1
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Weinreb V, Weinreb G, Carter CW. High-throughput thermal denaturation of tryptophanyl-tRNA synthetase combinatorial mutants reveals high-order energetic coupling determinants of conformational stability. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:044304. [PMID: 37637481 PMCID: PMC10449480 DOI: 10.1063/4.0000182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/13/2023] [Indexed: 08/29/2023]
Abstract
Landscape descriptions provide a framework for identifying functionally significant dynamic linkages in proteins but cannot supply details. Rate measurements of combinatorial mutations can implicate dynamic linkages in catalysis. A major difficulty is filtering dynamic linkages from the vastly more numerous static interactions that stabilize domain folding. The Geobacillus stearothermophilus (TrpRS) D1 switch is such a dynamic packing motif; it links domain movement to catalysis and specificity. We describe Thermofluor and far UV circular dichroism melting curves for all 16 D1 switch variants to determine their higher-order impact on unliganded TrpRS stability. A prominent transition at intermediate temperatures in TrpRS thermal denaturation is molten globule formation. Combinatorial analysis of thermal melting transcends the protein landscape in four significant respects: (i) bioinformatic methods identify dynamic linkages from coordinates of multiple conformational states. (ii) Relative mutant melting temperatures, δTM, are proportional to free energy changes. (iii) Structural analysis of thermal melting implicates unexpected coupling between the D1 switch packing and regions of high local frustration. Those segments develop molten globular characteristics at the point of greatest complementarity to the chemical transition state and are the first TrpRS structures to melt. (iv) Residue F37 stabilizes both native and molten globular states; its higher-order interactions modify the relative intrinsic impacts of mutations to other D1 switch residues from those estimated for single point mutants. The D1 switch is a central component of an escapement mechanism essential to free energy transduction. These conclusions begin to relate the escapement mechanism to differential TrpRS conformational stabilities.
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Affiliation(s)
- Violetta Weinreb
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260, USA
| | | | - Charles W. Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260, USA
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2
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Interaction and physicochemical parameters of dodecyltrimethylammonium bromide and crystal violet dye mixture in aqueous alcohols and urea solution: Effects of change in composition and temperature. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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3
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Gupta MN, Uversky VN. Pre-Molten, Wet, and Dry Molten Globules en Route to the Functional State of Proteins. Int J Mol Sci 2023; 24:ijms24032424. [PMID: 36768742 PMCID: PMC9916686 DOI: 10.3390/ijms24032424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Transitions between the unfolded and native states of the ordered globular proteins are accompanied by the accumulation of several intermediates, such as pre-molten globules, wet molten globules, and dry molten globules. Structurally equivalent conformations can serve as native functional states of intrinsically disordered proteins. This overview captures the characteristics and importance of these molten globules in both structured and intrinsically disordered proteins. It also discusses examples of engineered molten globules. The formation of these intermediates under conditions of macromolecular crowding and their interactions with nanomaterials are also reviewed.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, 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, FL 33612, USA
- Correspondence: ; Tel.: +1-813-494-5816
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4
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Piersimoni L, Abd El Malek M, Bhatia T, Bender J, Brankatschk C, Calvo Sánchez J, Dayhoff GW, Di Ianni A, Figueroa Parra JO, Garcia-Martinez D, Hesselbarth J, Köppen J, Lauth LM, Lippik L, Machner L, Sachan S, Schmidt L, Selle R, Skalidis I, Sorokin O, Ubbiali D, Voigt B, Wedler A, Wei AAJ, Zorn P, Dunker AK, Köhn M, Sinz A, Uversky VN. Lighting up Nobel Prize-winning studies with protein intrinsic disorder. Cell Mol Life Sci 2022; 79:449. [PMID: 35882686 PMCID: PMC11072364 DOI: 10.1007/s00018-022-04468-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/18/2022] [Accepted: 07/04/2022] [Indexed: 11/03/2022]
Abstract
Intrinsically disordered proteins and regions (IDPs and IDRs) and their importance in biology are becoming increasingly recognized in biology, biochemistry, molecular biology and chemistry textbooks, as well as in current protein science and structural biology curricula. We argue that the sequence → dynamic conformational ensemble → function principle is of equal importance as the classical sequence → structure → function paradigm. To highlight this point, we describe the IDPs and/or IDRs behind the discoveries associated with 17 Nobel Prizes, 11 in Physiology or Medicine and 6 in Chemistry. The Nobel Laureates themselves did not always mention that the proteins underlying the phenomena investigated in their award-winning studies are in fact IDPs or contain IDRs. In several cases, IDP- or IDR-based molecular functions have been elucidated, while in other instances, it is recognized that the respective protein(s) contain IDRs, but the specific IDR-based molecular functions have yet to be determined. To highlight the importance of IDPs and IDRs as general principle in biology, we present here illustrative examples of IDPs/IDRs in Nobel Prize-winning mechanisms and processes.
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Affiliation(s)
- Lolita Piersimoni
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Marina Abd El Malek
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Twinkle Bhatia
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Julian Bender
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Christin Brankatschk
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Jaime Calvo Sánchez
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL, 33620, USA
| | - Alessio Di Ianni
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | | | - Dailen Garcia-Martinez
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Julia Hesselbarth
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Janett Köppen
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Luca M Lauth
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Laurin Lippik
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Lisa Machner
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Shubhra Sachan
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Lisa Schmidt
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Robin Selle
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Ioannis Skalidis
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Oleksandr Sorokin
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Daniele Ubbiali
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Bruno Voigt
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alice Wedler
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alan An Jung Wei
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Peter Zorn
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alan Keith Dunker
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Marcel Köhn
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
| | - Andrea Sinz
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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Bychkova VE, Dolgikh DA, Balobanov VA, Finkelstein AV. The Molten Globule State of a Globular Protein in a Cell Is More or Less Frequent Case Rather than an Exception. Molecules 2022; 27:molecules27144361. [PMID: 35889244 PMCID: PMC9319461 DOI: 10.3390/molecules27144361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 02/01/2023] Open
Abstract
Quite a long time ago, Oleg B. Ptitsyn put forward a hypothesis about the possible functional significance of the molten globule (MG) state for the functioning of proteins. MG is an intermediate between the unfolded and the native state of a protein. Its experimental detection and investigation in a cell are extremely difficult. In the last decades, intensive studies have demonstrated that the MG-like state of some globular proteins arises from either their modifications or interactions with protein partners or other cell components. This review summarizes such reports. In many cases, MG was evidenced to be functionally important. Thus, the MG state is quite common for functional cellular proteins. This supports Ptitsyn’s hypothesis that some globular proteins may switch between two active states, rigid (N) and soft (MG), to work in solution or interact with partners.
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Affiliation(s)
- Valentina E. Bychkova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (V.E.B.); (A.V.F.)
| | - Dmitry A. Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117871 Moscow, Russia;
| | - Vitalii A. Balobanov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (V.E.B.); (A.V.F.)
- Correspondence:
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (V.E.B.); (A.V.F.)
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6
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Kulkarni P, Bhattacharya S, Achuthan S, Behal A, Jolly MK, Kotnala S, Mohanty A, Rangarajan G, Salgia R, Uversky V. Intrinsically Disordered Proteins: Critical Components of the Wetware. Chem Rev 2022; 122:6614-6633. [PMID: 35170314 PMCID: PMC9250291 DOI: 10.1021/acs.chemrev.1c00848] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Despite the wealth of knowledge gained about intrinsically disordered proteins (IDPs) since their discovery, there are several aspects that remain unexplored and, hence, poorly understood. A living cell is a complex adaptive system that can be described as a wetware─a metaphor used to describe the cell as a computer comprising both hardware and software and attuned to logic gates─capable of "making" decisions. In this focused Review, we discuss how IDPs, as critical components of the wetware, influence cell-fate decisions by wiring protein interaction networks to keep them minimally frustrated. Because IDPs lie between order and chaos, we explore the possibility that they can be modeled as attractors. Further, we discuss how the conformational dynamics of IDPs manifests itself as conformational noise, which can potentially amplify transcriptional noise to stochastically switch cellular phenotypes. Finally, we explore the potential role of IDPs in prebiotic evolution, in forming proteinaceous membrane-less organelles, in the origin of multicellularity, and in protein conformation-based transgenerational inheritance of acquired characteristics. Together, these ideas provide a new conceptual framework to discern how IDPs may perform critical biological functions despite their lack of structure.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
- Address for correspondence: Prakash Kulkarni, Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, , Vladimir N. Uversky, Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612,
| | - Supriyo Bhattacharya
- Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA, USA
| | - Srisairam Achuthan
- Division of Research Informatics, Center for Informatics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Amita Behal
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Sourabh Kotnala
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
- Center for Neuroscience, Indian Institute of Science, Bangalore 560012, India
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Vladimir Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, Moscow region 141700, Russia
- Address for correspondence: Prakash Kulkarni, Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, , Vladimir N. Uversky, Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612,
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7
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Investigation of the effect of temperature and electrolytes on the physicochemical parameters for the self-assembly of dodecyltrimethylammonium bromide. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01952-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Sultana S, Rub MA, Rahman M, Rana S, Rahman MM, Hoque MA, Alghamdi YG, Asiri AM. Effect of composition of mono/di-hydroxy organic compounds and temperature on the aggregation behavior and physico-chemical properties of polyvinyl alcohol + TTAB mixture. J DISPER SCI TECHNOL 2021. [DOI: 10.1080/01932691.2021.1960171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Sharmin Sultana
- Department of Chemistry, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Malik Abdul Rub
- Center of Excellence for Advanced Materials Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Marzia Rahman
- Department of Chemistry, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Shahed Rana
- Department of Chemistry, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | | | - Md. Anamul Hoque
- Department of Chemistry, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Yousef G. Alghamdi
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdullah M. Asiri
- Center of Excellence for Advanced Materials Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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9
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Islam M, Hossain M, Mahbub S, Hoque MA, Kumar D, Wabaidur SM, Habila MA, AL-Anazy MM, Kabir M. Influences of alcohol and diol on the aggregation behaviour, modes of interaction and the thermodynamic properties of the mixture of bromocresol green dye and sodium dodecyl sulphate at numerous temperatures. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1925364] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Mohaiminul Islam
- Department of Chemistry, Jahangirnagar University, Dhaka, Bangladesh
| | - Mezbah Hossain
- Department of Chemistry, Hajee Mohammad Danesh Science & Technology University, Dinajpur, Bangladesh
| | - Shamim Mahbub
- Department of Chemistry & Physics, Gono Bishwabidyalay, Dhaka, Bangladesh
| | - Md. Anamul Hoque
- Department of Chemistry, Jahangirnagar University, Dhaka, Bangladesh
| | - Dileep Kumar
- Division of Computational Physics, Institute for Computational Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Saikh M. Wabaidur
- Advanced Materials Research Chair, Chemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed A. Habila
- Advanced Materials Research Chair, Chemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Murefah Mana AL-Anazy
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mahbub Kabir
- Department of Chemistry, Jahangirnagar University, Dhaka, Bangladesh
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10
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Hoque MA, Rahman MM, Alam MM, Mahbub S, Khan MA, Kumar D, Albaqami MD, Wabaidur SM. Interaction of cephalexin monohydrate with surfactants in aqueous and sodium chloride solution at variable temperatures: Conductivity and spectroscopic measurements. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115337] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Carter CW, Wills PR. Reciprocally-Coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis. Biomolecules 2021; 11:265. [PMID: 33670192 PMCID: PMC7916928 DOI: 10.3390/biom11020265] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/04/2021] [Accepted: 02/06/2021] [Indexed: 12/12/2022] Open
Abstract
Bioenergetics, genetic coding, and catalysis are all difficult to imagine emerging without pre-existing historical context. That context is often posed as a "Chicken and Egg" problem; its resolution is concisely described by de Grasse Tyson: "The egg was laid by a bird that was not a chicken". The concision and generality of that answer furnish no details-only an appropriate framework from which to examine detailed paradigms that might illuminate paradoxes underlying these three life-defining biomolecular processes. We examine experimental aspects here of five examples that all conform to the same paradigm. In each example, a paradox is resolved by coupling "if, and only if" conditions for reciprocal transitions between levels, such that the consequent of the first test is the antecedent for the second. Each condition thus restricts fluxes through, or "gates" the other. Reciprocally-coupled gating, in which two gated processes constrain one another, is self-referential, hence maps onto the formal structure of "strange loops". That mapping uncovers two different kinds of forces that may help unite the axioms underlying three phenomena that distinguish biology from chemistry. As a physical analog for Gödel's logic, biomolecular strange-loops provide a natural metaphor around which to organize a large body of experimental data, linking biology to information, free energy, and the second law of thermodynamics.
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Affiliation(s)
- Charles W. Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7260, USA
| | - Peter R. Wills
- Department of Physics and Te Ao Marama Centre for Fundamental Inquiry, University of Auckland, PB 92019, Auckland 1142, New Zealand;
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12
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Amin MR, Alissa SA, Saha M, Hossian J, Shahriar I, Halim MA, Hoque MA, Alothman ZA, Wabaidur SM, Kabir SE. Investigation of the impacts of temperature and electrolyte on the interaction of cationic surfactant with promethazine hydrochloride: Combined conductivity and molecular dynamics studies. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113246] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Nur A, Mahbub S, Rahman MM, Khan F, Rub MA, Hoque MA, Khan MA, Azum N, Asiri AM. Influence of Additives and Temperature on the Interaction of Acid Red 151 Dye with Cetyltrimethylammonium Bromide: A Conductometric Study. J SURFACTANTS DETERG 2020. [DOI: 10.1002/jsde.12419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Asaduzzaman Nur
- Department of ChemistryJahangirnagar University Savar, Dhaka‐1342 Bangladesh
| | - Shamim Mahbub
- Department of ChemistryJahangirnagar University Savar, Dhaka‐1342 Bangladesh
- Department of Chemistry and PhysicsGono Bishwabidyalay Savar, Dhaka‐1344 Bangladesh
| | | | - Farah Khan
- Department of ChemistryAligarh Muslim University Aligarh‐202 002 India
| | - Malik Abdul Rub
- Chemistry Department, Faculty of ScienceKing Abdulaziz University Jeddah‐21589 Saudi Arabia
- Center of Excellence for Advanced Materials ResearchKing Abdulaziz University Jeddah‐21589 Saudi Arabia
| | - Md. Anamul Hoque
- Department of ChemistryJahangirnagar University Savar, Dhaka‐1342 Bangladesh
| | | | - Naved Azum
- Chemistry Department, Faculty of ScienceKing Abdulaziz University Jeddah‐21589 Saudi Arabia
| | - Abdullah M. Asiri
- Chemistry Department, Faculty of ScienceKing Abdulaziz University Jeddah‐21589 Saudi Arabia
- Center of Excellence for Advanced Materials ResearchKing Abdulaziz University Jeddah‐21589 Saudi Arabia
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14
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Aktar S, Saha M, Mahbub S, Halim MA, Rub MA, Hoque MA, Islam DS, Kumar D, Alghamdi YG, Asiri AM. Influence of polyethylene glycol on the aggregation/clouding phenomena of cationic and non-ionic surfactants in attendance of electrolytes (NaCl & Na2SO4): An experimental and theoretical analysis. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112880] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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15
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Rahim MA, Mahbub S, Islam MK, Ahsan SMA, Rana S, Rub MA, Khan A, Hoque MA. Influence of Different Additives on the Interaction of Quinolone Antibiotic Drug with Surfactant: Conductivity and Cloud Point Measurement Study. J SURFACTANTS DETERG 2019. [DOI: 10.1002/jsde.12377] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Md. Abdur Rahim
- Department of ChemistryJahangirnagar University Savar Dhaka 1342 Bangladesh
| | - Shamim Mahbub
- Department of ChemistryJahangirnagar University Savar Dhaka 1342 Bangladesh
| | - Md. Kamrul Islam
- Department of Biochemistry and Molecular BiologyJahangirnagar University Savar Dhaka 1342 Bangladesh
| | - Sk. Md. Ali Ahsan
- Department of ChemistryJahangirnagar University Savar Dhaka 1342 Bangladesh
| | - Shahed Rana
- Department of ChemistryJahangirnagar University Savar Dhaka 1342 Bangladesh
| | - Malik Abdul Rub
- Chemistry Department, Faculty of ScienceKing Abdulaziz University Jeddah 21589 Saudi Arabia
- Center of Excellence for Advanced Materials ResearchKing Abdulaziz University Jeddah 21589 Saudi Arabia
| | - Anish Khan
- Chemistry Department, Faculty of ScienceKing Abdulaziz University Jeddah 21589 Saudi Arabia
- Center of Excellence for Advanced Materials ResearchKing Abdulaziz University Jeddah 21589 Saudi Arabia
| | - Md. Anamul Hoque
- Department of ChemistryJahangirnagar University Savar Dhaka 1342 Bangladesh
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16
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Rahman M, Hoque MA, Rub MA, Khan MA. Interaction of cetyltrimethylammonium bromide with cefixime trihydrate drug at different temperatures and compositions: Effect of different electrolytes. Chin J Chem Eng 2019. [DOI: 10.1016/j.cjche.2018.10.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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17
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Bunzel HA, Kries H, Marchetti L, Zeymer C, Mittl PRE, Mulholland AJ, Hilvert D. Emergence of a Negative Activation Heat Capacity during Evolution of a Designed Enzyme. J Am Chem Soc 2019; 141:11745-11748. [PMID: 31282667 DOI: 10.1021/jacs.9b02731] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Temperature influences the reaction kinetics and evolvability of all enzymes. To understand how evolution shapes the thermodynamic drivers of catalysis, we optimized the modest activity of a computationally designed enzyme for an elementary proton-transfer reaction by nearly 4 orders of magnitude over 9 rounds of mutagenesis and screening. As theorized for primordial enzymes, the catalytic effects of the original design were almost entirely enthalpic in origin, as were the rate enhancements achieved by laboratory evolution. However, the large reductions in ΔH⧧ were partially offset by a decrease in TΔS⧧ and unexpectedly accompanied by a negative activation heat capacity, signaling strong adaptation to the operating temperature. These findings echo reports of temperature-dependent activation parameters for highly evolved natural enzymes and are relevant to explanations of enzymatic catalysis and adaptation to changing thermal environments.
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Affiliation(s)
- H Adrian Bunzel
- Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland
| | - Hajo Kries
- Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland
| | - Luca Marchetti
- Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland
| | - Cathleen Zeymer
- Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland
| | - Peer R E Mittl
- Department of Biochemistry , University of Zurich , 8057 Zurich , Switzerland
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , United Kingdom
| | - Donald Hilvert
- Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland
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18
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Hoque MA, Molla MR, Amin MR, Alam MM, Hossain MF, Rub MA. Investigation of the Effect of Temperature, Salt and Solvent Composition on the Micellization Behavior of Tetradecyltrimethylammonium Bromide in the Presence of the Antibiotic Drug Levofloxacin Hemihydrate. J SOLUTION CHEM 2019. [DOI: 10.1007/s10953-019-00850-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Amin MR, Mahbub S, Hidayathulla S, Alam MM, Hoque MA, Rub MA. An estimation of the effect of mono/poly-hydroxy organic compounds on the interaction of tetradecyltrimethylammonium bromide with levofloxacin hemihydrate antibiotic drug. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.08.043] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Kulkarni P, Uversky VN. Intrinsically Disordered Proteins: The Dark Horse of the Dark Proteome. Proteomics 2018; 18:e1800061. [DOI: 10.1002/pmic.201800061] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/07/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research; City of Hope National Medical Center; Duarte CA 91010 USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa FL 33612 USA
- Laboratory of New methods in Biology; Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino Moscow Region 142290 Russia
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21
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Dijkstra M, Fokkink W, Heringa J, van Dijk E, Abeln S. The characteristics of molten globule states and folding pathways strongly depend on the sequence of a protein. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1496290] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- M.J.J. Dijkstra
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - W.J. Fokkink
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - J. Heringa
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - E. van Dijk
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - S. Abeln
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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22
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Bychkova VE, Semisotnov GV, Balobanov VA, Finkelstein AV. The Molten Globule Concept: 45 Years Later. BIOCHEMISTRY (MOSCOW) 2018; 83:S33-S47. [DOI: 10.1134/s0006297918140043] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Cooperativity and flexibility in enzyme evolution. Curr Opin Struct Biol 2018; 48:83-92. [DOI: 10.1016/j.sbi.2017.10.020] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/24/2017] [Indexed: 11/23/2022]
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24
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Li J, Xie Y, Wang R, Fang Z, Fang W, Zhang X, Xiao Y. Mechanism of salt-induced activity enhancement of a marine-derived laccase, Lac15. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 47:225-236. [PMID: 28875401 DOI: 10.1007/s00249-017-1251-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/07/2017] [Accepted: 08/23/2017] [Indexed: 10/18/2022]
Abstract
Laccase (benzenediol: oxygen oxidoreductases, EC1.10.3.2) is a multi-copper oxidase capable of oxidizing a variety of phenolic and other aromatic organic compounds. The catalytic power of laccase makes it an attractive candidate for potential applications in many areas of industry including biodegradation of organic pollutants and synthesis of novel drugs. Most laccases are vulnerable to high salt and have limited applications. However, some laccases are not only tolerant to but also activated by certain concentrations of salt and thus have great application potential. The mechanisms of salt-induced activity enhancement of laccases are unclear as yet. In this study, we used dynamic light scattering, size exclusion chromatography, analytical ultracentrifugation, intrinsic fluorescence emission, circular dichroism, ultraviolet-visible light absorption, and an enzymatic assay to investigate the potential correlation between the structure and activity of the marine-derived laccase, Lac15, whose activity is promoted by low concentrations of NaCl. The results showed that low concentrations of NaCl exert little influence on the protein structure, which was partially folded in the absence of the salt; moreover, the partially folded rather than the fully folded state seemed to be favorable for enzyme activity, and this partially folded state was distinctive from the so-called 'molten globule' occasionally observed in active enzymes. More data indicated that salt might promote laccase activity through mechanisms involving perturbation of specific local sites rather than a change in global structure. Potential binding sites for chloride ions and their roles in enzyme activity promotion are proposed.
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Affiliation(s)
- Jie Li
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Key Laboratory of Modern Biomanufacturing, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Yanan Xie
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Key Laboratory of Modern Biomanufacturing, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Rui Wang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Key Laboratory of Modern Biomanufacturing, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Key Laboratory of Modern Biomanufacturing, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Wei Fang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, 230601, Anhui, China.,Anhui Key Laboratory of Modern Biomanufacturing, 111 Jiulong Road, Hefei, 230601, Anhui, China
| | - Xuecheng Zhang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China. .,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, 230601, Anhui, China. .,Anhui Key Laboratory of Modern Biomanufacturing, 111 Jiulong Road, Hefei, 230601, Anhui, China.
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, China. .,Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, 230601, Anhui, China. .,Anhui Key Laboratory of Modern Biomanufacturing, 111 Jiulong Road, Hefei, 230601, Anhui, China.
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25
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Hoque MA, Patoary MOF, Rashid MM, Molla MR, Rub MA. Physico-chemical Investigation of Mixed Micelle Formation Between Tetradecyltrimethylammonium Bromide and Dodecyltrimethylammonium Chloride in Water and Aqueous Solutions of Sodium Chloride. J SOLUTION CHEM 2017. [DOI: 10.1007/s10953-017-0594-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Hoque MA, Patoary MOF, Molla MR, Halim MA, Khan MA, Rub MA. Interaction between cetylpyridinium chloride and amino acids: A conductomertic and computational method study. J DISPER SCI TECHNOL 2017. [DOI: 10.1080/01932691.2016.1262779] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Md. Anamul Hoque
- Department of Chemistry, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | | | | | - Mohammad A. Halim
- Division of Quantum Chemistry, BICCB, Green Research Centre, Dhaka, Bangladesh
- Institut Lumière Matière, Université Lyon 1 – CNRS, Université de Lyon, Villeurbanne Cedex, France
| | | | - Malik Abdul Rub
- Chemistry Department, Faculty of Science, King Abdul Aziz University, Jeddah, Saudi Arabia
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27
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Rahman M, Khan MA, Rub MA, Hoque MA. Effect of temperature and salts on the interaction of cetyltrimethylammonium bromide with ceftriaxone sodium trihydrate drug. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.08.049] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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28
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Sammond DW, Kastelowitz N, Himmel ME, Yin H, Crowley MF, Bomble YJ. Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms. PLoS One 2016; 11:e0145848. [PMID: 26741367 PMCID: PMC4704809 DOI: 10.1371/journal.pone.0145848] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.
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Affiliation(s)
- Deanne W Sammond
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, United States of America
| | - Noah Kastelowitz
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, Colorado, 80309, United States of America
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, United States of America
| | - Hang Yin
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, Colorado, 80309, United States of America
| | - Michael F Crowley
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, United States of America
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, United States of America
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29
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Biophysical Methods to Investigate Intrinsically Disordered Proteins: Avoiding an “Elephant and Blind Men” Situation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:215-60. [DOI: 10.1007/978-3-319-20164-1_7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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An Energetic Analysis of the Phase Separation in Non-Ionic Surfactant Mixtures: The Role of the Headgroup Structure. ENTROPY 2014. [DOI: 10.3390/e16084375] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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31
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Brucale M, Schuler B, Samorì B. Single-molecule studies of intrinsically disordered proteins. Chem Rev 2014; 114:3281-317. [PMID: 24432838 DOI: 10.1021/cr400297g] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marco Brucale
- Institute for the Study of Nanostructured Materials (ISMN), Italian National Council of Research (CNR) , Area della Ricerca Roma1, Via Salaria km 29.3 00015 Monterotondo (Rome), Italy
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32
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Wild-type and molten globular chorismate mutase achieve comparable catalytic rates using very different enthalpy/entropy compensations. Sci China Chem 2013. [DOI: 10.1007/s11426-013-5021-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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33
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Okura H, Mihara H, Takahashi T. Construction of proteins with molecular recognition capabilities using α3β3 de novo protein scaffolds. Protein Eng Des Sel 2013; 26:705-11. [PMID: 24046439 DOI: 10.1093/protein/gzt046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The molecular recognition ability of proteins is essential in biological systems, and therefore a considerable amount of effort has been devoted to constructing desired target-binding proteins using a variety of naturally occurring proteins as scaffolds. However, since generating a binding site in a native protein can often affect its structural properties, highly stable de novo protein scaffolds may be more amenable than the native proteins. We previously reported the generation of de novo proteins comprising three α-helices and three β-strands (α3β3) from a genetic library coding simplified amino acid sets. Two α3β3 de novo proteins, vTAJ13 and vTAJ36, fold into a native-like stable and molten globule-like structures, respectively, even though the proteins have similar amino acid compositions. Here, we attempted to create binding sites for the vTAJ13 and vTAJ36 proteins to prove the utility of de novo designed artificial proteins as a molecular recognition tool. Randomization of six amino acids at two linker sites of vTAJ13 and vTAJ36 followed by biopanning generated binding proteins that recognize the target molecules, fluorescein and green fluorescent protein, with affinities of 10(-7)-10(-8) M. Of note, the selected proteins from the vTAJ13-based library tended to recognize the target molecules with high specificity, probably due to the native-like stable structure of vTAJ13. Our studies provide an example of the potential of de novo protein scaffolds, which are composed of a simplified amino acid set, to recognize a variety of target compounds.
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Affiliation(s)
- Hiromichi Okura
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B40 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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34
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Lin YW, Wang J. Structure and function of heme proteins in non-native states: a mini-review. J Inorg Biochem 2013; 129:162-71. [PMID: 23916118 DOI: 10.1016/j.jinorgbio.2013.07.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/11/2013] [Accepted: 07/13/2013] [Indexed: 12/12/2022]
Abstract
Heme proteins perform various biological functions ranging from electron transfer, oxygen binding and transport, catalysis, to signaling. Although adopting proper native states is very important for these functions, progresses in representative heme proteins, including cytochrome c (cyt c), cytochrome b5 (cyt b5), myoglobin (Mb), neuroglobin (Ngb), cytochrome P450 (CYP) and heme-based sensor proteins such as CO sensor CooA, showed that various native functions, or new functions evolved, are also closely associated with non-native states. The structure and function relationship of heme proteins in non-native states is thus as important as that in native states for elucidating the precise roles of heme proteins in biological systems.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
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35
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Uversky VN. A decade and a half of protein intrinsic disorder: biology still waits for physics. Protein Sci 2013; 22:693-724. [PMID: 23553817 PMCID: PMC3690711 DOI: 10.1002/pro.2261] [Citation(s) in RCA: 364] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 03/23/2013] [Accepted: 03/25/2013] [Indexed: 12/28/2022]
Abstract
The abundant existence of proteins and regions that possess specific functions without being uniquely folded into unique 3D structures has become accepted by a significant number of protein scientists. Sequences of these intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) are characterized by a number of specific features, such as low overall hydrophobicity and high net charge which makes these proteins predictable. IDPs/IDPRs possess large hydrodynamic volumes, low contents of ordered secondary structure, and are characterized by high structural heterogeneity. They are very flexible, but some may undergo disorder to order transitions in the presence of natural ligands. The degree of these structural rearrangements varies over a very wide range. IDPs/IDPRs are tightly controlled under the normal conditions and have numerous specific functions that complement functions of ordered proteins and domains. When lacking proper control, they have multiple roles in pathogenesis of various human diseases. Gaining structural and functional information about these proteins is a challenge, since they do not typically "freeze" while their "pictures are taken." However, despite or perhaps because of the experimental challenges, these fuzzy objects with fuzzy structures and fuzzy functions are among the most interesting targets for modern protein research. This review briefly summarizes some of the recent advances in this exciting field and considers some of the basic lessons learned from the analysis of physics, chemistry, and biology of IDPs.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, USA.
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36
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Musiani F, Ippoliti E, Micheletti C, Carloni P, Ciurli S. Conformational fluctuations of UreG, an intrinsically disordered enzyme. Biochemistry 2013; 52:2949-54. [PMID: 23560717 DOI: 10.1021/bi4001744] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
UreG proteins are small GTP binding (G) proteins that catalyze the hydrolysis of GTP necessary for the maturation of urease, a virulence factor in bacterial pathogenesis. UreG proteins are the first documented cases of intrinsically disordered enzymes. The comprehension of the dynamics of folding-unfolding events occurring in this protein could shed light on the enzymatic mechanism of UreG. Here, we used the recently developed replica exchange with solute tempering (REST2) computational methodology to explore the conformational space of UreG from Helicobacter pylori (HpUreG) and to identify its structural fluctuations. The same simulation and analysis protocol has been applied to HypB from Methanocaldococcus jannaschii (MjHypB), which is closely related to UreG in both sequence and function, even though it is not intrinsically disordered. A comparison of the two systems reveals that both HpUreG and MjHypB feature a substantial rigidity of the protein regions involved in catalysis, justifying its residual catalytic activity. On the other hand, HpUreG tends to unfold more than MjHypB in portions involved in protein-protein interactions with metallochaperones necessary for the formation of multiprotein complexes known to be involved in urease activation.
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Affiliation(s)
- Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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37
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Baldwin RL, Rose GD. Molten globules, entropy-driven conformational change and protein folding. Curr Opin Struct Biol 2013; 23:4-10. [DOI: 10.1016/j.sbi.2012.11.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/14/2012] [Accepted: 11/15/2012] [Indexed: 10/27/2022]
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38
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Abstract
Though lacking a well-defined three-dimensional structure, intrinsically unstructured proteins are ubiquitous in nature. These molecules play crucial roles in many cellular processes, especially signaling and regulation. Surprisingly, even enzyme catalysis can tolerate substantial disorder. This observation contravenes conventional wisdom but is relevant to an understanding of how protein dynamics modulates enzyme function. This chapter reviews properties and characteristics of disordered proteins, emphasizing examples of enzymes that lack defined structures, and considers implications of structural disorder for catalytic efficiency and evolution.
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39
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Cherny I, Korolev M, Koehler AN, Hecht MH. Proteins from an unevolved library of de novo designed sequences bind a range of small molecules. ACS Synth Biol 2012; 1:130-8. [PMID: 23651114 PMCID: PMC4104770 DOI: 10.1021/sb200018e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The availability of large collections of de novo designed proteins presents new opportunities to harness novel macromolecules for synthetic biological functions. Many of these new functions will require binding to small molecules. Is the ability to bind small molecules a property that arises only in response to biological selection or computational design? Or alternatively, is small molecule binding a property of folded proteins that occurs readily amidst collections of unevolved sequences? These questions can be addressed by assessing the binding potential of de novo proteins that are designed to fold into stable structures, but are "naïve" in the sense that they (i) share no significant sequence similarity with natural proteins and (ii) were neither selected nor designed to bind small molecules. We chose three naïve proteins from a library of sequences designed to fold into 4-helix bundles and screened for binding to 10,000 compounds displayed on small molecule microarrays. Several binders were identified, and binding was characterized by a series of biophysical assays. Surprisingly, despite the similarity of the three de novo proteins to one another, they exhibit selective ligand binding. These findings demonstrate the potential of novel proteins for molecular recognition and have significant implications for a range of applications in synthetic biology.
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Affiliation(s)
- Izhack Cherny
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Maria Korolev
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Angela N. Koehler
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Michael H. Hecht
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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40
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Uversky VN, Dunker AK. Multiparametric Analysis of Intrinsically Disordered Proteins: Looking at Intrinsic Disorder through Compound Eyes. Anal Chem 2012; 84:2096-104. [DOI: 10.1021/ac203096k] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Vladimir N. Uversky
- Department
of Molecular Medicine, University of South Florida, Tampa, Florida 33612, United States
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow
Region, Russia
| | - A. Keith Dunker
- Center for
Computational Biology and Bioinformatics, Department of Biochemistry
and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
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41
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Automated selection of stabilizing mutations in designed and natural proteins. Proc Natl Acad Sci U S A 2012; 109:1494-9. [PMID: 22307603 DOI: 10.1073/pnas.1115172109] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability to engineer novel protein folds, conformations, and enzymatic activities offers enormous potential for the development of new protein therapeutics and biocatalysts. However, many de novo and redesigned proteins exhibit poor hydrophobic packing in their predicted structures, leading to instability or insolubility. The general utility of rational, structure-based design would greatly benefit from an improved ability to generate well-packed conformations. Here we present an automated protocol within the RosettaDesign framework that can identify and improve poorly packed protein cores by selecting a series of stabilizing point mutations. We apply our method to previously characterized designed proteins that exhibited a decrease in stability after a full computational redesign. We further demonstrate the ability of our method to improve the thermostability of a well-behaved native protein. In each instance, biophysical characterization reveals that we were able to stabilize the original proteins against chemical and thermal denaturation. We believe our method will be a valuable tool for both improving upon designed proteins and conferring increased stability upon native proteins.
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42
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Zambelli B, Cremades N, Neyroz P, Turano P, Uversky VN, Ciurli S. Insights in the (un)structural organization of Bacillus pasteurii UreG, an intrinsically disordered GTPase enzyme. MOLECULAR BIOSYSTEMS 2011; 8:220-8. [PMID: 21922108 DOI: 10.1039/c1mb05227f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In the past, enzymatic activity has always been expected to be dependent on overall protein rigidity, necessary for substrate recognition and optimal orientation. However, increasing evidence is now accumulating, revealing that some proteins characterized by intrinsic disorder are actually able to perform catalysis. Among them, the only known natural intrinsically disordered enzyme is UreG, a GTPase that, in plants and bacteria, is involved in the protein interaction network leading to Ni(2+) ions delivery into the active site of urease. In this paper, we report a detailed analysis of the unfolding behaviour of UreG from Bacillus pasteurii (BpUreG), following its thermal and chemical denaturation with a combination of fluorescence spectroscopy, calorimetry, CD and NMR. The results demonstrate that BpUreG exists as an ensemble of inter-converting conformations, whose degrees of secondary structure depend on temperature and denaturant concentration. In particular, three major types of conformational ensembles with different degrees of residual structure were identified, with major structural characteristics resembling those of a molten globule (low temperature, absence of denaturant), pre-molten globule (high temperature, absence or presence of denaturant) and random coil (low temperature, presence of denaturant). Transitions among these ensembles of conformational states occur non-cooperatively although reversibly, with a gradual loss or acquisition of residual structure depending on the conditions. A possible role of disorder in the biological function of UreG is envisaged and discussed.
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Affiliation(s)
- Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, University of Bologna, Bologna, Italy.
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Butz M, Neuenschwander M, Kast P, Hilvert D. An N-terminal protein degradation tag enables robust selection of highly active enzymes. Biochemistry 2011; 50:8594-602. [PMID: 21916414 DOI: 10.1021/bi2011338] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Degradation tags are short peptide sequences that target proteins for destruction by housekeeping proteases. We previously utilized the C-terminal SsrA tag in directed evolution experiments to decrease the intracellular lifetime of a growth-limiting enzyme and thereby facilitate selection of highly active variants. In this study, we examine the N-terminal RepA tag as an alternative degradation signal for laboratory evolution. Although RepA proved to be less effective than SsrA at lowering protein concentrations in the cell, its N-terminal location dramatically reduced the occurrence of truncation and frameshift artifacts in selection experiments. We exploited this improvement to evolve a topologically redesigned chorismate mutase that is intrinsically disordered but already highly active for the conversion of chorismate to prephenate. After three rounds of mutagenesis and high-stringency selection, a robust and more nativelike variant was obtained that exhibited a catalytic efficiency (k(cat)/K(M) = 84000 M(-1) s(-1)) comparable to that of a natural dimeric chorismate mutase. Because of concomitant increases in catalyst yield, the level of intracellular prephenate production increased approximately 30-fold overall over the course of evolution.
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Affiliation(s)
- Maren Butz
- Laboratory of Organic Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
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Abstract
One of the fundamental questions of enzymology is how catalytic power is derived. This review focuses on recent developments in the structure--function relationships of chorismate-utilizing enzymes involved in siderophore biosynthesis to provide insight into the biocatalysis of pericyclic reactions. Specifically, salicylate synthesis by the two-enzyme pathway in Pseudomonas aeruginosa is examined. The isochorismate-pyruvate lyase is discussed in the context of its homologues, the chorismate mutases, and the isochorismate synthase is compared to its homologues in the MST family (menaquinone, siderophore, or tryptophan biosynthesis) of enzymes. The tentative conclusion is that the activities observed cannot be reconciled by inspection of the active site participants alone. Instead, individual activities must arise from unique dynamic properties of each enzyme that are tuned to promote specific chemistries.
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Affiliation(s)
- Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States.
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Luo Y, Huang P, Fu Q, Du W, Sun S, Li Y, Liu M, Chang C. Preparation of Monolithic Imprinted Stationary Phase for Clenbuterol by In Situ Polymerization and Application in Biological Samples Pretreatment. Chromatographia 2011. [DOI: 10.1007/s10337-011-2129-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Higo J, Nishimura Y, Nakamura H. A free-energy landscape for coupled folding and binding of an intrinsically disordered protein in explicit solvent from detailed all-atom computations. J Am Chem Soc 2011; 133:10448-58. [PMID: 21627111 DOI: 10.1021/ja110338e] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The N-terminal repressor domain of neural restrictive silencer factor (NRSF) is an intrinsically disordered protein (IDP) that binds to the paired amphipathic helix (PAH) domain of mSin3. An NMR experiment revealed that the minimal binding unit of NRSF is a 15-residue segment that adopts a helical structure upon binding to a cleft of mSin3. We computed a free-energy landscape of this system by an enhanced conformational sampling method, all-atom multicanonical molecular dynamics. The simulation started from a configuration where the NRSF segment was fully disordered and distant from mSin3 in explicit solvent. In the absence of mSin3, the disordered NRSF segment thermally fluctuated between hairpins, helices, and bent structures. In the presence of mSin3, the segment bound to mSin3 by adopting the structures involved in the isolated state, and non-native and native complexes were formed. The free-energy landscape comprised three superclusters, and free-energy barriers separated the superclusters. The native complex was located at the center of the lowest free-energy cluster. When NRSF landed in the largest supercluster, the generated non-native complex moved on the landscape to fold into the native complex, by increasing the interfacial hydrophobic contacts and the helix content. When NRSF landed in other superclusters, the non-native complex overcame the free-energy barriers between the various segment orientations in the binding cleft of mSin3. Both population-shift and induced-fit (or induced-folding) mechanisms work cooperatively in the coupled folding and binding. The diverse structural adaptability of NRSF may be related to the hub properties of the IDP.
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Affiliation(s)
- Junichi Higo
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
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Enzyme catalysis from improved packing in their transition-state structures. Curr Opin Chem Biol 2011; 14:666-70. [PMID: 20810304 DOI: 10.1016/j.cbpa.2010.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 08/05/2010] [Accepted: 08/05/2010] [Indexed: 11/22/2022]
Abstract
The binding of ligands to proteins can be enhanced through improved packing within the proteins that may, or may not, occur with conformational change. Enzymes can similarly improve their catalytic magic through better packing in the transition state (TS) for reaction. In principle, the improved packing demands no more than the minute shortening of non-covalent interactions throughout much of the structure of the protein (positively cooperative binding). Improved protein packing can account for the remarkably high biotin/streptavidin affinity, and perhaps also for a major part of the catalytic function of hypoxanthine-guanine phosphoribosyltransferase and purine nucleoside phosphorylase (PNP). As successive NAD(+) molecules bind to the glyceraldehyde phosphate dehydrogenase tetramer, they do so with positively cooperative binding (using the term as applied in crystallization and protein folding) that decreases at each step. This binding is negatively cooperative in the usage stemming from Monod and co-workers.
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Kandeel M, Kitade Y. Binding dynamics and energetic insight into the molecular forces driving nucleotide binding by guanylate kinase. J Mol Recognit 2010; 24:322-32. [PMID: 21360614 DOI: 10.1002/jmr.1074] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 07/16/2010] [Accepted: 07/16/2010] [Indexed: 11/11/2022]
Abstract
Plasmodium deoxyguanylate pathways are an attractive area of investigation for future metabolic and drug discovery studies due to their unique substrate specificities. We investigated the energetic contribution to guanylate kinase substrate binding and the forces underlying ligand recognition. In the range from 20 to 35°C, the thermodynamic profiles displayed marked decrease in binding enthalpy, while the free energy of binding showed little changes. GMP produced a large binding heat capacity change of -356 cal mol(-1) K(-1), indicating considerable conformational changes upon ligand binding. Interestingly, the calculated ΔCp was -32 cal mol(-1) K(-1), indicating that the accessible surface area is not the central change in substrate binding, and that other entropic forces, including conformational changes, are more predominant. The thermodynamic signature for GMP is inconsistent with rigid-body association, while dGMP showed more or less rigid-body association. These binding profiles explain the poor catalytic efficiency and low affinity for dGMP compared with GMP. At low temperature, the ligands bind to the receptor site under the effect of hydrophobic forces. Interestingly, by increasing the temperature, the entropic forces gradually vanish and proceed to a nonfavorable contribution, and the interaction occurs mainly through bonding, electrostatic forces, and van der Waals interactions.
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Affiliation(s)
- Mahmoud Kandeel
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafr El-Shikh University, Kafr El-Shikh 33516, Egypt.
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Vendruscolo M. Enzymatic activity in disordered states of proteins. Curr Opin Chem Biol 2010; 14:671-5. [PMID: 20832351 DOI: 10.1016/j.cbpa.2010.08.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 08/18/2010] [Accepted: 08/19/2010] [Indexed: 11/28/2022]
Abstract
Although disordered proteins are able to carry out a variety of different functions, particularly those involved in signalling and regulation, they have been observed to perform catalysis only in a small number of cases. The presence of structural disorder is indeed expected to be poorly compatible with enzymatic catalysis, which requires a well-organised environment in the active site of the enzyme in order to facilitate the formation of the transition state of the chemical reaction to be catalysed. Despite this stringent requirement, current evidence suggests that certain partially disordered proteins could be catalytically active by becoming structured in the regions of their active sites, even if their overall states retain a significant degree of conformational heterogeneity. This type of mechanism, however, does not appear to be not very common, perhaps because the time required to the conformational search within a disordered state to establish a catalytic environment in the presence of the substrate should not be longer than the overall turnover time required for optimal function. In addition, the catalytic environment should be maintained for long enough despite the structural fluctuations to enable the catalytic reaction to take place. As some partially unstructured proteins have been reported to be capable of overcoming these severe limitations and act as enzymes, their study can increase our general understanding of the mechanism of enzymatic catalysis, as well as extend our ability to control the range of functions that can be performed by disordered proteins.
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Affiliation(s)
- Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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50
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How do new proteins arise? Curr Opin Struct Biol 2010; 20:390-6. [PMID: 20347587 DOI: 10.1016/j.sbi.2010.02.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 02/24/2010] [Accepted: 02/25/2010] [Indexed: 11/23/2022]
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