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Izzi G, Paladino A, Oliva R, Barra G, Ruggiero A, Del Vecchio P, Vitagliano L, Graziano G. Destabilization of the D2 domain of Thermotoga maritima arginine binding protein induced by guanidinium thiocyanate and its counteraction by stabilizing agents. Protein Sci 2024; 33:e5146. [PMID: 39150147 PMCID: PMC11328109 DOI: 10.1002/pro.5146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/17/2024]
Abstract
D2 is a structural and cooperative domain of Thermotoga maritima Arginine Binding Protein, that possesses a remarkable conformational stability, with a denaturation temperature of 102.6°C, at pH 7.4. The addition of potassium thiocyanate causes a significant decrease in the D2 denaturation temperature. The interactions of thiocyanate ions with D2 have been studied by means of isothermal titration calorimetry measurements and molecular dynamics simulations. It emerged that: (a) 20-30 thiocyanate ions interact with the D2 surface and are present in its first solvation shell; (b) each of them makes several contacts with protein groups, both polar and nonpolar ones. The addition of guanidinium thiocyanate causes a marked destabilization of the D2 native state, because both the ions are denaturing agents. However, on adding to the solution containing D2 and guanidinium thiocyanate a stabilizing agent, such as TMAO, sucrose or sodium sulfate, a significant increase in denaturation temperature occurs. The present results confirm that counteraction is a general phenomenon for globular proteins.
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Affiliation(s)
- Guido Izzi
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | | | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Giovanni Barra
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | | | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | | | - Giuseppe Graziano
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis snc, Benevento, Italy
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Hussain M, Khan I, Chaudhary MN, Ali K, Mushtaq A, Jiang B, Zheng L, Pan Y, Hu J, Zou X. Phosphatidylserine: A comprehensive overview of synthesis, metabolism, and nutrition. Chem Phys Lipids 2024:105422. [PMID: 39097133 DOI: 10.1016/j.chemphyslip.2024.105422] [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: 06/07/2024] [Revised: 07/21/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024]
Abstract
Phosphatidylserine (PtdS) is classified as a glycerophospholipid and a primary anionic phospholipid and is particularly abundant in the inner leaflet of the plasma membrane in neural tissues. It is synthesized from phosphatidylcholine or phosphatidylethanolamine by exchanging the base head group with serine, and this reaction is catalyzed by PtdS synthase-1 and PtdS synthase-2 located in the endoplasmic reticulum. PtdS exposure on the outside surface of the cell is essential for eliminating apoptotic cells and initiating the blood clotting cascade. It is also a precursor of phosphatidylethanolamine, produced by PtdS decarboxylase in bacteria, yeast, and mammalian cells. Furthermore, PtdS acts as a cofactor for several necessary enzymes that participate in signaling pathways. Beyond these functions, several studies indicate that PtdS plays a role in various cerebral functions, including activating membrane signaling pathways, neuroinflammation, neurotransmission, and synaptic refinement associated with the central nervous system (CNS). This review discusses the occurrence of PtdS in nature and biosynthesis via enzymes and genes in plants, yeast, prokaryotes, mammalian cells, and the brain, and enzymatic synthesis through phospholipase D (PLD). Furthermore, we discuss metabolism, its role in the CNS, the fortification of foods, and supplementation for improving some memory functions, the results of which remain unclear. PtdS can be a potentially beneficial addition to foods for kids, seniors, athletes, and others, especially with the rising consumer trend favoring functional foods over conventional pills and capsules. Clinical studies have shown that PtdS is safe and well tolerated by patients.
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Affiliation(s)
- Mudassar Hussain
- State Key Laboratory of Food Science and Resources, National Engineering Research Center for Functional Food, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Imad Khan
- State Key Laboratory of Food Science and Resources, National Engineering Research Center for Functional Food, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | | | - Khubaib Ali
- State Key Laboratory of Food Science and Resources, National Engineering Research Center for Functional Food, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Anam Mushtaq
- State Key Laboratory of Food Science and Resources, National Engineering Research Center for Functional Food, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Bangzhi Jiang
- State Key Laboratory of Food Science and Resources, National Engineering Research Center for Functional Food, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Lei Zheng
- State Key Laboratory of Food Science and Resources, National Engineering Research Center for Functional Food, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Yuechao Pan
- State Key Laboratory of Food Science and Resources, National Engineering Research Center for Functional Food, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Jijie Hu
- State Key Laboratory of Food Science and Resources, National Engineering Research Center for Functional Food, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Xiaoqiang Zou
- State Key Laboratory of Food Science and Resources, National Engineering Research Center for Functional Food, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China; College of Food Science, Southwest University, Chongqing 400711, China.
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Kondratyev MS, Kabanov AV, Samchenko AA, Komarov VM, Khechinashvili NN. Parallel Computations in the Development of Thermostable Lipase Mutants. J STRUCT CHEM+ 2019. [DOI: 10.1134/s0022476618080292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Khechinashvili NN, Kabanov AV, Kondratyev MS, Polozov RV. Thermodynamics of globular proteins. J Biomol Struct Dyn 2017; 36:701-710. [PMID: 28278028 DOI: 10.1080/07391102.2017.1294112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The analysis of temperature-induced unfolding of proteins in aqueous solutions was performed. Based on the data of thermodynamic parameters of protein unfolding and using the method of semi-empirical calculations of hydration parameters at reference temperature 298 K, we obtained numerical values of enthalpy, free energy, and entropy which characterize the unfolding of proteins in the 'gas phase'. It was shown that specific values of the energy of weak intramolecular bonds (∆Hint), conformational free energy (∆Gconf) and entropy (∆Sconf) are the same for proteins with molecular weight 7-25 kDa. Using the energy value (∆Hint) and the proposed approach for estimation of the conformational entropy of native protein (SNC), numerical values of the absolute free energy (GNC) were obtained.
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Affiliation(s)
- Nikolay N Khechinashvili
- a Institute of Cell Biophysics, Russian Academy of Sciences , Pushchino , Moscow Region 142290 , Russia
| | - Artem V Kabanov
- a Institute of Cell Biophysics, Russian Academy of Sciences , Pushchino , Moscow Region 142290 , Russia
| | - Maxim S Kondratyev
- a Institute of Cell Biophysics, Russian Academy of Sciences , Pushchino , Moscow Region 142290 , Russia
| | - Robert V Polozov
- b Institute of Theoretical and Experimental Biophysics , Russian Academy of Sciences , Pushchino , Moscow Region 142290 , Russia
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5
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Pica A, Graziano G. Shedding light on the extra thermal stability of thermophilic proteins. Biopolymers 2017; 105:856-63. [PMID: 27449333 DOI: 10.1002/bip.22923] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 07/12/2016] [Accepted: 07/20/2016] [Indexed: 11/08/2022]
Abstract
An entropic stabilization mechanism has recently gained attention and credibility as the physical ground for the extra thermal stability of globular proteins from thermophilic microorganisms. An empirical result, obtained from the analysis of thermodynamic data for a large set of proteins, strengthens the general reliability of the theoretical approach originally devised to rationalize the occurrence of cold denaturation [Graziano, PCCP 2014, 16, 21755-21767]. It is shown that this theoretical approach can readily account for the entropic stabilization mechanism. On decreasing the conformational entropy gain associated with denaturation, the thermal stability of a model globular protein increases markedly.
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Affiliation(s)
- Andrea Pica
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, Napoli, 80126, Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port'Arsa 11, Benevento, 82100, Italy.
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Balcão VM, Vila MMDC. Structural and functional stabilization of protein entities: state-of-the-art. Adv Drug Deliv Rev 2015; 93:25-41. [PMID: 25312675 DOI: 10.1016/j.addr.2014.10.005] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 08/03/2014] [Accepted: 10/01/2014] [Indexed: 12/13/2022]
Abstract
Within the context of biomedicine and pharmaceutical sciences, the issue of (therapeutic) protein stabilization assumes particular relevance. Stabilization of protein and protein-like molecules translates into preservation of both structure and functionality during storage and/or targeting, and such stabilization is mostly attained through establishment of a thermodynamic equilibrium with the (micro)environment. The basic thermodynamic principles that govern protein structural transitions and the interactions of the protein molecule with its (micro)environment are, therefore, tackled in a systematic fashion. Highlights are given to the major classes of (bio)therapeutic molecules, viz. enzymes, recombinant proteins, (macro)peptides, (monoclonal) antibodies and bacteriophages. Modification of the microenvironment of the biomolecule via multipoint covalent attachment onto a solid surface followed by hydrophilic polymer co-immobilization, or physical containment within nanocarriers, are some of the (latest) strategies discussed aiming at full structural and functional stabilization of said biomolecules.
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Affiliation(s)
- Victor M Balcão
- LaBNUS - Biomaterials and Nanotechnology Laboratory, i(bs)(2) - intelligent biosensing and biomolecule stabilization research group, University of Sorocaba, Sorocaba, SP, Brazil; CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
| | - Marta M D C Vila
- LaBNUS - Biomaterials and Nanotechnology Laboratory, i(bs)(2) - intelligent biosensing and biomolecule stabilization research group, University of Sorocaba, Sorocaba, SP, Brazil
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Murakami S, Oshima H, Hayashi T, Kinoshita M. On the physics of thermal-stability changes upon mutations of a protein. J Chem Phys 2015; 143:125102. [DOI: 10.1063/1.4931814] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Shota Murakami
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hiraku Oshima
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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Khechinashvili NN, Capital Ka Cyrillicabanov AV, Kondratyev MS, Polozov RV. The entropic nature of protein thermal stabilization. J Biomol Struct Dyn 2013; 32:1396-405. [PMID: 23879480 DOI: 10.1080/07391102.2013.819788] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We performed thermodynamic analysis of temperature-induced unfolding of mesophilic and thermophilic proteins. It was shown that the variability in protein thermostability associated with pH-dependent unfolding or linked to the substitution of amino acid residues on the protein surface is evidence of the governing role of the entropy factor. Numerical values of conformational components in enthalpy, entropy and free energy which characterize protein unfolding in the "gas phase" were obtained. Based on the calculated absolute values of entropy and free energy, a model of protein unfolding is proposed in which the driving force is the conformational entropy of native protein, as an energy of the heat motion (T·S(NC)) increasing with temperature and acting as an factor devaluating the energy of intramolecular weak bonds in the transition state.
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Affiliation(s)
- Nikolay N Khechinashvili
- a Institute of Cell Biophysics, Russian Academy of Sciences , Pushchino, Moscow Region 142290 , Russia
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Tretyakova T, Shushanyan M, Partskhaladze T, Makharadze M, van Eldik R, Khoshtariya DE. Simplicity within the complexity: bilateral impact of DMSO on the functional and unfolding patterns of α-chymotrypsin. Biophys Chem 2013; 175-176:17-27. [PMID: 23524288 DOI: 10.1016/j.bpc.2013.02.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 02/05/2013] [Accepted: 02/09/2013] [Indexed: 10/27/2022]
Abstract
New understanding of the fundamental links between protein stability, conformational flexibility and function, can be gained through synergic studies on their catalytic and folding/unfolding properties under the influence of stabilizing/destabilizing additives. We explored an impact of dimethyl sulfoxide (DMSO), the moderate effector of multilateral action, on the kinetic (functional) and thermodynamic (thermal unfolding) patterns of a hydrolytic enzyme, α-chymotrypsin (α-CT), over a wide range of additive concentrations, 0-70% (v/v). Both the calorimetric and kinetic data exhibited rich behavior pointing to the complex interplay of global/local stability (and flexibility) patterns. The complex action of DMSO is explained through the negative and positive preferential solvation motifs that prevail for the extreme opposite, native-like and unfolded states, respectively, implying essential stabilization of compact domains by enhancement of interfacial water networks and destabilization of a flexible active site by direct binding of DMSO to the unoccupied specific positions intended for elongated polypeptide substrates.
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Affiliation(s)
- Tatyana Tretyakova
- Institute for Biophysics and Bionanosciences at the Department of Physics, I. Javakhishvili Tbilisi State University, I. Chavchavadze Ave. 3, 0128 Tbilisi, Georgia
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Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA. Structure fluctuations and conformational changes in protein binding. J Bioinform Comput Biol 2012; 10:1241002. [PMID: 22809338 DOI: 10.1142/s0219720012410028] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the residue centers of mass in proteins and a statistical analysis of conformation changes in the side-chains upon binding. Normal mode analysis and an elastic network model were applied to a set of protein complexes to calculate the residue fluctuations and develop the residue classification. Comparison with a classification based on normalized B-factors suggests that the B-factors may underestimate protein flexibility in solvent. Our classification shows that protein loops and disordered fragments are enriched with highly fluctuating residues and depleted with weakly fluctuating residues. Strategies for engineering thermostable proteins are discussed. To calculate the dihedral angles distribution functions, the configuration space was divided into cells by a cubic grid. The effect of protein association on the distribution functions depends on the amino acid type and a grid step in the dihedral angles space. The changes in the dihedral angles increase from the near-backbone dihedral angle to the most distant one, for most residues. On average, one fifth of the interface residues change the rotamer state upon binding, whereas the rest of the interface residues undergo local readjustments within the same rotamer.
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Affiliation(s)
- Anatoly M Ruvinsky
- Center for Bioinformatics, University of Kansas, Lawrence, KS 66047, USA.
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11
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Kondrat’ev MS, Kabanov AV, Komarov VM, Khechinashvili NN, Samchenko AA. Experience in simulating the structural and dynamic features of small proteins using table supercomputers. Biophysics (Nagoya-shi) 2011. [DOI: 10.1134/s0006350911060108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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12
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Durdenko EV, Kuznetsova SM, Basova LV, Tikhonenko SA, Saburova EA. Interaction of protein with charged colloidal particles. Biophysics (Nagoya-shi) 2011. [DOI: 10.1134/s0006350911040051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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