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Gupta MN, Uversky VN. Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure. Protein Sci 2024; 33:e4968. [PMID: 38532700 DOI: 10.1002/pro.4968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/18/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
The rationale for replacing the old binary of structure-function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disorder is actually critical for understanding the protein-protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation of amyloids and function of prions is often discussed, the roles of intrinsic disorder in infectious diseases and protein function under extreme conditions are also becoming clear. This review is an attempt to discuss how our current understanding of protein function, specificity, and evolution fit better with the continuum model. This integration of structure and disorder under a single model may bring greater clarity in our continuing quest for understanding proteins and molecular mechanisms of their functionality.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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2
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Melnik TN, Majorina MA, Vorobeva DE, Nagibina GS, Veselova VR, Glukhova KA, Pak MA, Ivankov DN, Uversky VN, Melnik BS. Design of stable circular permutants of the GroEL chaperone apical domain. Cell Commun Signal 2024; 22:90. [PMID: 38303060 PMCID: PMC10836027 DOI: 10.1186/s12964-023-01426-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/08/2023] [Indexed: 02/03/2024] Open
Abstract
Enhancing protein stability holds paramount significance in biotechnology, therapeutics, and the food industry. Circular permutations offer a distinctive avenue for manipulating protein stability while keeping intra-protein interactions intact. Amidst the creation of circular permutants, determining the optimal placement of the new N- and C-termini stands as a pivotal, albeit largely unexplored, endeavor. In this study, we employed PONDR-FIT's predictions of disorder propensity to guide the design of circular permutants for the GroEL apical domain (residues 191-345). Our underlying hypothesis posited that a higher predicted disorder value would correspond to reduced stability in the circular permutants, owing to the increased likelihood of fluctuations in the novel N- and C-termini. To substantiate this hypothesis, we engineered six circular permutants, positioning glycines within the loops as locations for the new N- and C-termini. We demonstrated the validity of our hypothesis along the set of the designed circular permutants, as supported by measurements of melting temperatures by circular dichroism and differential scanning microcalorimetry. Consequently, we propose a novel computational methodology that rationalizes the design of circular permutants with projected stability. Video Abstract.
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Affiliation(s)
- Tatiana N Melnik
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia
| | - Maria A Majorina
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia
| | - Daria E Vorobeva
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia
| | - Galina S Nagibina
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia
| | - Victoria R Veselova
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia
| | - Ksenia A Glukhova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaja Str. 3, Puschino, Moscow Region, 142290, Russia
| | - Marina A Pak
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow, 121205, Russia
| | - Dmitry N Ivankov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, Moscow, 121205, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Center and Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| | - Bogdan S Melnik
- Institute of Protein Research, Russian Academy of Sciences, Institutskaja Str. 4, Pushchino, Moscow Region, 142290, Russia.
- Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Prospekt Nauki 6, Pushchino, Moscow Region, 142290, Russia.
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Wang H, Chen H, Li Q, Yu F, Yan Y, Liu S, Tian J, Tan J. Enhancing the thermostability of transglutaminase from Streptomyces mobaraensis based on the rational design of a disulfide bond. Protein Expr Purif 2022. [DOI: 10.1016/j.pep.2022.106079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 11/22/2022]
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4
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Sen S, Dey A, Bandhyopadhyay S, Uversky VN, Maulik U. Understanding structural malleability of the SARS-CoV-2 proteins and relation to the comorbidities. Brief Bioinform 2021; 22:6304388. [PMID: 34143202 DOI: 10.1093/bib/bbab232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/13/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a causative agent of the coronavirus disease (COVID-19), is a part of the $\beta $-Coronaviridae family. The virus contains five major protein classes viz., four structural proteins [nucleocapsid (N), membrane (M), envelop (E) and spike glycoprotein (S)] and replicase polyproteins (R), synthesized as two polyproteins (ORF1a and ORF1ab). Due to the severity of the pandemic, most of the SARS-CoV-2-related research are focused on finding therapeutic solutions. However, studies on the sequences and structure space throughout the evolutionary time frame of viral proteins are limited. Besides, the structural malleability of viral proteins can be directly or indirectly associated with the dysfunctionality of the host cell proteins. This dysfunctionality may lead to comorbidities during the infection and may continue at the post-infection stage. In this regard, we conduct the evolutionary sequence-structure analysis of the viral proteins to evaluate their malleability. Subsequently, intrinsic disorder propensities of these viral proteins have been studied to confirm that the short intrinsically disordered regions play an important role in enhancing the likelihood of the host proteins interacting with the viral proteins. These interactions may result in molecular dysfunctionality, finally leading to different diseases. Based on the host cell proteins, the diseases are divided in two distinct classes: (i) proteins, directly associated with the set of diseases while showing similar activities, and (ii) cytokine storm-mediated pro-inflammation (e.g. acute respiratory distress syndrome, malignancies) and neuroinflammation (e.g. neurodegenerative and neuropsychiatric diseases). Finally, the study unveils that males and postmenopausal females can be more vulnerable to SARS-CoV-2 infection due to the androgen-mediated protein transmembrane serine protease 2.
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Affiliation(s)
- Sagnik Sen
- Department of Computer Science and Engineering, Jadavpur University, Kolkata-32, West Bengal, India
| | - Ashmita Dey
- Department of Computer Science and Engineering, Jadavpur University, Kolkata-32, West Bengal, India
| | | | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region, 142290 Russia
| | - Ujjwal Maulik
- Department of Computer Science and Engineering, Jadavpur University, Kolkata-32, West Bengal, India
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Meric G, Naik S, Hunter AK, Robinson AS, Roberts CJ. Challenges for design of aggregation-resistant variants of granulocyte colony-stimulating factor. Biophys Chem 2021; 277:106630. [PMID: 34119805 DOI: 10.1016/j.bpc.2021.106630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/14/2021] [Accepted: 05/31/2021] [Indexed: 01/15/2023]
Abstract
Non-native protein aggregation is a long-standing issue in pharmaceutical biotechnology. A rational design approach was used in order to identify variants of recombinant human granulocyte colony-stimulating factor (rhG-CSF) with lower aggregation propensity at solution conditions that are typical of commercial formulation. The approach used aggregation-prone-region (APR) predictors to select single amino acid substitutions that were predicted to decrease intrinsic aggregation propensity (IAP). The results of static light scattering temperature-ramps and chemical unfolding experiments demonstrated that none of the selected variants exhibited improved aggregation resistance, and the apparent conformational stability of each variant was lower than that of WT. Aggregation studies under partly denaturing conditions suggested that the IAP of at least one variant remained unaltered. Overall, this study highlights a general challenge in designing aggregation resistance for proteins, due to the need to accurately predict both APRs and conformational stability.
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Affiliation(s)
- Gulsum Meric
- Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States.
| | - Subhashchandra Naik
- Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States.
| | - Alan K Hunter
- Biopharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD 20878, United States.
| | - Anne S Robinson
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, United States.
| | - Christopher J Roberts
- Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States.
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6
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Wang R, Wang S, Xu Y, Yu X. Engineering of a thermo-alkali-stable lipase from Rhizopus chinensis by rational design of a buried disulfide bond and combinatorial mutagenesis. J Ind Microbiol Biotechnol 2020; 47:1019-1030. [PMID: 33070231 DOI: 10.1007/s10295-020-02324-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/09/2020] [Indexed: 01/21/2023]
Abstract
To improve the thermostability of the lipase (r27RCL) from Rhizopus chinensis through rational design, a newly introduced buried disulfide bond F223C/G247C was proved to be beneficial to thermostability. Interestingly, F223C/G247C was also found to improve the alkali tolerance of the lipase. Subsequently, six other thermostabilizing mutations from our previous work were integrated into the mutant F223C/G247C, leading to a thermo-alkali-stable mutant m32. Compared to the wild-type lipase, the associative effect of the beneficial mutations showed significant improvements on the thermostability of m32, with a 74.7-fold increase in half-life at 60 °C, a 21.2 °C higher [Formula: see text] value and a 10 °C elevation in optimum temperature. The mutated m32 was also found stable at pH 9.0-10.0. Furthermore, the molecular dynamics simulations of m32 indicated that its rigidity was enhanced due to the decreased solvent-accessible surface area, a newly formed salt bridge, and the increased ΔΔG values.
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Affiliation(s)
- Rui Wang
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Shang Wang
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Xiaowei Yu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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7
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Abstract
Directed stabilization of globular proteins via substitution of a minimal number of amino acid residues is one of the most complicated experimental tasks. In this work, we have successfully used algorithms for the evaluation of intrinsic disorder predisposition (such as PONDR® FIT and IsUnstruct) as tools for searching for the weakened regions in structured globular proteins. We have shown that the weakened regions found by these programs as regions with highest levels of predicted intrinsic disorder predisposition are a suitable target for introduction of stabilizing mutations.
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Affiliation(s)
- Galina S Nagibina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Tatiana N Melnik
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Ksenia A Glukhova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States; Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia.
| | - Bogdan S Melnik
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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8
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Zhang Y, Yang J, Yu X, Hu X, Zhang H. Engineering Leuconostoc mesenteroides dextransucrase by inserting disulfide bridges for enhanced thermotolerance. Enzyme Microb Technol 2020; 139:109603. [PMID: 32732025 DOI: 10.1016/j.enzmictec.2020.109603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/28/2020] [Accepted: 05/19/2020] [Indexed: 11/23/2022]
Abstract
The disulfide bridge is a very important part of the peptide chain and plays an important role in stabilizing the protein structure and maintaining its active function. One hundred and fourteen potential disulfide bridges were determined by Disulfide by Design™, and 4 disulfide bridges were constructed for the purpose of obtaining new enzyme species with high thermotolerance. High thermotolerance is achieved by increasing the number of hydrogen bonds between amino acids. The optimum temperatures of mutant L838C-V887C and A948C-A1013C were improved by 10 °C compared to that of the original enzyme, which was beneficial to reduce the viscosity of the reaction system. Some of the mutations resulted in the alteration of catalytic specificity, and the products D739C-F932C and A948C-A1013C catalyzed synthesis of dextran containing a new α(1-4) glycosidic linkage and α(1-2) glycosidic linkage. This study may provide information valuable for increasing the reaction temperature of recombinant dextransucrase. The molecular docking study presents a plausible explanation for reaction specificity alteration and optimum temperature improvement for the mutants.
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9
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Nagibina GS, Glukhova KA, Uversky VN, Melnik TN, Melnik BS. Intrinsic Disorder-Based Design of Stable Globular Proteins. Biomolecules 2019; 10:E64. [PMID: 31906016 PMCID: PMC7022990 DOI: 10.3390/biom10010064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/18/2019] [Accepted: 12/20/2019] [Indexed: 11/24/2022] Open
Abstract
Directed stabilization of globular proteins via substitution of a minimal number of amino acid residues is one of the most complicated experimental tasks. This work summarizes our research on the effect of amino acid substitutions on the protein stability utilizing the outputs of the analysis of intrinsic disorder predisposition of target proteins. This allowed us to formulate the basis of one of the possible approaches to the stabilization of globular proteins. The idea is quite simple. To stabilize a protein as a whole, one needs to find its "weakest spot" and stabilize it, but the question is how this weak spot can be found in a query protein. Our approach is based on the utilization of the computational tools for the per-residue evaluation of intrinsic disorder predisposition to search for the "weakest spot" of a query protein (i.e., the region(s) with the highest local predisposition for intrinsic disorder). When such "weakest spot" is found, it can be stabilized through a limited number of point mutations by introducing order-promoting residues at hot spots, thereby increasing structural stability of a protein as a whole. Using this approach, we were able to obtain stable mutant forms of several globular proteins, such as Gαo, GFP, ribosome protein L1, and circular permutant of apical domain of GroEL.
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Affiliation(s)
- Galina S. Nagibina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (G.S.N.); (K.A.G.); (T.N.M.)
| | - Ksenia A. Glukhova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (G.S.N.); (K.A.G.); (T.N.M.)
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA;
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Moscow Region, Russia
| | - Tatiana N. Melnik
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (G.S.N.); (K.A.G.); (T.N.M.)
| | - Bogdan S. Melnik
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (G.S.N.); (K.A.G.); (T.N.M.)
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Roura Padrosa D, Castro J, Romero-Casañas A, Ribó M, Vilanova M, Benito A. Construction of Highly Stable Cytotoxic Nuclear-Directed Ribonucleases. Molecules 2018; 23:E3273. [PMID: 30544927 DOI: 10.3390/molecules23123273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/05/2018] [Accepted: 12/08/2018] [Indexed: 02/01/2023] Open
Abstract
Ribonucleases are proteins whose use is promising in anticancer therapy. We have previously constructed different human pancreatic ribonuclease variants that are selectively cytotoxic for tumor cells by introducing a nuclear localization signal into their sequence. However, these modifications produced an important decrease in their stability compromising their behavior in vivo. Here, we show that we can significantly increase the thermal stability of these cytotoxic proteins by introducing additional disulfide bonds by site-directed mutagenesis. One of these variants increases its thermal stability by around 17 °C, without affecting its catalytic activity while maintaining the cytotoxic activity against tumor cells. We also show that the most stable variant is significantly more resistant to proteolysis when incubated with proteinase K or with human sera, suggesting that its half-live could be increased in vivo once administered.
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11
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Melnik TN, Nagibina GS, Surin AK, Glukhova KA, Melnik BS. Artificial Cysteine Bridges on the Surface of Green Fluorescent Protein Affect Hydration of Its Transition and Intermediate States. Mol Biol 2018. [DOI: 10.1134/s0026893318010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Affiliation(s)
- Gulsum Meric
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716
| | - Anne S. Robinson
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118
| | - Christopher J. Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716
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Fanaei Kahrani Z, Emamzadeh R, Nazari M, Rasa SMM. Molecular basis of thermostability enhancement of Renilla luciferase at higher temperatures by insertion of a disulfide bridge into the structure. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2017; 1865:252-9. [DOI: 10.1016/j.bbapap.2016.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 10/31/2016] [Accepted: 11/14/2016] [Indexed: 11/20/2022]
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14
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Stepanenko OV, Roginskii DO, Stepanenko OV, Kuznetsova IM, Uversky VN, Turoverov KK. Structure and stability of recombinant bovine odorant-binding protein: I. Design and analysis of monomeric mutants. PeerJ 2016; 4:e1933. [PMID: 27114880 PMCID: PMC4841250 DOI: 10.7717/peerj.1933] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 03/23/2016] [Indexed: 02/02/2023] Open
Abstract
Bovine odorant-binding protein (bOBP) differs from other lipocalins by lacking the conserved disulfide bond and for being able to form the domain-swapped dimers. To identify structural features responsible for the formation of the bOBP unique dimeric structure and to understand the role of the domain swapping on maintaining the native structure of the protein, structural properties of the recombinant wild type bOBP and its mutant that cannot dimerize via the domain swapping were analyzed. We also looked at the effect of the disulfide bond by designing a monomeric bOBPs with restored disulfide bond which is conserved in other lipocalins. Finally, to understand which features in the microenvironment of the bOBP tryptophan residues play a role in the defining peculiarities of the intrinsic fluorescence of this protein we designed and investigated single-tryptophan mutants of the monomeric bOBP. Our analysis revealed that the insertion of the glycine after the residue 121 of the bOBP prevents domain swapping and generates a stable monomeric protein bOBP-Gly121+. We also show that the restored disulfide bond in the GCC-bOBP mutant leads to the noticeable stabilization of the monomeric structure. Structural and functional analysis revealed that none of the amino acid substitutions introduced to the bOBP affected functional activity of the protein and that the ligand binding leads to the formation of a more compact and stable state of the recombinant bOBP and its mutant monomeric forms. Finally, analysis of the single-tryptophan mutants of the monomeric bOBP gave us a unique possibility to find peculiarities of the microenvironment of tryptophan residues which were not previously described.
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Affiliation(s)
- Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science , St. Petersburg , Russia
| | - Denis O Roginskii
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science , St. Petersburg , Russia
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science , St. Petersburg , Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science , St. Petersburg , Russia
| | - Vladimir N Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Russia; Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Russia; Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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15
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Perret P, Ahmadi M, Riou L, Bacot S, Pecher J, Poillot C, Broisat A, Ghezzi C, De Waard M. Biodistribution, Stability, and Blood Distribution of the Cell Penetrating Peptide Maurocalcine in Mice. Int J Mol Sci 2015; 16:27730-40. [PMID: 26610471 PMCID: PMC4661912 DOI: 10.3390/ijms161126054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/22/2015] [Accepted: 10/22/2015] [Indexed: 12/05/2022] Open
Abstract
Maurocalcine (MCa) is the first natural cell penetrating peptide to be discovered in animal venom. In addition to the fact that it represents a potent vector for the cell penetration of structurally diverse therapeutic compounds, MCa also displays several distinguishing features that make it a potential peptide of choice for clinical and biotechnological applications. The aim of the present study was to gain new information about the properties of MCa in vivo in order to delineate the future potential applications of this vector. For this purpose, two analogues of this peptide with (Tyr-MCa) and without (Lin-Tyr-MCa) disulfide bridges were synthesized, radiolabeled with 125I, and their in vitro stabilities were first evaluated in mouse blood. The results indicated that 125I-Tyr-MCa was stable in vitro and that the disulfide bridges conferred a competitive advantage for the stability of peptide. Following in vivo injection in mice, 125I-Tyr-MCa targeted peripheral organs with interesting quantitative differences and the main route of peptide elimination was renal.
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Affiliation(s)
- Pascale Perret
- Grenoble Alpes University, 38041 Saint-Martin-d'Hères, France.
- Radiopharmaceutiques Biocliniques, INSERM, UMR S1039, 38700 La Tronche, France.
| | - Mitra Ahmadi
- Grenoble Alpes University, 38041 Saint-Martin-d'Hères, France.
- Radiopharmaceutiques Biocliniques, INSERM, UMR S1039, 38700 La Tronche, France.
| | - Laurent Riou
- Grenoble Alpes University, 38041 Saint-Martin-d'Hères, France.
- Radiopharmaceutiques Biocliniques, INSERM, UMR S1039, 38700 La Tronche, France.
| | - Sandrine Bacot
- Grenoble Alpes University, 38041 Saint-Martin-d'Hères, France.
- Radiopharmaceutiques Biocliniques, INSERM, UMR S1039, 38700 La Tronche, France.
| | - Julien Pecher
- Smartox Biotechnologies, Bâtiment Nanobio, 570 rue de la Chimie, 38400 Saint Martin d'Hères, France.
| | - Cathy Poillot
- Grenoble Alpes University, 38041 Saint-Martin-d'Hères, France.
- Science and Therapeutics, LabEx Ion Channels, Grenoble Institute of Neuroscience, INSERM, U836, 38700 La Tronche, France.
| | - Alexis Broisat
- Grenoble Alpes University, 38041 Saint-Martin-d'Hères, France.
- Radiopharmaceutiques Biocliniques, INSERM, UMR S1039, 38700 La Tronche, France.
| | - Catherine Ghezzi
- Grenoble Alpes University, 38041 Saint-Martin-d'Hères, France.
- Radiopharmaceutiques Biocliniques, INSERM, UMR S1039, 38700 La Tronche, France.
| | - Michel De Waard
- Grenoble Alpes University, 38041 Saint-Martin-d'Hères, France.
- Smartox Biotechnologies, Bâtiment Nanobio, 570 rue de la Chimie, 38400 Saint Martin d'Hères, France.
- Science and Therapeutics, LabEx Ion Channels, Grenoble Institute of Neuroscience, INSERM, U836, 38700 La Tronche, France.
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16
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Abstract
There is a wide variety of ion channel types with various types of blockers, making research in this field very complicated. To reduce this complexity, it is essential to study ion channels and their blockers independently. Scorpion toxins, a major class of blockers, are charged short peptides with high affinities for potassium channels. Their high selectivity and inhibitory properties make them an important pharmacological tool for treating autoimmune or nervous system disorders. Scorpion toxins typically have highly charged surfaces and-like other proteins-an intrinsic ability to bind ions (Friedman J Phys Chem B 115(29):9213-9223, 1996; Baldwin Biophys J 71(4):2056-2063, 1996; Vrbka et al. Proc Natl Acad Sci USA 103(42):15440-15444, 2006a; Vrbka et al. J Phys Chem B 110(13):7036-43, 2006b). Thus, their effects on potassium channels are usually investigated in various ionic solutions. In this work, computer simulations of protein structures were performed to analyze the structural properties of the key residues (i.e., those that are presumably involved in contact with the surfaces of the ion channels) of 12 scorpion toxins. The presence of the two most physiologically abundant cations, Na(+) and K(+), was considered. The results indicated that the ion-binding properties of the toxin residues vary. Overall, all of the investigated toxins had more stable structures in ionic solutions than in water. We found that both the number and length of elements in the secondary structure varied depending on the ionic solution used (i.e., in the presence of NaCl or KCl). This study revealed that the ionic solution should be chosen carefully before performing experiments on these toxins. Similarly, the influence of these ions should be taken into consideration in the design of toxin-based pharmaceuticals.
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Affiliation(s)
- Azadeh Nikouee
- Institute of Applied Physiology, Ulm University, Ulm, Germany
| | - Morteza Khabiri
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Prague 6, Czech Republic.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Lukasz Cwiklik
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
- J. Heyrovský Institute of Physical Chemistry Academy of Sciences of the Czech Republic v.v.i., Dolejskova 3, 18223, Prague 8, Czech Republic
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17
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Pitman DJ, Banerjee S, Macari SJ, Castaldi CA, Crone DE, Bystroff C. Exploring the folding pathway of green fluorescent protein through disulfide engineering. Protein Sci 2015; 24:341-53. [PMID: 25516354 PMCID: PMC4353360 DOI: 10.1002/pro.2621] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 12/09/2014] [Indexed: 11/12/2022]
Abstract
We have introduced two disulfide crosslinks into the loop regions on opposite ends of the beta barrel in superfolder green fluorescent protein (GFP) in order to better understand the nature of its folding pathway. When the disulfide on the side opposite the N/C-termini is formed, folding is 2× faster, unfolding is 2000× slower, and the protein is stabilized by 16 kJ/mol. But when the disulfide bond on the side of the termini is formed we see little change in the kinetics and stability. The stabilization upon combining the two crosslinks is approximately additive. When the kinetic effects are broken down into multiple phases, we observe Hammond behavior in the upward shift of the kinetic m-value of unfolding. We use these results in conjunction with structural analysis to assign folding intermediates to two parallel folding pathways. The data are consistent with a view that the two fastest transition states of folding are "barrel closing" steps. The slower of the two phases passes through an intermediate with the barrel opening occurring between strands 7 and 8, while the faster phase opens between 9 and 4. We conclude that disulfide crosslink-induced perturbations in kinetics are useful for mapping the protein folding pathway.
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Affiliation(s)
- Derek J Pitman
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies
| | - Shounak Banerjee
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies
| | - Stephen J Macari
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies
| | - Christopher A Castaldi
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies
| | - Donna E Crone
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies
| | - Christopher Bystroff
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies
- Department of Computer Science, Rensselaer Polytechnic InstituteTroy, New York
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18
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Floor RJ, Wijma HJ, Colpa DI, Ramos-Silva A, Jekel PA, Szymański W, Feringa BL, Marrink SJ, Janssen DB. Computational library design for increasing haloalkane dehalogenase stability. Chembiochem 2014; 15:1660-72. [PMID: 24976371 DOI: 10.1002/cbic.201402128] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Indexed: 11/05/2022]
Abstract
We explored the use of a computational design framework for the stabilization of the haloalkane dehalogenase LinB. Energy calculations, disulfide bond design, molecular dynamics simulations, and rational inspection of mutant structures predicted many stabilizing mutations. Screening of these in small mutant libraries led to the discovery of seventeen point mutations and one disulfide bond that enhanced thermostability. Mutations located in or contacting flexible regions of the protein had a larger stabilizing effect than mutations outside such regions. The combined introduction of twelve stabilizing mutations resulted in a LinB mutant with a 23 °C increase in apparent melting temperature (Tm,app , 72.5 °C) and an over 200-fold longer half-life at 60 °C. The most stable LinB variants also displayed increased compatibility with co-solvents, thus allowing substrate conversion and kinetic resolution at much higher concentrations than with the wild-type enzyme.
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Affiliation(s)
- Robert J Floor
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands)
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19
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Costanzo JA, O'Brien CJ, Tiller K, Tamargo E, Robinson AS, Roberts CJ, Fernandez EJ. Conformational stability as a design target to control protein aggregation. Protein Eng Des Sel 2014; 27:157-67. [DOI: 10.1093/protein/gzu008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Craig DB, Dombkowski AA. Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins. BMC Bioinformatics 2013; 14:346. [PMID: 24289175 PMCID: PMC3898251 DOI: 10.1186/1471-2105-14-346] [Citation(s) in RCA: 292] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 11/24/2013] [Indexed: 01/14/2023] Open
Abstract
Background Disulfide engineering is an important biotechnological tool that has advanced a wide range of research. The introduction of novel disulfide bonds into proteins has been used extensively to improve protein stability, modify functional characteristics, and to assist in the study of protein dynamics. Successful use of this technology is greatly enhanced by software that can predict pairs of residues that will likely form a disulfide bond if mutated to cysteines. Results We had previously developed and distributed software for this purpose: Disulfide by Design (DbD). The original DbD program has been widely used; however, it has a number of limitations including a Windows platform dependency. Here, we introduce Disulfide by Design 2.0 (DbD2), a web-based, platform-independent application that significantly extends functionality, visualization, and analysis capabilities beyond the original program. Among the enhancements to the software is the ability to analyze the B-factor of protein regions involved in predicted disulfide bonds. Importantly, this feature facilitates the identification of potential disulfides that are not only likely to form but are also expected to provide improved thermal stability to the protein. Conclusions DbD2 provides platform-independent access and significantly extends the original functionality of DbD. A web server hosting DbD2 is provided at http://cptweb.cpt.wayne.edu/DbD2/.
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Affiliation(s)
| | - Alan A Dombkowski
- Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan 48201, USA.
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21
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Abstract
Improving the stability of proteins is an important goal in many biomedical and industrial applications. A logical approach is to emulate stabilizing molecular interactions found in nature. Disulfide bonds are covalent interactions that provide substantial stability to many proteins and conform to well-defined geometric conformations, thus making them appealing candidates in protein engineering efforts. Disulfide engineering is the directed design of novel disulfide bonds into target proteins. This important biotechnological tool has achieved considerable success in a wide range of applications, yet the rules that govern the stabilizing effects of disulfide bonds are not fully characterized. Contrary to expectations, many designed disulfide bonds have resulted in decreased stability of the modified protein. We review progress in disulfide engineering, with an emphasis on the issue of stability and computational methods that facilitate engineering efforts.
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Affiliation(s)
- Alan A Dombkowski
- Carman and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Kazi Zakia Sultana
- Department of Computer Science & Engineering, Chittagong University of Engineering & Technology, Chittagong 4349, Bangladesh
| | - Douglas B Craig
- Carman and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI 48201, USA
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22
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Santambrogio C, Sperandeo P, Villa R, Sobott F, Polissi A, Grandori R. LptA assembles into rod-like oligomers involving disorder-to-order transitions. J Am Soc Mass Spectrom 2013; 24:1593-1602. [PMID: 23897621 DOI: 10.1007/s13361-013-0687-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/20/2013] [Accepted: 05/20/2013] [Indexed: 06/02/2023]
Abstract
LptA is a periplasmic protein involved in the transport of lipopolysaccharide (LPS) from the inner membrane (IM) to the outer membrane (OM) of Gram-negative bacteria. Growing evidence supports a model in which LptA assembles into oligomers, forming a physical bridge connecting IM and OM. This work investigates assembly and architecture of LptA oligomers. Circular dichroism and "native" electrospray-ionization ion-mobility mass spectrometry (ESI-IM-MS) are employed to test concentration dependence of LptA structural features and to analyze the morphology of higher-order aggregates. The results show that LptA progressively assembles into rod-like oligomers without fixed stoichiometry, and grows by an n + 1 mechanism up to at least the pentamer. The oligomerization process induces disorder-to-order transitions in the polypeptide chain. Comparison with crystallographic and computational data suggests that these conformational changes likely involve short disordered regions at the N- and C-termini of monomeric LptA. The protein response to thermal denaturation displays strong concentration dependence, indicating that oligomerization increases protein stability. LptA conformational stability can also be enhanced by in vitro LPS binding. The genesis of these fibrillar structures could be relevant for the correct transport of LPS across the bacterial periplasm.
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Affiliation(s)
- Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milan, Italy
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23
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Melnik TN, Povarnitsyna TV, Glukhov AS, Melnik BS. Multi-state proteins: approach allowing experimental determination of the formation order of structure elements in the green fluorescent protein. PLoS One 2012; 7:e48604. [PMID: 23155397 PMCID: PMC3498258 DOI: 10.1371/journal.pone.0048604] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 09/26/2012] [Indexed: 11/19/2022] Open
Abstract
The most complex problem in studying multi-state protein folding is the determination of the sequence of formation of protein intermediate states. A far more complex issue is to determine at what stages of protein folding its various parts (secondary structure elements) develop. The structure and properties of different intermediate states depend in particular on these parts. An experimental approach, named μ-analysis, which allows understanding the order of formation of structural elements upon folding of a multi-state protein was used in this study. In this approach the same elements of the protein secondary structure are “tested” by substitutions of single hydrophobic amino acids and by incorporation of cysteine bridges. Single substitutions of hydrophobic amino acids contribute to yielding information on the late stages of protein folding while incorporation of ss-bridges allows obtaining data on the initial stages of folding. As a result of such an μ-analysis, we have determined the order of formation of beta-hairpins upon folding of the green fluorescent protein.
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Affiliation(s)
- Tatiana N. Melnik
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | | | | | - Bogdan S. Melnik
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
- * E-mail:
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