactants was observed. The results also indicate that for Cyt c hydrolysis to occur, large unfolding of the protein is needed in order to accommodate the POMs. While SDS readily unfolds Cyt c, the protein remains largely folded in the presence of CHAPS and Zw3 12. Addition of POMs to Cyt c solutions in CHAPS results in unfolding of the structure allowing the interaction with POMs to occur and results in protein hydrolysis. Zw3 12, however, locks Cyt c in a conformation that resists unfolding upon addition of POM, and therefore results in nearly complete inhibition of protein hydrolysis.
Collapse
Affiliation(s)
- Thomas Quanten
- Laboratory of Bio-Inorganic Chemistry, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Tessa De Mayaer
- Laboratory of Bio-Inorganic Chemistry, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Pavletta Shestakova
- NMR Centre, Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Tatjana N Parac-Vogt
- Laboratory of Bio-Inorganic Chemistry, Department of Chemistry, KU Leuven, Leuven, Belgium
| |
Collapse
|
10
|
Dahanayake JN, Mitchell-Koch KR. How Does Solvation Layer Mobility Affect Protein Structural Dynamics? Front Mol Biosci 2018; 5:65. [PMID: 30057902 PMCID: PMC6053501 DOI: 10.3389/fmolb.2018.00065] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/20/2018] [Indexed: 11/18/2022] Open
Abstract
Solvation is critical for protein structural dynamics. Spectroscopic studies have indicated relationships between protein and solvent dynamics, and rates of gas binding to heme proteins in aqueous solution were previously observed to depend inversely on solution viscosity. In this work, the solvent-compatible enzyme Candida antarctica lipase B, which functions in aqueous and organic solvents, was modeled using molecular dynamics simulations. Data was obtained for the enzyme in acetonitrile, cyclohexane, n-butanol, and tert-butanol, in addition to water. Protein dynamics and solvation shell dynamics are characterized regionally: for each α-helix, β-sheet, and loop or connector region. Correlations are seen between solvent mobility and protein flexibility. So, does local viscosity explain the relationship between protein structural dynamics and solvation layer dynamics? Halle and Davidovic presented a cogent analysis of data describing the global hydrodynamics of a protein (tumbling in solution) that fits a model in which the protein's interfacial viscosity is higher than that of bulk water's, due to retarded water dynamics in the hydration layer (measured in NMR τ2 reorientation times). Numerous experiments have shown coupling between protein and solvation layer dynamics in site-specific measurements. Our data provides spatially-resolved characterization of solvent shell dynamics, showing correlations between regional solvation layer dynamics and protein dynamics in both aqueous and organic solvents. Correlations between protein flexibility and inverse solvent viscosity (1/η) are considered across several protein regions and for a rather disparate collection of solvents. It is seen that the correlation is consistently higher when local solvent shell dynamics are considered, rather than bulk viscosity. Protein flexibility is seen to correlate best with either the local interfacial viscosity or the ratio of the mobility of an organic solvent in a regional solvation layer relative to hydration dynamics around the same region. Results provide insight into the function of aqueous proteins, while also suggesting a framework for interpreting and predicting enzyme structural dynamics in non-aqueous solvents, based on the mobility of solvents within the solvation layer. We suggest that Kramers' theory may be used in future work to model protein conformational transitions in different solvents by incorporating local viscosity effects.
Collapse
|
11
|
Hayashi T, Yasuda S, Škrbić T, Giacometti A, Kinoshita M. Unraveling protein folding mechanism by analyzing the hierarchy of models with increasing level of detail. J Chem Phys 2017; 147:125102. [DOI: 10.1063/1.4999376] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Satoshi Yasuda
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Tatjana Škrbić
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Edificio Alfa Campus Scientifico, Via Torino 155, Venezia-Mestre I-3010, Italy
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Edificio Alfa Campus Scientifico, Via Torino 155, Venezia-Mestre I-3010, Italy
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| |
Collapse
|
12
|
Correlating the Effects of Antimicrobial Preservatives on Conformational Stability, Aggregation Propensity, and Backbone Flexibility of an IgG1 mAb. J Pharm Sci 2017; 106:1508-1518. [DOI: 10.1016/j.xphs.2017.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/02/2017] [Accepted: 02/06/2017] [Indexed: 11/23/2022]
|
13
|
Nakamura S, Saotome T, Nakazawa A, Fukuda M, Kuroda Y, Kidokoro SI. Thermodynamics of the Thermal Denaturation of Acid Molten Globule State of Cytochrome c Indicate a Reversible High-Temperature Oligomerization Process. Biochemistry 2017; 56:2372-2378. [DOI: 10.1021/acs.biochem.6b01225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shigeyoshi Nakamura
- Department
of General Education, National Institute of Technology, Ube College, 2-14-1 Tokiwadai, Ube 755-8555, Japan
- Department
of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka 940-2188, Japan
| | - Tomonori Saotome
- Department
of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-15 Nakamachi, Koganei 184-8588, Japan
| | - Akiko Nakazawa
- Department
of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka 940-2188, Japan
| | - Masao Fukuda
- Department
of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka 940-2188, Japan
| | - Yutaka Kuroda
- Department
of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-15 Nakamachi, Koganei 184-8588, Japan
| | - Shun-ichi Kidokoro
- Department
of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka 940-2188, Japan
| |
Collapse
|
14
|
Murakami S, Kinoshita M. Effects of monohydric alcohols and polyols on the thermal stability of a protein. J Chem Phys 2016; 144:125105. [PMID: 27036482 DOI: 10.1063/1.4944680] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The thermal stability of a protein is lowered by the addition of a monohydric alcohol, and this effect becomes larger as the size of hydrophobic group in an alcohol molecule increases. By contrast, it is enhanced by the addition of a polyol possessing two or more hydroxyl groups per molecule, and this effect becomes larger as the number of hydroxyl groups increases. Here, we show that all of these experimental observations can be reproduced even in a quantitative sense by rigid-body models focused on the entropic effect originating from the translational displacement of solvent molecules. The solvent is either pure water or water-cosolvent solution. Three monohydric alcohols and five polyols are considered as cosolvents. In the rigid-body models, a protein is a fused hard spheres accounting for the polyatomic structure in the atomic detail, and the solvent is formed by hard spheres or a binary mixture of hard spheres with different diameters. The effective diameter of cosolvent molecules and the packing fractions of water and cosolvent, which are crucially important parameters, are carefully estimated using the experimental data of properties such as the density of solid crystal of cosolvent, parameters in the pertinent cosolvent-cosolvent interaction potential, and density of water-cosolvent solution. We employ the morphometric approach combined with the integral equation theory, which is best suited to the physical interpretation of the calculation result. It is argued that the degree of solvent crowding in the bulk is the key factor. When it is made more serious by the cosolvent addition, the solvent-entropy gain upon protein folding is magnified, leading to the enhanced thermal stability. When it is made less serious, the opposite is true. The mechanism of the effects of monohydric alcohols and polyols is physically the same as that of sugars. However, when the rigid-body models are employed for the effect of urea, its addition is predicted to enhance the thermal stability, which conflicts with the experimental fact. We then propose, as two essential factors, not only the solvent-entropy gain but also the loss of protein-solvent interaction energy upon protein folding. The competition of changes in these two factors induced by the cosolvent addition determines the thermal-stability change.
Collapse
Affiliation(s)
- Shota Murakami
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| |
Collapse
|
15
|
Dahanayake JN, Gautam DN, Verma R, Mitchell-Koch KR. To Keep or Not to Keep? The Question of Crystallographic Waters for Enzyme Simulations in Organic Solvent. MOLECULAR SIMULATION 2016; 42:1001-1013. [PMID: 27403032 DOI: 10.1080/08927022.2016.1139108] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The use of enzymes in non-aqueous solvents expands the use of biocatalysts to hydrophobic substrates, with the ability to tune selectivity of reactions through solvent selection. Non-aqueous enzymology also allows for fundamental studies on the role of water and other solvents in enzyme structure, dynamics, and function. Molecular dynamics simulations serve as a powerful tool in this area, providing detailed atomic information about the effect of solvents on enzyme properties. However, a common protocol for non-aqueous enzyme simulations does not exist. If you want to simulate enzymes in non-aqueous solutions, how many and which crystallographic waters do you keep? In the present work, this question is addressed by determining which crystallographic water molecules lead most quickly to an equilibrated protein structure. Five different methods of selecting and keeping crystallographic waters are used in order to discover which crystallographic waters lead the protein structure to reach an equilibrated structure more rapidly in organic solutions. It is found that buried waters contribute most to rapid equilibration in organic solvent, with slow-diffusing waters giving similar results.
Collapse
Affiliation(s)
- Jayangika N Dahanayake
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States
| | - Devaki N Gautam
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States
| | - Rajni Verma
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States
| | - Katie R Mitchell-Koch
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States
| |
Collapse
|
16
|
Meyer NA, Root K, Zenobi R, Vidal-de-Miguel G. Gas-Phase Dopant-Induced Conformational Changes Monitored with Transversal Modulation Ion Mobility Spectrometry. Anal Chem 2016; 88:2033-40. [PMID: 26845079 DOI: 10.1021/acs.analchem.5b02750] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The potential of a Transversal Modulation Ion Mobility Spectrometry (TMIMS) instrument for protein analysis applications has been evaluated. The Collision Cross Section (CCS) of cytochrome c measured with the TMIMS is in agreement with values reported in the literature. Additionally, it enables tandem IMS-IMS prefiltration in dry gas and in vapor doped gas. The chemical specificity of the different dopants enables interesting studies on the structure of proteins as CCS changed strongly depending on the specific dopant. Hexane produced an unexpectedly high CCS shift, which can be utilized to evaluate the exposure of hydrophobic parts of the protein. Alcohols produced higher shifts with a dual behavior: an increase in CCS due to vapor uptake at specific absorption sites, followed by a linear shift typical for unspecific and unstable vapor uptake. The molten globule +8 shows a very specific transition. Initially, its CCS follows the trend of the compact folded states, and then it rapidly increases to the levels of the unfolded states. This strong variation suggests that the +8 charge state undergoes a dopant-induced conformational change. Interestingly, more sterically demanding alcohols seem to unfold the protein more effectively also in the gas phase. This study shows the capabilities of the TMIMS device for protein analysis and how tandem IMS-IMS with dopants could provide better understanding of the conformational changes of proteins.
Collapse
Affiliation(s)
- Nicole Andrea Meyer
- Department of Chemistry and Applied Biosciences, ETH Zurich , CH-8093, Zurich, Switzerland
| | - Katharina Root
- Department of Chemistry and Applied Biosciences, ETH Zurich , CH-8093, Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich , CH-8093, Zurich, Switzerland
| | - Guillermo Vidal-de-Miguel
- Department of Chemistry and Applied Biosciences, ETH Zurich , CH-8093, Zurich, Switzerland.,Fossil Ion Technology (FIT) , Cipreses 18, 28036, Madrid, Spain
| |
Collapse
|
17
|
Parravicini F, Brocca S, Lotti M. Evaluation of the Conformational Stability of Recombinant Desulfurizing Enzymes from a Newly Isolated Rhodococcus sp. Mol Biotechnol 2015; 58:1-11. [PMID: 26515071 DOI: 10.1007/s12033-015-9897-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metabolic pathways of aerobic bacteria able to assimilate sulfur can provide biocatalysts for biodesulfurization of petroleum and of other sulfur-containing pollutants. Of major interest is the so-called "4S pathway," in that C-S bonds are specifically cleaved leaving the carbon skeleton of substrates intact. This pathway is carried out by four enzymes, named Dsz A, B, C, and D. In view of a possible application of recombinant Dsz enzymes in biodesulfurization treatments, we have investigated the structural features of enzymes cloned from a Rhodococcus strain isolated from polluted environmental samples and their resistance to temperature (20-95 °C) and to organic solvents (5, 10, and 20 % v/v methanol, acetonitrile, hexane, and toluene). Changes in protein structures were assessed by circular dichroism and intrinsic fluorescence spectroscopy. We found that all Dsz proteins are unfolded by temperatures in the range 45-60 °C and by all solvents tested, with the most dramatic effect being produced by toluene. These results suggest that stabilization of the biocatalysts by protein engineering will be necessary for developing biodesulfurization technologies based on Dsz enzymes.
Collapse
Affiliation(s)
- Federica Parravicini
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
| |
Collapse
|
18
|
Gong X, Xiong X, Wang S, Li Y, Zhang S, Fang X, Zhang X. Desalting by crystallization: detection of attomole biomolecules in picoliter buffers by mass spectrometry. Anal Chem 2015; 87:9745-51. [PMID: 26312607 DOI: 10.1021/acs.analchem.5b01877] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Sensitive detection of biomolecules in small-volume samples by mass spectrometry is, in many cases, challenging because of the use of buffers to maintain the biological activities of proteins and cells. Here, we report a highly effective desalting method for picoliter samples. It was based on the spontaneous separation of biomolecules from salts during crystallization of the salts. After desalting, the biomolecules were deposited in the tip of the quartz pipet because of the evaporation of the solvent. Subsequent detection of the separated biomolecules was achieved using solvent assisted electric field induced desorption/ionization (SAEFIDI) coupled with mass spectrometry. It allowed for direct desorption/ionization of the biomolecules in situ from the tip of the pipet. The organic component in the assistant solvent inhibited the desorption/ionization of salts, thus assured successful detection of biomolecules. Proteins and peptides down to 50 amol were successfully detected using our method even if there were 3 × 10(5) folds more amount of salts in the sample. The concentration and ion species of the salts had little influence on the detection results.
Collapse
Affiliation(s)
- Xiaoyun Gong
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University , Beijing 100084, China.,National Institute of Metrology , Beijing 100013, China
| | | | - Song Wang
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Yanyan Li
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Sichun Zhang
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Xiang Fang
- National Institute of Metrology , Beijing 100013, China
| | - Xinrong Zhang
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University , Beijing 100084, China
| |
Collapse
|
19
|
DeMuth JC, McLuckey SA. Electrospray Droplet Exposure to Organic Vapors: Metal Ion Removal from Proteins and Protein Complexes. Anal Chem 2014; 87:1210-8. [PMID: 25517019 DOI: 10.1021/ac503865v] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- J. Corinne DeMuth
- Department of Chemistry Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Scott A. McLuckey
- Department of Chemistry Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| |
Collapse
|
20
|
Giuliani A, Milosavljević AR, Canon F, Nahon L. Contribution of synchrotron radiation to photoactivation studies of biomolecular ions in the gas phase. MASS SPECTROMETRY REVIEWS 2014; 33:424-441. [PMID: 24375654 DOI: 10.1002/mas.21398] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Photon activation of ions in the visible and ultraviolet range attracts a growing interest, partly for its promising applications in tandem mass spectrometry. However, this task is not trivial, as it requires notably high brilliance photon sources. Hence, most of the work in that field has been performed using lasers. Synchrotron radiation is a source continuously tunable over a wide photon energy range and which possesses the necessary characteristics for ion activation. This review focuses on the array of applications of synchrotron radiation in photon activation of ions ranging from near UV to soft X-rays.
Collapse
Affiliation(s)
- Alexandre Giuliani
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, 91192, Gif-sur-Yvette, France; UAR1008 CEPIA, INRA, 44316, Nantes, France
| | | | | | | |
Collapse
|
21
|
Deshpande MS, Parui PP, Kamikubo H, Yamanaka M, Nagao S, Komori H, Kataoka M, Higuchi Y, Hirota S. Formation of Domain-Swapped Oligomer of Cytochrome c from Its Molten Globule State Oligomer. Biochemistry 2014; 53:4696-703. [DOI: 10.1021/bi500497s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Megha Subhash Deshpande
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Partha Pratim Parui
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Department
of Chemistry, Jadavpur University, Kolkata 700032, India
| | - Hironari Kamikubo
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Masaru Yamanaka
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Satoshi Nagao
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hirofumi Komori
- Faculty
of Education, Kagawa University, 1-1 Saiwai, Takamatsu, Kagawa 760-8522, Japan
| | - Mikio Kataoka
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yoshiki Higuchi
- Department
of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1
Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shun Hirota
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| |
Collapse
|
22
|
Trifluorosilane induced structural transitions in beta-lactoglobulin in sol and gel. Colloids Surf B Biointerfaces 2014; 119:6-13. [DOI: 10.1016/j.colsurfb.2014.04.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 04/21/2014] [Accepted: 04/22/2014] [Indexed: 11/17/2022]
|
23
|
Shao Q. Methanol Concentration Dependent Protein Denaturing Ability of Guanidinium/Methanol Mixed Solution. J Phys Chem B 2014; 118:6175-85. [DOI: 10.1021/jp500280v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Qiang Shao
- Drug Discovery and Design
Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| |
Collapse
|
24
|
Sashi P, Yasin UM, Balasubramanian H, Sree MU, Ramakrishna D, Bhuyan AK. Preferential water exclusion in protein unfolding. J Phys Chem B 2014; 118:717-23. [PMID: 24354363 DOI: 10.1021/jp4111103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Association of water with protein plays a central role in the latter's folding, structure acquisition, ligand binding, catalytic reactivity, oligomerization, and crystallization. Because these phenomena are also influenced by the net charge content on the protein, the present study examines the association of water with cytochrome c held at different pH values so as to allow its side chains to ionize to variable extents. Equilibrium unfolding of differently charged cytochrome c molecules in water-methanol binary mixtures, where the alcohol acts as the cosolvent denaturant, was used to quantify the preferential exclusion of water during the unfolding transition. The extent of exclusion was found to be related to the net-charge-dependent molecular expansion of the protein in an alcohol-free aqueous medium. The degree of water exclusion was also found to be linearly related to the observed rate of protein unfolding, where the net charge contents of the initial and final states are the same. The results suggest that side-chain ionization, molecular expansion due to charge repulsion, and hence the loss of tertiary contacts lead to additional water-protein association. Protein unfolding rates appear to be linearly correlated with the effective number of water molecules excluded across the end states of unfolding equilibria.
Collapse
Affiliation(s)
- Pulikallu Sashi
- School of Chemistry University of Hyderabad , Hyderabad 500 046, India
| | | | | | | | | | | |
Collapse
|
25
|
Cosolvents Induced Unfolding and Aggregation of Keyhole Limpet Hemocyanin. Cell Biochem Biophys 2013; 69:103-13. [DOI: 10.1007/s12013-013-9776-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
26
|
Yasin UM, Sashi P, Bhuyan AK. Expansion and Internal Friction in Unfolded Protein Chain. J Phys Chem B 2013; 117:12059-64. [DOI: 10.1021/jp408718c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- U. Mahammad Yasin
- School of Chemistry, University of Hyderabad, Hyderabad 500
046, India
| | - Pulikallu Sashi
- School of Chemistry, University of Hyderabad, Hyderabad 500
046, India
| | - Abani K. Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500
046, India
| |
Collapse
|
27
|
Shiu YJ, Su C, Yeh YL, Liang KK, Hayashi M, Mo Y, Yan Y, Lin SH. Experimental and Theoretical Studies of Protein Folding-Unfolding. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200400172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
28
|
Zaroog MS, Tayyab S. Halogenol- versus alkanol-induced structural transitions of acid-denatured glucoamylase: Characterization of alcohol-induced states. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
29
|
Yasuda S, Oshima H, Kinoshita M. Structural stability of proteins in aqueous and nonpolar environments. J Chem Phys 2013; 137:135103. [PMID: 23039615 DOI: 10.1063/1.4755755] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A protein folds into its native structure with the α-helix and∕or β-sheet in aqueous solution under the physiological condition. The relative content of these secondary structures largely varies from protein to protein. However, such structural variability is not exhibited in nonaqueous environment. For example, there is a strong trend that alcohol induces a protein to form α-helices, and many of the membrane proteins within the lipid bilayer consists of α-helices. Here we investigate the structural stability of proteins in aqueous and nonpolar environments using our recently developed free-energy function F = (Λ - TS)∕(k(B)T(0)) = Λ∕(k(B)T(0)) - S∕k(B) (T(0) = 298 K and the absolute temperature T is set at T(0)) which is based on statistical thermodynamics. Λ∕(k(B)T(0)) and S∕k(B) are the energetic and entropic components, respectively, and k(B) is Boltzmann's constant. A smaller value of the positive quantity, -S, represents higher efficiency of the backbone and side-chain packing promoted by the entropic effect arising from the translational displacement of solvent molecules or the CH(2), CH(3), and CH groups which constitute nonpolar chains of lipid molecules. As for Λ, in aqueous solution, a transition to a more compact structure of a protein accompanies the break of protein-solvent hydrogen bonds: As the number of donors and acceptors buried without protein intramolecular hydrogen bonding increases, Λ becomes higher. In nonpolar solvent, lower Λ simply implies more intramolecular hydrogen bonds formed. We find the following. The α-helix and β-sheet are advantageous with respect to -S as well as Λ and to be formed as much as possible. In aqueous solution, the solvent-entropy effect on the structural stability is so strong that the close packing of side chains is dominantly important, and the α-helix and β-sheet contents are judiciously adjusted to accomplish it. In nonpolar solvent, the solvent-entropy effect is substantially weaker than in aqueous solution. Λ is crucial and the α-helix is more stable than the β-sheet in terms of Λ, which develops a tendency that α-helices are exclusively chosen. For a membrane protein, α-helices are stabilized as fundamental structural units for the same reason, but their arrangement is performed through the entropic effect mentioned above.
Collapse
Affiliation(s)
- Satoshi Yasuda
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | | | | |
Collapse
|
30
|
Moore BN, Hamdy O, Julian RR. Protein structure evolution in liquid DESI as revealed by selective noncovalent adduct protein probing. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2012; 330-332:220-225. [PMID: 23526115 PMCID: PMC3601934 DOI: 10.1016/j.ijms.2012.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Previous experiments based on charge state distributions have suggested that liquid desorption electrospray ionization (DESI) is capable of preserving solution phase protein structure during transfer to the gas phase (Journal of the American Society for Mass Spectrometry 21 (2010) 1730-1736). In order to examine this possibility more carefully, we have utilized selective non-covalent adduct protein probing (SNAPP) to evaluate protein structural evolution in both liquid DESI and standard ESI under a variety of conditions. Experiments with cytochrome c (Cytc) demonstrated that methanol induced conformational shifts previously observed with ESI are also easily observed with liquid DESI. However, undesirable acid-induced unfolding becomes apparent at very high concentrations of methanol in liquid DESI due to acetic acid in the spray solvent, suggesting that there are conditions under which liquid DESI will not preserve solution phase structure. The effects of ammonium acetate buffer on liquid DESI SNAPP experiments were examined by monitoring structural changes in myoglobin. Heme retention and SNAPP distributions were both preserved better in liquid DESI than traditional ESI, suggesting superior performance for liquid DESI in buffered conditions. Finally, liquid DESI SNAPP was used to study the natively disordered proteins α, β, and γ synuclein with SNAPP. α-Synuclein, the main component of fibrils found in patients with Parkinson's disease, yielded a significantly different SNAPP distribution compared to β and γ synuclein. This difference is indicative of highly accessible protonated basic side chains, a property known to promote fibril formation in proteins.
Collapse
Affiliation(s)
| | | | - Ryan R. Julian
- Corresponding author. Tel.: +1 951 827 3958. (R.R. Julian)
| |
Collapse
|
31
|
Acid Denaturation and Refolding of Cytochromecon Silica Surface. J CHIN CHEM SOC-TAIP 2012. [DOI: 10.1002/jccs.201200417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
32
|
Takekiyo T, Yamazaki K, Yamaguchi E, Abe H, Yoshimura Y. High Ionic Liquid Concentration-Induced Structural Change of Protein in Aqueous Solution: A Case Study of Lysozyme. J Phys Chem B 2012; 116:11092-7. [DOI: 10.1021/jp3057064] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takahiro Takekiyo
- Department
of Applied Chemistry, and ‡Department of Materials Science and Engineering, National Defense Academy, 1-10-20, Hashirimizu,
Yokosuka, Japan 239-8686
| | - Kumiko Yamazaki
- Department
of Applied Chemistry, and ‡Department of Materials Science and Engineering, National Defense Academy, 1-10-20, Hashirimizu,
Yokosuka, Japan 239-8686
| | - Erika Yamaguchi
- Department
of Applied Chemistry, and ‡Department of Materials Science and Engineering, National Defense Academy, 1-10-20, Hashirimizu,
Yokosuka, Japan 239-8686
| | - Hiroshi Abe
- Department
of Applied Chemistry, and ‡Department of Materials Science and Engineering, National Defense Academy, 1-10-20, Hashirimizu,
Yokosuka, Japan 239-8686
| | - Yukihiro Yoshimura
- Department
of Applied Chemistry, and ‡Department of Materials Science and Engineering, National Defense Academy, 1-10-20, Hashirimizu,
Yokosuka, Japan 239-8686
| |
Collapse
|
33
|
Hirota S, Ueda M, Hayashi Y, Nagao S, Kamikubo H, Kataoka M. Maintenance of the secondary structure of horse cytochrome c during the conversion process of monomers to oligomers by addition of ethanol. ACTA ACUST UNITED AC 2012; 152:521-9. [DOI: 10.1093/jb/mvs098] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
34
|
Giuliani A, Milosavljević AR, Hinsen K, Canon F, Nicolas C, Réfrégiers M, Nahon L. Structure and Charge-State Dependence of the Gas-Phase Ionization Energy of Proteins. Angew Chem Int Ed Engl 2012; 51:9552-6. [DOI: 10.1002/anie.201204435] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Indexed: 11/09/2022]
|
35
|
Giuliani A, Milosavljević AR, Hinsen K, Canon F, Nicolas C, Réfrégiers M, Nahon L. Structure and Charge-State Dependence of the Gas-Phase Ionization Energy of Proteins. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204435] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
36
|
Sashi P, Yasin UM, Bhuyan AK. Unfolding action of alcohols on a highly negatively charged state of cytochrome C. Biochemistry 2012; 51:3273-83. [PMID: 22439732 DOI: 10.1021/bi201716r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is well-known that hydrophobic effect play a major role in alcohol-protein interactions leading to structure unfolding. Studies with extremely alkaline cytochrome c (U(B) state, pH 13) in the presence of the first four alkyl alcohols suggests that the hydrophobic effect persistently overrides even though the protein carries a net charge of -17 under these conditions. Equilibrium unfolding of the U(B) state is accompanied by an unusual expansion of the chain involving an intermediate, I(alc), from which water is preferentially excluded, the extent of water exclusion being greater with the hydrocarbon content of the alcohol. The mobility and environmental averaging of side chains in the I(alc) state are generally constrained relative to those in the U(B) state. A few nuclear magnetic resonance-detected tertiary interactions are also found in the I(alc) state. The fact that the I(alc) state populates at low concentrations of methanol and ethanol and the fact that the extent of chain expansion in this state approaches that of the U(B) state indicate a definite influence of electrostatic repulsion severed by the low dielectric of the water/alcohol mixture. Interestingly, the U(B) ⇌ I(alc) segment of the U(B) ⇌ I(alc) ⇌ U equilibrium, where U is the unfolded state, accounts for roughly 85% of the total number of water molecules preferentially excluded in unfolding. Stopped-flow refolding results report on a submillisecond hydrophobic collapse during which almost the entire buried surface area associated with the U(B) state is recovered, suggesting the overwhelming influence of hydrophobic interaction over electrostatic repulsions.
Collapse
Affiliation(s)
- Pulikallu Sashi
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
| | | | | |
Collapse
|
37
|
Shao Q, Fan Y, Yang L, Qin Gao Y. From protein denaturant to protectant: Comparative molecular dynamics study of alcohol/protein interactions. J Chem Phys 2012; 136:115101. [DOI: 10.1063/1.3692801] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
38
|
Douglass KA, Venter AR. Investigating the role of adducts in protein supercharging with sulfolane. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:489-497. [PMID: 22219044 DOI: 10.1007/s13361-011-0319-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 12/05/2011] [Accepted: 12/09/2011] [Indexed: 05/31/2023]
Abstract
The supercharging effect of sulfolane on cytochrome c (cyt c) during electrospray ionization mass spectrometry (ESI-MS) in the absence of conformational effects was investigated. The addition of sulfolane on the order of 1 mM or greater to denaturing solutions of cyt c results in supercharging independent of protein concentration over the range of 0.1 to 10 μM. While supercharging was observed in the positive mode, no change in the charge state distribution was observed in the negative mode, ruling out polarity-independent factors such as conformational changes or surface tension effects. A series of sulfolane adducts observed with increasing intensity concurrent with increasing charge state suggests that a direct interaction between sulfolane and the charged sites of cyt c plays an important role in supercharging. We propose that charge delocalization occurring through large-scale dipole reordering of the highly polar supercharging reagent reduces the electrostatic barrier for proximal charging along the cyt c amino acid chain. Supporting this claim, supercharging was shown to increase with increasing dipole moment for several supercharging reagents structurally related to sulfolane.
Collapse
Affiliation(s)
- Kevin Aart Douglass
- Department of Chemistry, Western Michigan University, 1901 W. Michigan Ave., Kalamazoo, MI 49008-5413, USA
| | | |
Collapse
|
39
|
Tao Y, Julian RR. Examining protein surface structure in highly conserved sequence variants with mass spectrometry. Biochemistry 2012; 51:1796-802. [PMID: 22320248 DOI: 10.1021/bi2018199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A simple mass spectrometry-based method capable of examining protein structure called SNAPP (selective noncovalent adduct protein probing) is used to evaluate the structural consequences of point mutations in naturally occurring sequence variants from different species. SNAPP monitors changes in the attachment of noncovalent adducts to proteins as a function of structural state. Mutations that lead to perturbations to the electrostatic surface structure of a protein affect noncovalent attachment and are easily observed with SNAPP. Mutations that do not alter the tertiary structure or electrostatic surface structure yield similar results by SNAPP. For example, bovine, porcine, and human insulin all have very similar backbone structures and no basic or acidic residue mutations, and the SNAPP distributions for all three proteins are very similar. In contrast, four variants of cytochrome c (cytc) have varying degrees of sequence homology, which are reflected in the observed SNAPP distributions. Bovine and pigeon cytc have several basic or acidic residue substitutions relative to horse cytc, but the SNAPP distributions for all three proteins are similar. This suggests that these mutations do not significantly influence the protein surface structure. On the other hand, yeast cytc has the least sequence homology and exhibits a unique, though related, SNAPP distribution. Even greater differences are observed for lysozyme. Hen and human lysozyme have identical tertiary structures but significant variations in the locations of numerous basic and acidic residues. The SNAPP distributions are quite distinct for the two forms of lysozyme, suggesting significant differences in the surface structures. In summary, SNAPP experiments are relatively easy to perform, require minimal sample consumption, and provide a facile route for comparison of protein surface structure between highly homologous proteins.
Collapse
Affiliation(s)
- Yuanqi Tao
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | | |
Collapse
|
40
|
Nakamura S, Kidokoro SI. Volumetric Properties of the Molten Globule State of Cytochrome c in the Thermal Three-State Transition Evaluated by Pressure Perturbation Calorimetry. J Phys Chem B 2012; 116:1927-32. [DOI: 10.1021/jp209686e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shigeyoshi Nakamura
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka 940-2188, Japan
| | - Shun-ichi Kidokoro
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka 940-2188, Japan
| |
Collapse
|
41
|
Top A, Zhong S, Yan C, Roberts CJ, Pochan DJ, Kiick KL. Controlling assembly of helical polypeptides via PEGylation strategies. SOFT MATTER 2011; 20:9758-9766. [PMID: 24039625 PMCID: PMC3769986 DOI: 10.1039/c1sm05686g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Recent studies in our laboratories have demonstrated that a helical polypeptide (17H6), equipped with a histidine tag and a helical alanine-rich, glutamic-acid-containing domain, exhibits pH-responsive assembly behavior useful in the production of polymorphological nanostructures. In this study, the histidine tag in these polypeptides was replaced by polyethylene glycol (PEG) with different molecular masses (5 kDa, or 10 kDa), and the self-association behavior of 17H6 and the PEGylated conjugates was characterized via dynamic light scattering (DLS), small angle neutron scattering (SANS), and cryogenic transmission electron microscopy (cryo-TEM). DLS experiments illustrated that the polypeptide and its PEG-conjugates undergo reversible assembly under acidic conditions, suggesting that the aggregation state of the polypeptide and the conjugates is controlled by the charged state of the glutamic acid residues. Nanoscale aggregates were detected at polypeptide/conjugate concentrations as low as 20 μM (∼0.3-0.5 mg ml-1) at physiological and ambient temperatures. Scattering and microscopy results showed that the size, the aggregation number, and the morphology of the aggregates can be tuned by the size and the nature of the hydrophilic tag. This tunable nature of the morphology of the aggregates, along with their low critical aggregation concentration, suggests that PEG-alanine-rich polypeptide conjugates may be useful as drug delivery vehicles in which the alanine-rich block serves as a drug attachment domain.
Collapse
Affiliation(s)
- Ayben Top
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, 19716, USA
| | | | | | | | | | | |
Collapse
|
42
|
Miura Y. NMR studies on thermal stability of α-helix conformation of melittin in pure ethanol and ethanol-water mixture solvents. J Pept Sci 2011; 17:798-804. [DOI: 10.1002/psc.1405] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 06/30/2011] [Accepted: 07/14/2011] [Indexed: 11/11/2022]
Affiliation(s)
- Yoshinori Miura
- Center for Advanced Instrumental Analysis; Kyushu University; Kasuga; Japan
| |
Collapse
|
43
|
Nakamura S, Seki Y, Katoh E, Kidokoro SI. Thermodynamic and structural properties of the acid molten globule state of horse cytochrome C. Biochemistry 2011; 50:3116-26. [PMID: 21388230 DOI: 10.1021/bi101806b] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To understand the stabilization, folding, and functional mechanisms of proteins, it is very important to understand the structural and thermodynamic properties of the molten globule state. In this study, the global structure of the acid molten globule state, which we call MG1, of horse cytochrome c at low pH and high salt concentrations was evaluated by solution X-ray scattering (SXS), dynamic light scattering, and circular dichroism measurements. MG1 was globular and slightly (3%) larger than the native state, N. Calorimetric methods, such as differential scanning calorimetry and isothermal acid-titration calorimetry, were used to evaluate the thermodynamic parameters in the transitions of N to MG1 and MG1 to denatured state D of horse cytochrome c. The heat capacity change, ΔC(p), in the N-to-MG1 transition was determined to be 2.56 kJ K(-1) mol(-1), indicating the increase in the level of hydration in the MG1 state. Moreover, the intermediate state on the thermal N-to-D transition of horse cytochrome c at pH 4 under low-salt conditions showed the same structural and thermodynamic properties of the MG1 state in both SXS and calorimetric measurements. The Gibbs free energy changes (ΔG) for the N-to-MG1 and N-to-D transitions at 15 °C were 10.9 and 42.2 kJ mol(-1), respectively.
Collapse
Affiliation(s)
- Shigeyoshi Nakamura
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | | | | | | |
Collapse
|
44
|
Acevedo-Vélez C, Andre G, Dufrêne YF, Gellman SH, Abbott NL. Single-Molecule Force Spectroscopy of β-Peptides That Display Well-Defined Three-Dimensional Chemical Patterns. J Am Chem Soc 2011; 133:3981-8. [DOI: 10.1021/ja1089183] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Claribel Acevedo-Vélez
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Guillaume Andre
- Institute of Condensed Matter and Nanosciences-Bio & Soft Matter, Université Catholique de Louvain, Croix du Sud 2/18, B-1348 Louvain-la-Neuve, Belgium
| | - Yves F. Dufrêne
- Institute of Condensed Matter and Nanosciences-Bio & Soft Matter, Université Catholique de Louvain, Croix du Sud 2/18, B-1348 Louvain-la-Neuve, Belgium
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Nicholas L. Abbott
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| |
Collapse
|
45
|
Khan MKA, Rahaman H, Ahmad F. Conformation and thermodynamic stability of pre-molten and molten globule states of mammalian cytochromes-c. Metallomics 2011; 3:327-38. [DOI: 10.1039/c0mt00078g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
46
|
Dimer structure and conformational variability in the N-terminal region of an archaeal small heat shock protein, StHsp14.0. J Struct Biol 2010; 174:92-9. [PMID: 21195185 DOI: 10.1016/j.jsb.2010.12.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 12/17/2010] [Accepted: 12/21/2010] [Indexed: 11/24/2022]
Abstract
Small heat shock proteins (sHsps), which are categorized into a class of molecular chaperones, bind and stabilize denatured proteins to prevent aggregation. The sHsps undergo transition between different oligomeric states to control their hydrophobicity. So far, only the structures of sHsps in large oligomeric states have been reported. Here we report the structure of StHsp14.0 from Sulfolobus tokodaii in the dimeric state, which is formed by means of a mutation at the C-terminal IXI/V motif. The dimer is the sole building block in two crystal forms, and the dimeric mode is the same as that in the large oligomers. The N-terminal helix has variety in its conformation. Furthermore, spectroscopic and biochemical experiments were performed to investigate the conformational variability at the N-terminus. The structural, dynamical and oligomeric properties suggest that chaperone activity of StHsp14.0 is mediated by partially dissolved oligomers.
Collapse
|
47
|
Singh SM, Cabello-Villegas J, Hutchings RL, Mallela KMG. Role of partial protein unfolding in alcohol-induced protein aggregation. Proteins 2010; 78:2625-37. [PMID: 20597088 DOI: 10.1002/prot.22778] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Proteins aggregate in response to various stresses including changes in solvent conditions. Addition of alcohols has been recently shown to induce aggregation of disease-related as well as nondisease-related proteins. Here we probed the biophysical mechanisms underlying alcohol-induced protein aggregation, in particular the role of partial protein unfolding in aggregation. We have studied aggregation mechanisms due to benzyl alcohol which is used in numerous biochemical and biotechnological applications. We chose cytochrome c as a model protein, for the reason that various optical and structural probes are available to monitor its global and partial unfolding reactions. Benzyl alcohol induced the aggregation of cytochrome c in isothermal conditions and decreased the temperature at which the protein aggregates. However, benzyl alcohol did not perturb the overall native conformation of cytochrome c. Instead, it caused partial unfolding of a local protein region around the methionine residue at position 80. Site-specific optical probes, two-dimensional NMR titrations, and hydrogen exchange all support this conclusion. The protein aggregation temperature varied linearly with the melting temperature of the Met80 region. Stabilizing the Met80 region by heme iron reduction drastically decreased protein aggregation, which confirmed that the local unfolding of this region causes protein aggregation. These results indicate that a possible mechanism by which alcohols induce protein aggregation is through partial rather than complete unfolding of native proteins.
Collapse
Affiliation(s)
- Surinder M Singh
- Department of Pharmaceutical Sciences and Center for Pharmaceutical Biotechnology, School of Pharmacy, University of Colorado Denver, 12700 E 19th Avenue, C238-P15, Aurora, Colorado 80045, USA
| | | | | | | |
Collapse
|
48
|
Raja M. Monitoring the effects of strong cosolvent hexafluoroisopropanol in investigation of the tetrameric structure and stability of K+-channel KcsA. Arch Biochem Biophys 2010; 498:1-6. [DOI: 10.1016/j.abb.2010.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 03/24/2010] [Indexed: 11/29/2022]
|
49
|
Hamid THTA, Rahman RNZRA, Salleh AB, Basri M. Molten globule-triggered inactivation of a thermostable and solvent stable lipase in hydrophilic solvents. Protein J 2010; 29:290-7. [PMID: 20509044 DOI: 10.1007/s10930-010-9251-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The use of lipase in hydrophilic solvent is usually hampered by inactivation. The solvent stability of a recombinant solvent stable lipase isolated from thermostable Bacillus sp. strain 42 (Lip 42), in DMSO and methanol were studied at different solvent-water compositions. The enzymatic activities were retained in up to 45% v/v solvent compositions. The near-UV CD spectra indicated that tertiary structures were perturbed at 60% v/v and above. Far-UV CD in methanol indicated the secondary structure in Lip 42 was retained throughout all solvent compositions. Fluorescence studies indicated formations of molten globules in solvent compositions of 60% v/v and above. The enzyme was able to retain its secondary structures in the presence of methanol; however, there was a general reduction in beta-sheet and an increase in alpha-helix contents. The H-bonding arrangements triggered in methanol and DMSO, respectively, caused different forms of tertiary structure perturbations on Lip 42, despite both showing partial denaturation with molten globule formations.
Collapse
|
50
|
Ahmad B, Haq SK, Varshney A, Moosavi-Movahedi AA, Khan RH. Effect of trifluoroethanol on native and acid-induced states of glucose oxidase from Aspergillus niger. BIOCHEMISTRY (MOSCOW) 2010; 75:486-530. [DOI: 10.1134/s0006297910040139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|