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Schön A, Clarkson BR, Jaime M, Freire E. Temperature stability of proteins: Analysis of irreversible denaturation using isothermal calorimetry. Proteins 2017; 85:2009-2016. [PMID: 28722205 DOI: 10.1002/prot.25354] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/10/2017] [Accepted: 07/18/2017] [Indexed: 01/17/2023]
Abstract
The structural stability of proteins has been traditionally studied under conditions in which the folding/unfolding reaction is reversible, since thermodynamic parameters can only be determined under these conditions. Achieving reversibility conditions in temperature stability experiments has often required performing the experiments at acidic pH or other nonphysiological solvent conditions. With the rapid development of protein drugs, the fastest growing segment in the pharmaceutical industry, the need to evaluate protein stability under formulation conditions has acquired renewed urgency. Under formulation conditions and the required high protein concentration (∼100 mg/mL), protein denaturation is irreversible and frequently coupled to aggregation and precipitation. In this article, we examine the thermal denaturation of hen egg white lysozyme (HEWL) under irreversible conditions and concentrations up to 100 mg/mL using several techniques, especially isothermal calorimetry which has been used to measure the enthalpy and kinetics of the unfolding and aggregation/precipitation at 12°C below the transition temperature measured by DSC. At those temperatures the rate of irreversible protein denaturation and aggregation of HEWL is measured to be on the order of 1 day-1 . Isothermal calorimetry appears a suitable technique to identify buffer formulation conditions that maximize the long term stability of protein drugs.
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Affiliation(s)
- Arne Schön
- Department of Biology, Johns Hopkins University, 3400 North Charles, Baltimore, Maryland, 21218
| | - Benjamin R Clarkson
- Department of Biology, Johns Hopkins University, 3400 North Charles, Baltimore, Maryland, 21218
| | - Maria Jaime
- Department of Biology, Johns Hopkins University, 3400 North Charles, Baltimore, Maryland, 21218
| | - Ernesto Freire
- Department of Biology, Johns Hopkins University, 3400 North Charles, Baltimore, Maryland, 21218
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Raza M, Ahmad A, Yue F, Khan Z, Jiang Y, Wei Y, Raza S, He WW, Khan FU, Qipeng Y. Biophysical and molecular docking approaches for the investigation of biomolecular interactions between amphotericin B and bovine serum albumin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 170:6-15. [DOI: 10.1016/j.jphotobiol.2017.03.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/20/2017] [Accepted: 03/21/2017] [Indexed: 12/16/2022]
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104
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Hermans SM, Pfleger C, Nutschel C, Hanke CA, Gohlke H. Rigidity theory for biomolecules: concepts, software, and applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1311] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Susanne M.A. Hermans
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christopher Pfleger
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christina Nutschel
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christian A. Hanke
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
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105
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Aggregation of t10,c12 conjugated linoleic Acid in presence of natural and modified cyclodextrins. A physicochemical, thermal and computational analysis. Chem Phys Lipids 2017; 204:57-64. [DOI: 10.1016/j.chemphyslip.2017.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/08/2017] [Accepted: 03/23/2017] [Indexed: 11/22/2022]
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106
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Privalov PL, Crane-Robinson C. Role of water in the formation of macromolecular structures. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2017; 46:203-224. [PMID: 27457765 PMCID: PMC5346440 DOI: 10.1007/s00249-016-1161-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/21/2016] [Accepted: 07/13/2016] [Indexed: 11/27/2022]
Abstract
This review shows that water in biological systems is not just a passive liquid solvent but also a partner in the formation of the structure of proteins, nucleic acids and their complexes, thereby contributing to the stability and flexibility required for their proper function. Reciprocally, biological macromolecules affect the state of the water contacting them, so that it is only partly in the normal liquid state, being somewhat ordered when bound to macromolecules. While the compaction of globular proteins results from the reluctance of their hydrophobic groups to interact with water, the collagen superhelix is maintained by water forming a hydroxyproline-controlled frame around this coiled-coil macromolecule. As for DNA, its stability and rigidity are linked to water fixed by AT pairs in the minor groove: this leads to the enthalpic contribution of AT pairs exceeding that of GC pairs, but this is overbalanced by their greater entropy contribution, with the result that AT pairs melt at lower temperatures than GCs. Loss of this water drives transcription factor binding to the minor groove.
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Affiliation(s)
- Peter L Privalov
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Colyn Crane-Robinson
- Biophysics Laboratories, School of Biology, University of Portsmouth, Portsmouth, PO1 2DT, UK.
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107
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Chakravorty D, Khan MF, Patra S. Multifactorial level of extremostability of proteins: can they be exploited for protein engineering? Extremophiles 2017; 21:419-444. [PMID: 28283770 DOI: 10.1007/s00792-016-0908-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 12/19/2016] [Indexed: 12/20/2022]
Abstract
Research on extremostable proteins has seen immense growth in the past decade owing to their industrial importance. Basic research of attributes related to extreme-stability requires further exploration. Modern mechanistic approaches to engineer such proteins in vitro will have more impact in industrial biotechnology economy. Developing a priori knowledge about the mechanism behind extreme-stability will nurture better understanding of pathways leading to protein molecular evolution and folding. This review is a vivid compilation about all classes of extremostable proteins and the attributes that lead to myriad of adaptations divulged after an extensive study of 6495 articles belonging to extremostable proteins. Along with detailing on the rationale behind extreme-stability of proteins, emphasis has been put on modern approaches that have been utilized to render proteins extremostable by protein engineering. It was understood that each protein shows different approaches to extreme-stability governed by minute differences in their biophysical properties and the milieu in which they exist. Any general rule has not yet been drawn regarding adaptive mechanisms in extreme environments. This review was further instrumental to understand the drawback of the available 14 stabilizing mutation prediction algorithms. Thus, this review lays the foundation to further explore the biophysical pleiotropy of extreme-stable proteins to deduce a global prediction model for predicting the effect of mutations on protein stability.
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Affiliation(s)
- Debamitra Chakravorty
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Mohd Faheem Khan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Sanjukta Patra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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108
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Lee SY, Khoiroh I, Ooi CW, Ling TC, Show PL. Recent Advances in Protein Extraction Using Ionic Liquid-based Aqueous Two-phase Systems. SEPARATION AND PURIFICATION REVIEWS 2017. [DOI: 10.1080/15422119.2017.1279628] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Sze Ying Lee
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham Malaysia Campus, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Ianatul Khoiroh
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham Malaysia Campus, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Chien Wei Ooi
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Tau Chuan Ling
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Pau Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham Malaysia Campus, Semenyih, Selangor Darul Ehsan, Malaysia
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Medvedev KE, Kolchanov NA, Afonnikov DA. High temperature and pressure influence the interdomain orientation of Nip7 proteins from P. abyssi and P. furiosus: MD simulations. J Biomol Struct Dyn 2017; 36:68-82. [DOI: 10.1080/07391102.2016.1268070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Kirill E. Medvedev
- Systems Biology Department, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nikolay A. Kolchanov
- Systems Biology Department, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Chair of Informational Biology, Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
| | - Dmitry A. Afonnikov
- Systems Biology Department, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Chair of Informational Biology, Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
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110
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Kashanian F, Habibi-Rezaei M, Bagherpour AR, Seyedarabi A, Moosavi-Movahedi AA. Magnetic nanoparticles as double-edged swords: concentration-dependent ordering or disordering effects on lysozyme. RSC Adv 2017. [DOI: 10.1039/c7ra08903a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The study of the interaction of nanoparticles (NPs) with proteins is of great importance due to its relevance in several fields including nano-biosafety, nano-bioscience, nano-biomedicine, and nano-biotechnology.
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Affiliation(s)
- F. Kashanian
- Department of Life Science Engineering
- Faculty of New Sciences and Technologies
- University of Tehran
- Tehran
- Iran
| | - M. Habibi-Rezaei
- School of Biology
- College of Science
- University of Tehran
- Tehran
- Iran
| | - A. R. Bagherpour
- School of Biology
- College of Science
- University of Tehran
- Tehran
- Iran
| | - A. Seyedarabi
- Institute of Biochemistry and Biophysics
- University of Tehran
- Tehran
- Iran
| | - A. A. Moosavi-Movahedi
- Institute of Biochemistry and Biophysics
- University of Tehran
- Tehran
- Iran
- Center of Excellence in Biothermodynamics
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111
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Kabir A, Honda RP, Kamatari YO, Endo S, Fukuoka M, Kuwata K. Effects of ligand binding on the stability of aldo-keto reductases: Implications for stabilizer or destabilizer chaperones. Protein Sci 2016; 25:2132-2141. [PMID: 27595938 PMCID: PMC5119574 DOI: 10.1002/pro.3036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/30/2016] [Indexed: 01/26/2023]
Abstract
Ligands such as enzyme inhibitors stabilize the native conformation of a protein upon binding to the native state, but some compounds destabilize the native conformation upon binding to the non-native state. The former ligands are termed "stabilizer chaperones" and the latter ones "destabilizer chaperones." Because the stabilization effects are essential for the medical chaperone (MC) hypothesis, here we have formulated a thermodynamic system consisting of a ligand and a protein in its native- and non-native state. Using the differential scanning fluorimetry and the circular dichroism varying the urea concentration and temperature, we found that when the coenzyme NADP+ was absent, inhibitors such as isolithocholic acid stabilized the aldo-keto reductase AKR1A1 upon binding, which showed actually the three-state folding, but destabilized AKR1B10. In contrast, in the presence of NADP+ , they destabilized AKR1A1 and stabilized AKR1B10. To explain these phenomena, we decomposed the free energy of stabilization (ΔΔG) into its enthalpy (ΔΔH) and entropy (ΔΔS) components. Then we found that in a relatively unstable protein showing the three-state folding, native conformation was stabilized by the negative ΔΔH in association with the negative ΔΔS, suggesting that the stabilizer chaperon decreases the conformational fluctuation of the target protein or increase its hydration. However, in other cases, ΔΔG was essentially determined by the delicate balance between ΔΔH and ΔΔS. The proposed thermodynamic formalism is applicable to the system including multiple ligands with allosteric interactions. These findings would promote the development of screening strategies for MCs to regulate the target conformations.
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Affiliation(s)
- Aurangazeb Kabir
- United Graduate School of Drug Discovery and Medical Information SciencesGifu UniversityGifu501‐1193Japan
| | - Ryo P. Honda
- Department of Molecular Pathobiochemistry, Graduate School of MedicineGifu UniversityGifu501‐1193Japan
| | | | - Satoshi Endo
- Laboratory of BiochemistryGifu Pharmaceutical UniversityGifu501‐1196Japan
| | - Mayuko Fukuoka
- United Graduate School of Drug Discovery and Medical Information SciencesGifu UniversityGifu501‐1193Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information SciencesGifu UniversityGifu501‐1193Japan
- Department of Gene and Development, Graduate School of MedicineGifu UniversityGifu501‐1193Japan
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112
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Malhotra P, Udgaonkar JB. How cooperative are protein folding and unfolding transitions? Protein Sci 2016; 25:1924-1941. [PMID: 27522064 PMCID: PMC5079258 DOI: 10.1002/pro.3015] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/09/2016] [Accepted: 08/09/2016] [Indexed: 11/12/2022]
Abstract
A thermodynamically and kinetically simple picture of protein folding envisages only two states, native (N) and unfolded (U), separated by a single activation free energy barrier, and interconverting by cooperative two-state transitions. The folding/unfolding transitions of many proteins occur, however, in multiple discrete steps associated with the formation of intermediates, which is indicative of reduced cooperativity. Furthermore, much advancement in experimental and computational approaches has demonstrated entirely non-cooperative (gradual) transitions via a continuum of states and a multitude of small energetic barriers between the N and U states of some proteins. These findings have been instrumental towards providing a structural rationale for cooperative versus noncooperative transitions, based on the coupling between interaction networks in proteins. The cooperativity inherent in a folding/unfolding reaction appears to be context dependent, and can be tuned via experimental conditions which change the stabilities of N and U. The evolution of cooperativity in protein folding transitions is linked closely to the evolution of function as well as the aggregation propensity of the protein. A large activation energy barrier in a fully cooperative transition can provide the kinetic control required to prevent the accumulation of partially unfolded forms, which may promote aggregation. Nevertheless, increasing evidence for barrier-less "downhill" folding, as well as for continuous "uphill" unfolding transitions, indicate that gradual non-cooperative processes may be ubiquitous features on the free energy landscape of protein folding.
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Affiliation(s)
- Pooja Malhotra
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India.
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113
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Structural and thermodynamic characterisation of L94F mutant of horse cytochrome c. Int J Biol Macromol 2016; 92:202-212. [DOI: 10.1016/j.ijbiomac.2016.06.096] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/24/2016] [Accepted: 06/30/2016] [Indexed: 12/11/2022]
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114
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Marsh D. Equation of State for Phospholipid Self-Assembly. Biophys J 2016; 110:188-96. [PMID: 26745421 DOI: 10.1016/j.bpj.2015.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/09/2015] [Accepted: 11/09/2015] [Indexed: 11/16/2022] Open
Abstract
Phospholipid self-assembly is the basis of biomembrane stability. The entropy of transfer from water to self-assembled micelles of lysophosphatidylcholines and diacyl phosphatidylcholines with different chain lengths converges to a common value at a temperature of 44°C. The corresponding enthalpies of transfer converge at ∼-18°C. An equation of state for the free energy of self-assembly formulated from this thermodynamic data depends on the heat capacity of transfer as the sole parameter needed to specify a particular lipid. For lipids lacking calorimetric data, measurement of the critical micelle concentration at a single temperature suffices to define an effective heat capacity according to the model. Agreement with the experimental temperature dependence of the critical micelle concentration is then good. The predictive powers should extend also to amphiphile partitioning and the kinetics of lipid-monomer transfer.
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Affiliation(s)
- Derek Marsh
- University of Southern Denmark, MEMPHYS, Odense, Denmark; Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany.
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115
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Diaz-Franulic I, Poblete H, Miño-Galaz G, González C, Latorre R. Allosterism and Structure in Thermally Activated Transient Receptor Potential Channels. Annu Rev Biophys 2016; 45:371-98. [DOI: 10.1146/annurev-biophys-062215-011034] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ignacio Diaz-Franulic
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago 8370146, Chile
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile; ,
- Fraunhofer Chile Research, Las Condes 7550296, Santiago, Chile
| | - Horacio Poblete
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802
| | - Germán Miño-Galaz
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago 8370146, Chile
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile; ,
| | - Carlos González
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile; ,
| | - Ramón Latorre
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile; ,
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116
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Extraction and purification of a highly thermostable alkaline caseinolytic protease from wastes Penaeus vannamei suitable for food and detergent industries. Food Chem 2016; 202:110-5. [DOI: 10.1016/j.foodchem.2016.01.104] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 01/14/2016] [Accepted: 01/25/2016] [Indexed: 11/21/2022]
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117
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Thermal protein unfolding by differential scanning calorimetry and circular dichroism spectroscopy Two-state model versus sequential unfolding. Q Rev Biophys 2016; 49:e9. [PMID: 27658613 DOI: 10.1017/s0033583516000044] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Thermally-induced protein unfolding is commonly described with the two-state model. This model assumes only two types of protein molecules in solution, the native (N) and the denatured, unfolded (U) protein. In reality, protein unfolding is a multistep process, even if intermediate states are only sparsely populated. As an alternative approach we explore the Zimm-Bragg theory, originally developed for the α-helix-to-random coil transition of synthetic polypeptides. The theory includes intermediate structures with concentrations determined by the cooperativity of the unfolding reaction. We illustrate the differences between the two-state model and the Zimm-Bragg theory with measurements of apolipoprotein A-1 and lysozyme by differential scanning calorimetry (DSC) and CD spectroscopy. Nine further protein examples are taken from the literature. The Zimm-Bragg theory provides a perfect fit of the calorimetric unfolding transitions for all proteins investigated. In contrast, the transition curves and enthalpies predicted by the two-state model differ considerably from the experimental results. Apolipoprotein A-1 is ~50% α-helical at ambient temperature and its unfolding follows the classical α-helix-to-random coil equilibrium. The unfolding of proteins with little α-helix content, such as lysozyme, can also be analyzed with the Zimm-Bragg theory by introducing the concept of 'folded' and 'unfolded' peptide units assuming an average unfolding enthalpy per peptide unit. DSC is the method of choice to measure the unfolding enthalpy, , but CD spectroscopy in combination with the two-state model is often used to deduce the unfolding enthalpy. This can lead to erroneous result. Not only are different enthalpies required to describe the CD and DSC transition curves but these values deviate distinctly from the experimental result. In contrast, the Zimm-Bragg theory predicts the DSC and CD unfolding transitions with the same set of parameters.
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118
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Liu J, Falke S, Drobot B, Oberthuer D, Kikhney A, Guenther T, Fahmy K, Svergun D, Betzel C, Raff J. Analysis of self-assembly of S-layer protein slp-B53 from Lysinibacillus sphaericus. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:77-89. [PMID: 27270294 DOI: 10.1007/s00249-016-1139-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/29/2016] [Accepted: 05/12/2016] [Indexed: 10/21/2022]
Abstract
The formation of stable and functional surface layers (S-layers) via self-assembly of surface-layer proteins on the cell surface is a dynamic and complex process. S-layers facilitate a number of important biological functions, e.g., providing protection and mediating selective exchange of molecules and thereby functioning as molecular sieves. Furthermore, S-layers selectively bind several metal ions including uranium, palladium, gold, and europium, some of them with high affinity. Most current research on surface layers focuses on investigating crystalline arrays of protein subunits in Archaea and bacteria. In this work, several complementary analytical techniques and methods have been applied to examine structure-function relationships and dynamics for assembly of S-layer protein slp-B53 from Lysinibacillus sphaericus: (1) The secondary structure of the S-layer protein was analyzed by circular dichroism spectroscopy; (2) Small-angle X-ray scattering was applied to gain insights into the three-dimensional structure in solution; (3) The interaction with bivalent cations was followed by differential scanning calorimetry; (4) The dynamics and time-dependent assembly of S-layers were followed by applying dynamic light scattering; (5) The two-dimensional structure of the paracrystalline S-layer lattice was examined by atomic force microscopy. The data obtained provide essential structural insights into the mechanism of S-layer self-assembly, particularly with respect to binding of bivalent cations, i.e., Mg2+ and Ca2+. Furthermore, the results obtained highlight potential applications of S-layers in the fields of micromaterials and nanobiotechnology by providing engineered or individual symmetric thin protein layers, e.g., for protective, antimicrobial, or otherwise functionalized surfaces.
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Affiliation(s)
- Jun Liu
- Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany.,Bioengineering Faculty, Sichuan University of Science and Engineering, Huixing Rd., Xueyuan Street 180, Zigong, 643000, Sichuan, China
| | - Sven Falke
- Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany
| | - Bjoern Drobot
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstr. 400, 01328, Dresden, Germany
| | - Dominik Oberthuer
- Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany.,Center for Free-Electron Laser Science (CFEL), DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Alexey Kikhney
- EMBL Hamburg, European Molecular Biology Laboratory, Notkestr. 85, 22607, Hamburg, Germany
| | - Tobias Guenther
- Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstr. 400, 01328, Dresden, Germany
| | - Karim Fahmy
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstr. 400, 01328, Dresden, Germany
| | - Dmitri Svergun
- EMBL Hamburg, European Molecular Biology Laboratory, Notkestr. 85, 22607, Hamburg, Germany
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King Platz 6, 20146, Hamburg, Germany
| | - Johannes Raff
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstr. 400, 01328, Dresden, Germany. .,Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstr. 400, 01328, Dresden, Germany.
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119
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Role of denatured-state properties in chaperonin action probed by single-molecule spectroscopy. Biophys J 2016; 107:2891-2902. [PMID: 25517154 DOI: 10.1016/j.bpj.2014.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/07/2014] [Accepted: 11/03/2014] [Indexed: 11/22/2022] Open
Abstract
The bacterial chaperonin GroEL/GroES assists folding of a broad spectrum of denatured and misfolded proteins. Here, we explore the limits of this remarkable promiscuity by mapping two denatured proteins with very different conformational properties, rhodanese and cyclophilin A, during binding and encapsulation by GroEL/GroES with single-molecule spectroscopy, microfluidic mixing, and ensemble kinetics. We find that both proteins bind to GroEL with high affinity in a reaction involving substantial conformational adaptation. However, whereas the compact denatured state of rhodanese is encapsulated efficiently upon addition of GroES and ATP, the more expanded and unstructured denatured cyclophilin A is not encapsulated but is expelled into solution. The origin of this surprising disparity is the weaker interactions of cyclophilin A with a transiently formed GroEL-GroES complex, which may serve as a crucial checkpoint for substrate discrimination.
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120
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Sedlák E, Varhač R, Musatov A, Robinson NC. The kinetic stability of cytochrome C oxidase: effect of bound phospholipid and dimerization. Biophys J 2016; 107:2941-2949. [PMID: 25517159 DOI: 10.1016/j.bpj.2014.10.055] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/14/2014] [Accepted: 10/22/2014] [Indexed: 12/21/2022] Open
Abstract
Thermally induced transitions of the 13-subunit integral membrane protein bovine cytochrome c oxidase (CcO) have been studied by differential scanning calorimetry (DSC) and circular dichroism (CD). Thermal denaturation of dodecyl maltoside solubilized CcO proceeds in two consecutive, irreversible, kinetically driven steps with the apparent transition temperatures at ∼ 51°C and ∼ 61°C (5μM CcO at scan rate of 1.5 K/min). The thermal denaturation data were analyzed according to the Lyubarev and Kurganov model of two consecutive irreversible steps. However, because of the limitation of the model to describe the complex mechanism of the thermal denaturation of CcO, the obtained results were utilized only for comparison purposes of kinetic stabilities of CcO under specific protein concentration (5μM) and scan rate (1.5 K/min). This enabled us to show that both the amphiphilic environment and the self-association state of CcO affect its kinetic stability. Kinetic stabilities of both steps are significantly decreased when all of the phospholipids are removed from CcO by phospholipase A2 (the half-life decreases at 37°C). Conversely, dimerization of CcO induced by sodium cholate significantly increases its kinetic stability of only the first step (the half-life increases at 37°C). Protein concentration-dependent nonspecific oligomerization also indicate mild stabilization of CcO. Both, reversed-phase high-performance liquid chromatography (HPLC) and SDS-PAGE subunit analysis reveal that the first step of thermal denaturation involves dissociation of subunits III, VIa, VIb, and VIIa, whereas the second step is less well defined and most likely involves global unfold and aggregation of the remaining subunits. Electron transport activity of CcO decreases in a sigmoidal manner during the first transition and this dependence is very well described by kinetic parameters for the first step of the thermal transition. Therefore, dissociation of subunit III and/or VIIa is responsible for temperature-induced inactivation of CcO because VIa and VIb can be removed from CcO without affecting the enzyme activity. These results demonstrate an important role of tightly bound phospholipids and oligomeric state (particularly the dimeric form) of CcO for kinetic stability of the protein.
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Affiliation(s)
- Erik Sedlák
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, Texas.
| | - Rastislav Varhač
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, Texas
| | - Andrej Musatov
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, Texas
| | - Neal C Robinson
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, Texas
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121
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Corkrey R, McMeekin TA, Bowman JP, Ratkowsky DA, Olley J, Ross T. The Biokinetic Spectrum for Temperature. PLoS One 2016; 11:e0153343. [PMID: 27088362 PMCID: PMC4835062 DOI: 10.1371/journal.pone.0153343] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/28/2016] [Indexed: 11/18/2022] Open
Abstract
We identify and describe the distribution of temperature-dependent specific growth rates for life on Earth, which we term the biokinetic spectrum for temperature. The spectrum has the potential to provide for more robust modeling in thermal ecology since any conclusions derived from it will be based on observed data rather than using theoretical assumptions. It may also provide constraints for systems biology model predictions and provide insights in physiology. The spectrum has a Δ-shape with a sharp peak at around 42°C. At higher temperatures up to 60°C there was a gap of attenuated growth rates. We found another peak at 67°C and a steady decline in maximum rates thereafter. By using Bayesian quantile regression to summarise and explore the data we were able to conclude that the gap represented an actual biological transition between mesophiles and thermophiles that we term the Mesophile-Thermophile Gap (MTG). We have not identified any organism that grows above the maximum rate of the spectrum. We used a thermodynamic model to recover the Δ-shape, suggesting that the growth rate limits arise from a trade-off between activity and stability of proteins. The spectrum provides underpinning principles that will find utility in models concerned with the thermal responses of biological processes.
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Affiliation(s)
- Ross Corkrey
- Tasmanian Institute of Agriculture / School of Land and Food, University of Tasmania, Hobart, Tasmania, Australia
- * E-mail:
| | - Tom A. McMeekin
- Tasmanian Institute of Agriculture / School of Land and Food, University of Tasmania, Hobart, Tasmania, Australia
| | - John P. Bowman
- Tasmanian Institute of Agriculture / School of Land and Food, University of Tasmania, Hobart, Tasmania, Australia
| | - David A. Ratkowsky
- Tasmanian Institute of Agriculture / School of Land and Food, University of Tasmania, Hobart, Tasmania, Australia
| | - June Olley
- Tasmanian Institute of Agriculture / School of Land and Food, University of Tasmania, Hobart, Tasmania, Australia
| | - Tom Ross
- Tasmanian Institute of Agriculture / School of Land and Food, University of Tasmania, Hobart, Tasmania, Australia
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122
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Yeggoni DP, Rachamallu A, Subramanyam R. Protein stability, conformational change and binding mechanism of human serum albumin upon binding of embelin and its role in disease control. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 160:248-59. [PMID: 27130964 DOI: 10.1016/j.jphotobiol.2016.04.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 04/12/2016] [Indexed: 12/26/2022]
Abstract
Here, we present the inclusive binding mode of phytochemical embelin, an anticancer drug with human serum albumin (HSA) established under physiological condition. Also, to understand the pharmacological role of embelin molecule, here, we have studied the anti-cancer activity of embelin on human cervical cancer cell line (HeLa cell line), which revealed that embelin showed dose dependent inhibition in the growth of cancer cells and also induces 26.3% of apoptosis at an IC50 value of 29μM. Further, embelin was titrated with HSA and the fluorescence emission quenching of HSA due to the formation of the HSA-embelin complex was observed. The binding constant of this complex is 5.9±.01×10(4)M(-1) and the number of bound embelin molecules is approximately 1.0. Consequently, molecular displacement and computational docking experiments show that the embelin is binding to subdomain IB to HSA. Further evidence from microTOF-Q mass spectrometry showed an increase in mass from 66,563Da to 66,857Da observed for free HSA and HSA+embelin complex, signifying that there is robust binding of embelin with HSA. In addition, the variations of HSA secondary structural elements in presence of embelin were confirmed by circular dichroism which indicates partial unfolding of protein. Furthermore, the transmission electron micrographs established that complex formation leads to aggregation of HSA plus embelin. Molecular dynamics simulations revealed that the stability of the HSA-embelin complexes and results suggests that at around 3500ps the complex reaches equilibration state which clearly contributes to the understanding of the stability of the HSA-embelin complexes.
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Affiliation(s)
- Daniel Pushparaju Yeggoni
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Aparna Rachamallu
- National Institute of Animal Biotechnology, Axis Clinicals Building, Miyapur, Hyderabad 500049, India
| | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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124
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Choi JM, Lee YJ, Cao TP, Shin SM, Park MK, Lee HS, di Luccio E, Kim SB, Lee SJ, Lee SJ, Lee SH, Lee DW. Structure of the thermophilic l-Arabinose isomerase from Geobacillus kaustophilus reveals metal-mediated intersubunit interactions for activity and thermostability. Arch Biochem Biophys 2016; 596:51-62. [DOI: 10.1016/j.abb.2016.02.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/27/2016] [Accepted: 02/29/2016] [Indexed: 11/27/2022]
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125
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Meti MD, Nandibewoor ST, Joshi SD, More UA, Chimatadar SA. Binding interaction and conformational changes of human serum albumin with ranitidine studied by spectroscopic and time-resolved fluorescence methods. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2016. [DOI: 10.1007/s13738-016-0847-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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126
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Yan XC, Tirado-Rives J, Jorgensen WL. Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water. J Phys Chem B 2016; 120:8102-14. [PMID: 26901452 DOI: 10.1021/acs.jpcb.6b00399] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Due to the importance of water in chemical and biological systems, a coarse-grained representation of the solvent can greatly simplify the description of the system while retaining key thermodynamic properties of the medium. A multiscale solvation model that couples all-atom solutes and polarizable Martini coarse-grained water (AAX/CGS) is developed to reproduce free energies of hydration of organic solutes. Using Monte Carlo/free energy perturbation (MC/FEP) calculations, results from multiscale and all-atom simulations are compared. Improved accuracy is obtained with the AAX/CGS approach for hydrophobic and sulfur- or halogen-containing solutes, but larger deviations are found for polar solute molecules where hydrogen bonding is featured. Furthermore, solvent effects on conformational and tautomeric equilibria of AA solutes were investigated using AA, CG, and GB/SA solvent models. It is found that the CG solvent model can reproduce well the medium effects from experiment and AA simulations; however, the GB/SA solvent model fails in some cases. A 7-30-fold reduction in computational cost is found for the present AAX/CGS multiscale simulations compared to the AA alternative.
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Affiliation(s)
- Xin Cindy Yan
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
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127
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Hentze N, Le Breton L, Wiesner J, Kempf G, Mayer MP. Molecular mechanism of thermosensory function of human heat shock transcription factor Hsf1. eLife 2016; 5. [PMID: 26785146 PMCID: PMC4775227 DOI: 10.7554/elife.11576] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 01/18/2016] [Indexed: 01/06/2023] Open
Abstract
The heat shock response is a universal homeostatic cell autonomous reaction of organisms to cope with adverse environmental conditions. In mammalian cells, this response is mediated by the heat shock transcription factor Hsf1, which is monomeric in unstressed cells and upon activation trimerizes, and binds to promoters of heat shock genes. To understand the basic principle of Hsf1 activation we analyzed temperature-induced alterations in the conformational dynamics of Hsf1 by hydrogen exchange mass spectrometry. We found a temperature-dependent unfolding of Hsf1 in the regulatory region happening concomitant to tighter packing in the trimerization region. The transition to the active DNA binding-competent state occurred highly cooperative and was concentration dependent. Surprisingly, Hsp90, known to inhibit Hsf1 activation, lowered the midpoint temperature of trimerization and reduced cooperativity of the process thus widening the response window. Based on our data we propose a kinetic model of Hsf1 trimerization.
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Affiliation(s)
- Nikolai Hentze
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Laura Le Breton
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Jan Wiesner
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Georg Kempf
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Matthias P Mayer
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
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128
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Kanbargi KD, Sonawane SK, Arya SS. Functional and antioxidant activity of Ziziphus jujube seed protein hydrolysates. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2015. [DOI: 10.1007/s11694-015-9297-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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129
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Ielo I, Lanza S, Campagna S, Giannetto A. The Reversible Formation of Tight Ion Pairs within Platinum(II) Complexes – A Study of Thermodynamic Parameters Governing Noncovalent Interactions. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ileana Ielo
- Dipartimento di Scienze Chimiche, Università di Messina, Via d'Alcontres 31, 98166 Messina, Italy
| | - Santo Lanza
- Dipartimento di Scienze Chimiche, Università di Messina, Via d'Alcontres 31, 98166 Messina, Italy
| | - Sebastiano Campagna
- Dipartimento di Scienze Chimiche, Università di Messina, Via d'Alcontres 31, 98166 Messina, Italy
| | - Antonino Giannetto
- Dipartimento di Scienze Chimiche, Università di Messina, Via d'Alcontres 31, 98166 Messina, Italy
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130
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Rhys NH, Soper AK, Dougan L. Hydrophilic Association in a Dilute Glutamine Solution Persists Independent of Increasing Temperature. J Phys Chem B 2015; 119:15644-51. [DOI: 10.1021/acs.jpcb.5b07413] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Natasha H. Rhys
- School
of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Alan K. Soper
- ISIS Facility,
STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxon OX11
OQX, U.K
| | - Lorna Dougan
- School
of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
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131
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Sanfelice D, Morandi E, Pastore A, Niccolai N, Temussi PA. Cold Denaturation Unveiled: Molecular Mechanism of the Asymmetric Unfolding of Yeast Frataxin. Chemphyschem 2015; 16:3599-602. [PMID: 26426928 PMCID: PMC4676917 DOI: 10.1002/cphc.201500765] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/01/2015] [Indexed: 11/11/2022]
Abstract
What is the mechanism that determines the denaturation of proteins at low temperatures, which is, by now, recognized as a fundamental property of all proteins? We present experimental evidence that clarifies the role of specific interactions that favor the entrance of water into the hydrophobic core, a mechanism originally proposed by Privalov but never proved experimentally. By using a combination of molecular dynamics simulation, molecular biology, and biophysics, we identified a cluster of negatively charged residues that represents a preferential gate for the entrance of water molecules into the core. Even single-residue mutations in this cluster, from acidic to neutral residues, affect cold denaturation much more than heat denaturation, suppressing cold denaturation at temperatures above zero degrees. The molecular mechanism of the cold denaturation of yeast frataxin is intrinsically different from that of heat denaturation.
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Affiliation(s)
- Domenico Sanfelice
- Department of Basic and Clinical Neurosciences, Kings College London, London, SE5 9RX, UK
| | - Edoardo Morandi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100, Siena, Italy
| | - Annalisa Pastore
- Department of Basic and Clinical Neurosciences, Kings College London, London, SE5 9RX, UK.
| | - Neri Niccolai
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100, Siena, Italy
| | - Piero Andrea Temussi
- Department of Basic and Clinical Neurosciences, Kings College London, London, SE5 9RX, UK.
- Department of Chemical Sciences, Università di Napoli Federico II, via Cinthia, 80126, Napoli, Italy.
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132
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Mills EA, Plotkin SS. Protein Transfer Free Energy Obeys Entropy-Enthalpy Compensation. J Phys Chem B 2015; 119:14130-44. [DOI: 10.1021/acs.jpcb.5b09219] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eric A. Mills
- Department of Physics & Astronomy, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Steven S. Plotkin
- Department of Physics & Astronomy, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
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133
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Thermodynamics of protein denaturation at temperatures over 100 °C: CutA1 mutant proteins substituted with hydrophobic and charged residues. Sci Rep 2015; 5:15545. [PMID: 26497062 PMCID: PMC4620440 DOI: 10.1038/srep15545] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/28/2015] [Indexed: 11/08/2022] Open
Abstract
Although the thermodynamics of protein denaturation at temperatures over 100 °C is essential for the rational design of highly stable proteins, it is not understood well because of the associated technical difficulties. We designed certain hydrophobic mutant proteins of CutA1 from Escherichia coli, which have denaturation temperatures (Td) ranging from 101 to 113 °C and show a reversible heat denaturation. Using a hydrophobic mutant as a template, we successfully designed a hyperthermostable mutant protein (Td = 137 °C) by substituting six residues with charged ones. Thermodynamic analyses of these mutant proteins indicated that the hydrophobic mutants were stabilized by the accumulation of denaturation enthalpy (ΔH) with no entropic gain from hydrophobic solvation around 100 °C, and that the stabilization due to salt bridges resulted from both the increase in ΔH from ion-ion interactions and the entropic effect of the electrostatic solvation over 113 °C. This is the first experimental evidence that has successfully overcome the typical technical difficulties.
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134
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Rabdano SO, Donets AV, Vovk MA, Michel D, Chizhik VI. "Hydration Shells" of CH2 Groups of ω-Amino Acids as Studied by Deuteron NMR Relaxation. J Phys Chem B 2015; 119:13358-66. [PMID: 26322528 DOI: 10.1021/acs.jpcb.5b06584] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydration phenomena play a very important role in various processes, in particular in biological systems. Water molecules in aqueous solutions of organic compounds can be distributed among the following substructures: (i) hydration shells of hydrophilic functional groups of molecules, (ii) water in the environment of nonpolar moieties, and (iii) bulk water. Up to now, the values of hydration parameters suggested for the description of various solutions of organic compounds were not thoroughly analyzed in the aspect of the consideration of the total molecular composition. The temperature and concentration dependences of relaxation rates of water deuterons were studied in a wide range of concentration and temperature in aqueous (D2O) solutions of a set of ω-amino acids. Assuming the coordination number of the CH2 group equal to 7, which was determined from quantum-chemical calculations, it was found that the rotational correlation times of water molecules near the methylene group is 1.5-2 times greater than one for pure water. The average rotational mobility of water molecules in the hydration shells of hydrophilic groups of ω-amino acids is a bit slower than that in pure solvent at temperatures higher that 60 °C, but at lower temperatures, it is 0.8-1.0 of values of correlation times for bulk water. The technique suggested provides the basis for the characterization of different hydrophobic and hydrophilic species in the convenient terms of the rotational correlation times for the nearest water molecules.
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Affiliation(s)
- Sevastyan O Rabdano
- Laboratory of Biomolecular NMR, St. Petersburg State University , St. Petersburg 199034, Russia.,Department of Physics, St. Petersburg State University , St. Petersburg 198504, Russia
| | - Alexey V Donets
- Department of Physics, St. Petersburg State University , St. Petersburg 198504, Russia
| | - Mikhail A Vovk
- Center for Magnetic Resonance, St. Petersburg State University , St. Petersburg 198504, Russia
| | - Dieter Michel
- Institute of Experimental Physics II, University of Leipzig , Linnéstr. 5, D-04103 Leipzig, Germany
| | - Vladimir I Chizhik
- Department of Physics, St. Petersburg State University , St. Petersburg 198504, Russia
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135
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Akazawa-Ogawa Y, Uegaki K, Hagihara Y. The role of intra-domain disulfide bonds in heat-induced irreversible denaturation of camelid single domain VHH antibodies. J Biochem 2015; 159:111-21. [PMID: 26289739 DOI: 10.1093/jb/mvv082] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 07/05/2015] [Indexed: 01/14/2023] Open
Abstract
Camelid-derived single domain VHH antibodies are highly heat resistant, and the mechanism of heat-induced VHH denaturation predominantly relies on the chemical modification of amino acids. Although chemical modification of disulfide bonds has been recognized as a cause for heat-induced denaturation of many proteins, there have been no mutagenesis studies, in which the number of disulfide bonds was controlled. In this article, we examined a series of mutants of two different VHHs with single, double or no disulfide bonds, and scrutinized the effects of these disulfide bond modifications on VHH denaturation. With the exception of one mutant, the heat resistance of VHHs decreased when the number of disulfide bonds increased. The effect of disulfide bonds on heat denaturation was more striking if the VHH had a second disulfide bond, suggesting that the contribution of disulfide shuffling is significant in proteins with multiple disulfide bonds. Furthermore, our results directly indicate that removal of a disulfide bond can indeed increase the heat resistance of a protein, irrespective of the negative impact on equilibrium thermodynamic stability.
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Affiliation(s)
- Yoko Akazawa-Ogawa
- National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Koichi Uegaki
- National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Yoshihisa Hagihara
- National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
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136
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Polley S, Chakravarty D, Chakrabarti G, Chattopadhyaya R, Sau S. Proline substitutions in a Mip-like peptidyl-prolyl cis-trans isomerase severely affect its structure, stability, shape and activity. BIOCHIMIE OPEN 2015; 1:28-39. [PMID: 29632827 PMCID: PMC5889476 DOI: 10.1016/j.biopen.2015.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 07/12/2015] [Indexed: 01/28/2023]
Abstract
FKBP22, an Escherichia coli-specific peptidyl-prolyl cis-trans isomerase, shows substantial homology with the Mip-like virulence factors. Mip-like proteins are homodimeric and possess a V-shaped conformation. Their N-terminal domains form dimers, whereas their C-terminal domains bind protein/peptide substrates and distinct inhibitors such as rapamycin and FK506. Interestingly, the two domains of the Mip-like proteins are separated by a lengthy, protease-susceptible α-helix. To delineate the structural requirement of this domain-connecting region in Mip-like proteins, we have investigated a recombinant FKBP22 (rFKBP22) and its three point mutants I65P, V72P and A82P using different probes. Each mutant harbors a Pro substitution mutation at a distinct location in the hinge region. We report that the three mutants are not only different from each other but also different from rFKBP22 in structure and activity. Unlike rFKBP22, the three mutants were unfolded by a non-two state mechanism in the presence of urea. In addition, the stabilities of the mutants, particularly I65P and V72P, differed considerably from that of rFKBP22. Conversely, the rapamycin binding affinity of no mutant was different from that of rFKBP22. Of the mutants, I65P showed the highest levels of structural/functional loss and dissociated partly in solution. Our computational study indicated a severe collapse of the V-shape in I65P due to the anomalous movement of its C-terminal domains. The α-helical nature of the domain-connecting region is, therefore, critical for the Mip-like proteins.
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Key Words
- A82P, a FKBP22/rFKBP22 derivative harboring a Ala to Pro change at position 82 in the helix α3
- CTD, C-terminal domain of FKBP22
- FKBP22, a PPIase from Escherichia coli
- Helix α3
- I65P, a FKBP22/rFKBP22 variant carrying a Ile to Pro replacement at position 65 in the helix α3
- Mip, macrophage infectivity potentiator
- Mutation
- NTD, N-terminal domain of FKBP22
- PPIase, peptidyl-prolyl cis-trans isomerase
- Peptidyl-prolyl cis-trans isomerase
- Stability
- Structure
- TUGE, transverse urea gradient gel electrophoresis
- V72P, a FKBP22/rFKBP22 variant with a Val to Pro substitution at position 72 in the helix α3
- rFKBP22, a polyhistidine-tagged FKBP22
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Affiliation(s)
- Soumitra Polley
- Department of Biochemistry, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, West Bengal, India
| | - Devlina Chakravarty
- Department of Biochemistry, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, West Bengal, India
| | - Gopal Chakrabarti
- Dr. B.C. Guha Centre for Genetic Engineering, University of Calcutta, Ballygunge Circular Road, Kolkata 700019, West Bengal, India
| | - Rajagopal Chattopadhyaya
- Department of Biochemistry, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, West Bengal, India
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, P-1/12, CIT Scheme VII M, Kolkata 700054, West Bengal, India
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137
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Rathi PC, Jaeger KE, Gohlke H. Structural Rigidity and Protein Thermostability in Variants of Lipase A from Bacillus subtilis. PLoS One 2015; 10:e0130289. [PMID: 26147762 PMCID: PMC4493141 DOI: 10.1371/journal.pone.0130289] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 05/18/2015] [Indexed: 11/24/2022] Open
Abstract
Understanding the origin of thermostability is of fundamental importance in protein biochemistry. Opposing views on increased or decreased structural rigidity of the folded state have been put forward in this context. They have been related to differences in the temporal resolution of experiments and computations that probe atomic mobility. Here, we find a significant (p = 0.004) and fair (R2 = 0.46) correlation between the structural rigidity of a well-characterized set of 16 mutants of lipase A from Bacillus subtilis (BsLipA) and their thermodynamic thermostability. We apply the rigidity theory-based Constraint Network Analysis (CNA) approach, analyzing directly and in a time-independent manner the statics of the BsLipA mutants. We carefully validate the CNA results on macroscopic and microscopic experimental observables and probe for their sensitivity with respect to input structures. Furthermore, we introduce a robust, local stability measure for predicting thermodynamic thermostability. Our results complement work that showed for pairs of homologous proteins that raising the structural stability is the most common way to obtain a higher thermostability. Furthermore, they demonstrate that related series of mutants with only a small number of mutations can be successfully analyzed by CNA, which suggests that CNA can be applied prospectively in rational protein design aimed at higher thermodynamic thermostability.
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Affiliation(s)
- Prakash Chandra Rathi
- Institute of Pharmaceutical and Medical Chemistry, Heinrich-Heine-University, Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University, Düsseldorf, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Research Centre Jülich, Jülich, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medical Chemistry, Heinrich-Heine-University, Düsseldorf, Germany
- * E-mail:
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138
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Thomas JL, Bose HS. Regulation of human 3-beta-hydroxysteroid dehydrogenase type-2 (3βHSD2) by molecular chaperones and the mitochondrial environment affects steroidogenesis. J Steroid Biochem Mol Biol 2015; 151:74-84. [PMID: 25448736 DOI: 10.1016/j.jsbmb.2014.11.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/09/2014] [Accepted: 11/19/2014] [Indexed: 10/24/2022]
Abstract
Human 3-β-hydroxysteroid dehydrogenase/isomerase types 1 and 2 (3βHSD1 and 3βHSD2, respectively) are expressed in a tissue-specific pattern by different genes. Site-directed mutagenesis studies have confirmed the function of the catalytic amino acids (Tyr154, Lys 158, Ser124 in both isoenzymes), substrate/inhibitor isoform-specific residues (His156 and Arg195 in 3βHSD1) and cofactor binding residues (Asp36 provides NAD(+) specificity in both isoenzymes). However, detailed analysis of isoform-specific organelle localization and characterization is difficult due to the 93% amino acid identity between the two isoforms. With recent advances in the knowledge of mitochondrial architecture and localization of the various translocases, our laboratory has studied the mechanisms regulating mitochondrial 3βHSD2 localization. The mitochondrial N-terminal leader sequence of 3βHSD2 directs its entry into the mitochondria where it is localized to the intermembrane space (IMS). Unlike other mitochondrial proteins, the N-terminal signal sequence of 3βHSD2 is not cleaved upon mitochondrial import. 3βHSD2 interacts with the mitochondrial translocase, Tim50, to regulate progesterone and androstenedione formation. Our studies suggest that its activity at the IMS is facilitated in a partially unfolded "molten globule" conformation by the proton pump between the matrix and IMS. The unfolded protein is refolded by the mitochondrial chaperones. The protons at the IMS are absorbed by the lipid vesicles, to maintain the proton pump and recycle 3βHSD2. As a result, one molecule of 3βHSD2 may participate in multiple catalytic reactions. In summary, the steroidogenic cell recycles 3βHSD2 to catalyze the reactions needed to produce androstenedione, progesterone and 17α-hydroxyprogesterone on demand in coordination with the mitochondrial translocase, Tim50. This article is part of a Special Issue entitled 'Steroid/Sterol signaling'.
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Affiliation(s)
- James L Thomas
- Division of Basic Medical Sciences, Mercer University School of Medicine, Macon, GA 31207, USA
| | - Himangshu S Bose
- Departments of Biochemistry, Biomedical Sciences, Mercer University School of Medicine, Savannah, GA 31404, USA; Memorial University Medical Center, Anderson Cancer Institute, Savannah, GA 31404, USA.
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139
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Ferrante A, Templeton M, Hoffman M, Castellini MJ. The Thermodynamic Mechanism of Peptide-MHC Class II Complex Formation Is a Determinant of Susceptibility to HLA-DM. THE JOURNAL OF IMMUNOLOGY 2015; 195:1251-61. [PMID: 26116504 DOI: 10.4049/jimmunol.1402367] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 05/28/2015] [Indexed: 11/19/2022]
Abstract
Peptides bind MHC class II molecules through a thermodynamically nonadditive process consequent to the flexibility of the reactants. Currently, how the specific outcome of this binding process affects the ensuing epitope selection needs resolution. Calorimetric assessment of binding thermodynamics for hemagglutinin 306-319 peptide variants to the human MHC class II HLA-DR1 (DR1) and a mutant DR1 reveals that peptide/DR1 complexes can be formed with different enthalpic and entropic contributions. Complexes formed with a smaller entropic penalty feature circular dichroism spectra consistent with a non-compact form, and molecular dynamics simulation shows a more flexible structure. The opposite binding mode, compact and less flexible, is associated with greater entropic penalty. These structural variations are associated with rearrangements of residues known to be involved in HLA-DR (DM) binding, affinity of DM for the complex, and complex susceptibility to DM-mediated peptide exchange. Thus, the thermodynamic mechanism of peptide binding to DR1 correlates with the structural rigidity of the complex, and DM mediates peptide exchange by "sensing" flexible complexes in which the aforementioned residues are rearranged at a higher frequency than in more rigid ones.
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Affiliation(s)
- Andrea Ferrante
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775;
| | - Megan Templeton
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775; Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, AK 99775; and
| | - Megan Hoffman
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK 99775
| | - Margaret J Castellini
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK 99775
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140
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Hande VR, Chakrabarty S. Structural Order of Water Molecules around Hydrophobic Solutes: Length-Scale Dependence and Solute–Solvent Coupling. J Phys Chem B 2015; 119:11346-57. [DOI: 10.1021/acs.jpcb.5b03449] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vrushali R. Hande
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune-411008, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune-411008, India
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141
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Meadows JA, Wargo MJ. Carnitine in bacterial physiology and metabolism. MICROBIOLOGY (READING, ENGLAND) 2015; 161:1161-74. [PMID: 25787873 PMCID: PMC4635513 DOI: 10.1099/mic.0.000080] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/17/2015] [Indexed: 12/23/2022]
Abstract
Carnitine is a quaternary amine compound found at high concentration in animal tissues, particularly muscle, and is most well studied for its contribution to fatty acid transport into mitochondria. In bacteria, carnitine is an important osmoprotectant, and can also enhance thermotolerance, cryotolerance and barotolerance. Carnitine can be transported into the cell or acquired from metabolic precursors, where it can serve directly as a compatible solute for stress protection or be metabolized through one of a few distinct pathways as a nutrient source. In this review, we summarize what is known about carnitine physiology and metabolism in bacteria. In particular, recent advances in the aerobic and anaerobic metabolic pathways as well as the use of carnitine as an electron acceptor have addressed some long-standing questions in the field.
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Affiliation(s)
- Jamie A. Meadows
- Department of Microbiology and Molecular Genetics, University of Vermont College of Medicine, 95 Carrigan Drive, Burlington, VT, 05405, USA
| | - Matthew J. Wargo
- Department of Microbiology and Molecular Genetics, University of Vermont College of Medicine, 95 Carrigan Drive, Burlington, VT, 05405, USA
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142
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Sodium-reduced lean sausages with fish oil optimized by a mixture design approach. Meat Sci 2015; 104:67-77. [DOI: 10.1016/j.meatsci.2015.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 11/05/2014] [Accepted: 02/13/2015] [Indexed: 11/19/2022]
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143
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Gharanlar J, Hosseinkhani S, Sajedi RH, Yaghmaei P. The Effect of Surface Charge Saturation on Heat-induced Aggregation of Firefly Luciferase. Photochem Photobiol 2015; 91:1156-64. [PMID: 25989897 DOI: 10.1111/php.12467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/27/2015] [Indexed: 10/23/2022]
Abstract
We present here the effect of firefly luciferase surface charge saturation and the presence of some additives on its thermal-induced aggregation. Three mutants of firefly luciferase prepared by introduction of surface Arg residues named as 2R, 3R and 5R have two, three and five additional arginine residues substituted at their surface compared to native luciferase; respectively. Turbidimetric study of heat-induced aggregation indicates that all three mutants were reproducibly aggregated at higher rates relative to wild type in spite of their higher thermostability. Among them, 2R had most evaluated propensity to heat-induced aggregation. Therefore, the hydrophilization followed by appearing of more substituted arginine residues with positive charge on the firefly luciferase surface was not reduced its thermal aggregation. Nevertheless, at the same condition in the presence of charged amino acids, e.g. Arg, Lys and Glu, as well as a hydrophobic amino acid, e.g. Val, the heat-induced aggregation of wild type and mutants of firefly luciferases was markedly decelerated than those in the absence of additives. On the basis of obtained results it seems, relinquishment of variety in charge of amino acid side chains, they via local interactions with proteins cause to decrease rate and extent of their thermal aggregation.
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Affiliation(s)
- Jamileh Gharanlar
- Department of Biology, Faculty of Basic Sciences, Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Parichehr Yaghmaei
- Department of Biology, Faculty of Basic Sciences, Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran
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144
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145
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Sikosek T, Chan HS. Biophysics of protein evolution and evolutionary protein biophysics. J R Soc Interface 2015; 11:20140419. [PMID: 25165599 DOI: 10.1098/rsif.2014.0419] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence-structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by 'hidden' conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution.
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Affiliation(s)
- Tobias Sikosek
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Physics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Physics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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146
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Grinberg VY, Senin AA, Grinberg NV, Burova TV, Dubovik AS, Potekhin SA, Erukhimovich IY. High pressure effects under phase separation of aqueous solutions of poly(N-isopropylacryamide): A HS-DSC study. POLYMER 2015. [DOI: 10.1016/j.polymer.2015.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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147
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The Calorimetry Conference Celebrates Professor Robert H. Wood’s Eightieth Birthday. J SOLUTION CHEM 2015. [DOI: 10.1007/s10953-015-0340-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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148
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Faure G, Koonin EV. Universal distribution of mutational effects on protein stability, uncoupling of protein robustness from sequence evolution and distinct evolutionary modes of prokaryotic and eukaryotic proteins. Phys Biol 2015; 12:035001. [PMID: 25927823 DOI: 10.1088/1478-3975/12/3/035001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Robustness to destabilizing effects of mutations is thought of as a key factor of protein evolution. The connections between two measures of robustness, the relative core size and the computationally estimated effect of mutations on protein stability (ΔΔG), protein abundance and the selection pressure on protein-coding genes (dN/dS) were analyzed for the organisms with a large number of available protein structures including four eukaryotes, two bacteria and one archaeon. The distribution of the effects of mutations in the core on protein stability is universal and indistinguishable in eukaryotes and bacteria, centered at slightly destabilizing amino acid replacements, and with a heavy tail of more strongly destabilizing replacements. The distribution of mutational effects in the hyperthermophilic archaeon Thermococcus gammatolerans is significantly shifted toward strongly destabilizing replacements which is indicative of stronger constraints that are imposed on proteins in hyperthermophiles. The median effect of mutations is strongly, positively correlated with the relative core size, in evidence of the congruence between the two measures of protein robustness. However, both measures show only limited correlations to the expression level and selection pressure on protein-coding genes. Thus, the degree of robustness reflected in the universal distribution of mutational effects appears to be a fundamental, ancient feature of globular protein folds whereas the observed variations are largely neutral and uncoupled from short term protein evolution. A weak anticorrelation between protein core size and selection pressure is observed only for surface residues in prokaryotes but a stronger anticorrelation is observed for all residues in eukaryotic proteins. This substantial difference between proteins of prokaryotes and eukaryotes is likely to stem from the demonstrable higher compactness of prokaryotic proteins.
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Affiliation(s)
- Guilhem Faure
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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149
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Micklitsch CM, Medina SH, Yucel T, Nagy-Smith KJ, Pochan DJ, Schneider JP. Influence of Hydrophobic Face Amino Acids on the Hydrogelation of β-Hairpin Peptide Amphiphiles. Macromolecules 2015; 48:1281-1288. [PMID: 33223568 DOI: 10.1021/ma5024796] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hydrophobic residues provide much of the thermodynamic driving force for the folding, self-assembly, and consequent hydrogelation of amphiphilic β-hairpin peptides. We investigate how the identity of hydrophobic side chains displayed from the hydrophobic face of these amphiphilic peptides influences their behavior to expound on the design criteria important to gel formation. Six peptides were designed that globally incorporate valine, aminobutyric acid, norvaline, norleucine, phenylalanine, or isoleucine on the hydrophobic face of the hairpin to study how systematic changes in hydrophobic content, β-sheet propensity, and aromaticity affect gelation. Circular dichroism (CD) spectroscopy indicates that hydrophobic content, rather than β-sheet propensity, dictates the temperature- and pH-dependent folding and assembly behavior of these peptides. Transmission electron microscopy (TEM) and small-angle neutron scattering (SANS) show that the local morphology of the fibrils formed via self-assembly is little affected by amino acid type. However, residue type does influence the propensity of peptide fibrils to undergo higher order assembly events. Oscillatory rheology shows that the mechanical rigidity of the peptide gels is highly influenced by residue type, but there is no apparent correlation between rigidity and residue hydrophobicity nor β-sheet propensity. Lastly, the large planar aromatic side chain of phenylalanine supports hairpin folding and assembly, affording a gel characterized by a rate of formation and storage modulus similar to the parent valine-containing peptide.
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Affiliation(s)
- Christopher M Micklitsch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Scott H Medina
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21701, United States
| | - Tuna Yucel
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Katelyn J Nagy-Smith
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.,Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21701, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Joel P Schneider
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21701, United States
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150
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Cheng B, Wu S, Liu S, Rodriguez-Aliaga P, Yu J, Cui S. Protein denaturation at a single-molecule level: the effect of nonpolar environments and its implications on the unfolding mechanism by proteases. NANOSCALE 2015; 7:2970-2977. [PMID: 25597693 DOI: 10.1039/c4nr07140a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Most proteins are typically folded into predetermined three-dimensional structures in the aqueous cellular environment. However, proteins can be exposed to a nonpolar environment under certain conditions, such as inside the central cavity of chaperones and unfoldases during protein degradation. It remains unclear how folded proteins behave when moved from an aqueous solvent to a nonpolar one. Here, we employed single-molecule atomic force microscopy and molecular dynamics (MD) simulations to investigate the structural and mechanical variations of a polyprotein, I278, during the change from a polar to a nonpolar environment. We found that the polyprotein was unfolded into an unstructured polypeptide spontaneously when pulled into nonpolar solvents. This finding was corroborated by MD simulations where I27 was dragged from water into a nonpolar solvent, revealing details of the unfolding process at the water/nonpolar solvent interface. These results highlight the importance of water in maintaining folding stability, and provide insights into the response of folded proteins to local hydrophobic environments.
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Affiliation(s)
- Bo Cheng
- Key Lab of Advanced Technologies of Materials, Ministry of Education of China, Southwest Jiaotong University, Chengdu 610031, China.
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