1
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Hait S, Kundu S. Revisiting structural organization of proteins at high temperature from a network perspective. Comput Biol Chem 2024; 108:107978. [PMID: 37956471 DOI: 10.1016/j.compbiolchem.2023.107978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/08/2023] [Accepted: 10/29/2023] [Indexed: 11/15/2023]
Abstract
Interactions between distantly placed amino acids in the primary chain (long-range) play a very crucial role in the formation and stabilization of the tertiary structure of a protein, while interactions between closely placed amino acids in the primary chain (short-range) mostly stabilize the secondary structures. Every protein needs to maintain marginal stability in order to perform its physiological functions in its native environment. The requirements for this stability in mesophilic and thermophilic proteins are different. Thermophilic proteins need to form more interactions as well as more stable interactions to survive in the extreme environment, they live in. Here, we aim to find out how the interacting amino acids in three-dimensional space are positioned in the primary chains in thermophilic and mesophilic. How does this arrangement help thermophiles to maintain their structural integrity at high temperatures? Working on a dataset of 1560 orthologous pairs we perceive that thermophiles are not only enriched with long-range interactions, they feature bigger connected clusters and higher network densities compared to their mesophilic orthologs, at higher interaction strengths between the amino acids. Moreover, we have observed the enrichment of different types of interactions at different secondary structural regions.
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Affiliation(s)
- Suman Hait
- Department of Biophysics, Molecular Biology and Bioinformatics, 92, Acharya Prafulla Chandra Road, Kolkata 700009, India.
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, 92, Acharya Prafulla Chandra Road, Kolkata 700009, India.
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2
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Hait S, Basu S, Kundu S. Charge reversal mutations in mesophilic-thermophilic orthologous protein pairs and their role in enhancing coulombic interaction energy. J Biomol Struct Dyn 2023; 41:1745-1752. [PMID: 34996344 DOI: 10.1080/07391102.2021.2024258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Proteins from thermophilic organisms are a matter of immense interest for decades because of its application in fields like de-novo protein design, thermostable variants of biocatalysts etc. Previous studies have found several sequence and structural adaptations related to thermal stability, while charge reversal study remains ignored. Here we address whether charge reversal mutations naturally occur in mesophilic-thermophilic/hyperthermophilic orthologous proteins. Do they contribute to thermal stability? Our systematic study on 1550 mesophilic-thermophilic/hyperthermophilic orthologous protein pairs with remarkable structural and topological similarity, shows gain in coulombic interaction energy in thermophilic/hyperthermophilic proteins at short range associated with partially exposed and buried charge reversal mutations, which may enhance thermostability. Our findings call forth its application in future protein engineering studies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suman Hait
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Sudipto Basu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
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3
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Wang S, Ma C. Stability profile of the neuronal SNARE complex reflects its potency to drive fast membrane fusion. Biophys J 2022; 121:3081-3102. [PMID: 35810329 PMCID: PMC9463651 DOI: 10.1016/j.bpj.2022.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/24/2022] [Accepted: 07/07/2022] [Indexed: 11/02/2022] Open
Abstract
Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) form the SNARE complex to mediate most fusion events of the secretory pathway. The neuronal SNARE complex is featured by its high stability and half-zippered conformation required for driving robust and fast synaptic exocytosis. However, these two features seem to be thermodynamically mutually exclusive. In this study, we have employed temperature-dependent disassociation assays and single-molecule Förster resonance energy transfer (FRET) experiments to analyze the stability and conformation of the neuronal SNARE complex. We reclassified the amino acids of the SNARE motif into four sub-groups (core, core-side I and II, and non-contact). Our data showed that the core residues predominantly contribute to the complex stability to meet a basal requirement for SNARE-mediated membrane fusion, while the core-side residues exert an unbalanced effect on the N- and C-half bundle stability that determines the half-zippered conformation of the neuronal SNARE complex, which would accommodate essential regulations by complexins and synaptotagmins for fast Ca2+-triggered membrane fusion. Furthermore, our data confirmed a strong coupling of folding energy between the N- and C-half assembly of the neuronal SNARE complex, which rationalizes the strong potency of the half-zippered conformation to conduct robust and fast fusion. Overall, these results uncovered that the stability profile of the neuronal SNARE complex reflects its potency to drive fast and robust membrane fusion. Based on these results, we also developed a new parameter, the stability factor (Fs), to characterize the overall stability of the neuronal SNARE complex and resolved a linear correlation between the stability and inter-residue coulombic interactions of the neuronal SNARE complex, which would help rationally design artificial SNARE complexes and remold functional SNARE complexes with desirable stability.
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Affiliation(s)
- Shen Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Cong Ma
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
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4
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5
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Khan JM, Sen P, Malik A, Rehman MT, AlAjmi MF, Ahmed A, Alghamdi OHA, Ahmad A, Ahmed MZ, Khan RH, Anwer MK. Industrially important enzyme bovine liver catalase forms amyloid in the presence of 14-4-14 Gemini surfactant at physiological pH. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2020.125909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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6
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Kashif M, Bharati AP, Chaturvedi SK, Khan RH, Ahmad A, Kumar B, Zamzami MA, Ahmad V, Kumari S. pH and alcohol induced structural transition in Ntf2 a nuclear transport factor of Saccharomyces cerevisiae. Int J Biol Macromol 2020; 159:79-86. [PMID: 32407943 DOI: 10.1016/j.ijbiomac.2020.05.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 10/24/2022]
Abstract
Ntf2 is a nuclear envelope protein, which play a pivotal role in nucleocytoplasmic transport and mediates the nuclear import of RanGDP. It interacts with various nucleoporins along with Ran-GDP and part of a multicomponent system that assembles at the nuclear pore complex (NCP) during nuclear import. Here, we have described the biophysical characterization of Ntf2 from Saccharomyces cerevisiae. Recombinant Ntf2 showed increment in the β-sheet content as well as decrement in the α-helix content from pH-7.0 to pH-4.0. A subsequent decrease in the pH led to increment in the α-helical content along with decrement in β-sheet content. Intrinsic fluorescence studies demonstrated the unfolding of the protein below physiological pH. Ntf2 showed stabilization as well as phenomenal phase transition (β sheet to α helix) by increase in alcohol concentration from 10% to 70%. Further increase in alcohol concentration (90%) resulted in residual secondary structure in Ntf2 protein. Presence of ammonium sulfate also stabilizes the secondary structure of Ntf2 protein. The structural characterization reveals the flexibility and the stability of Ntf2 at various conditions. These structural alterations in Ntf2 protein probably occurs in the course of nucleocytoplasmic transport when it interacts with other proteins moving towards its final destination.
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Affiliation(s)
- Mohd Kashif
- Center for Plant Molecular Biology Division, CSIR-NBRI, Lucknow, India.
| | | | | | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Bhupendra Kumar
- Center for Plant Molecular Biology Division, CSIR-NBRI, Lucknow, India
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Varish Ahmad
- Department of Health and Information Technology, Faculty of Applied Studies, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sunita Kumari
- ICAR-Indian Institute of Seed Science, Mau, Uttar Pradesh 275103, India
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7
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Spielmann A, Brack Y, van Beek H, Flachbart L, Sundermeyer L, Baumgart M, Bott M. NADPH biosensor-based identification of an alcohol dehydrogenase variant with improved catalytic properties caused by a single charge reversal at the protein surface. AMB Express 2020; 10:14. [PMID: 31955268 PMCID: PMC6969876 DOI: 10.1186/s13568-020-0946-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/06/2020] [Indexed: 01/29/2023] Open
Abstract
Alcohol dehydrogenases (ADHs) are used in reductive biotransformations for the production of valuable chiral alcohols. In this study, we used a high-throughput screening approach based on the NADPH biosensor pSenSox and fluorescence-activated cell sorting (FACS) to search for variants of the NADPH-dependent ADH of Lactobacillus brevis (LbADH) with improved activity for the reduction of 2,5-hexanedione to (2R,5R)-hexanediol. In a library of approx. 1.4 × 106 clones created by random mutagenesis we identified the variant LbADHK71E. Kinetic analysis of the purified enzyme revealed that LbADHK71E had a ~ 16% lowered KM value and a 17% higher Vmax for 2,5-hexanedione compared to the wild-type LbADH. Higher activities were also observed for the alternative substrates acetophenone, acetylpyridine, 2-hexanone, 4-hydroxy-2-butanone, and methyl acetoacetate. K71 is solvent-exposed on the surface of LbADH and not located within or close to the active site. Therefore, K71 is not an obvious target for rational protein engineering. The study demonstrates that high-throughput screening using the NADPH biosensor pSenSox represents a powerful method to find unexpected beneficial mutations in NADPH-dependent alcohol dehydrogenases that can be favorable in industrial biotransformations.
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8
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Hait S, Mallik S, Basu S, Kundu S. Finding the generalized molecular principles of protein thermal stability. Proteins 2019; 88:788-808. [PMID: 31872464 DOI: 10.1002/prot.25866] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/05/2019] [Accepted: 12/14/2019] [Indexed: 11/09/2022]
Abstract
Are there any generalized molecular principles of thermal adaptation? Here, integrating the concepts of structural bioinformatics, sequence analysis, and classical knot theory, we develop a robust computational framework that seeks for mechanisms of thermal adaptation by comparing orthologous mesophilic-thermophilic and mesophilic-hyperthermophilic proteins of remarkable structural and topological similarities, and still leads us to context-independent results. A comprehensive analysis of 4741 high-resolution, non-redundant X-ray crystallographic structures collected from 11 hyperthermophilic, 32 thermophilic and 53 mesophilic prokaryotes unravels at least five "nearly universal" signatures of thermal adaptation, irrespective of the enormous sequence, structure, and functional diversity of the proteins compared. A careful investigation further extracts a set of amino acid changes that can potentially enhance protein thermal stability, and remarkably, these mutations are overrepresented in protein crystallization experiments, in disorder-to-order transitions and in engineered thermostable variants of existing mesophilic proteins. These results could be helpful to find a precise, global picture of thermal adaptation.
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Affiliation(s)
- Suman Hait
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Saurav Mallik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sudipto Basu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, Kolkata, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, Kolkata, India
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9
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Khan JM, Ahmed A, Freeh Alamery S, Farah MA, Hussain T, Khan MI, Khan RH, Malik A, Fatima S, Sen P. Millimolar concentration of sodium dodecyl sulfate inhibit thermal aggregation in hen egg white lysozyme via increased α-helicity. Colloids Surf A Physicochem Eng Asp 2019. [DOI: 10.1016/j.colsurfa.2019.03.085] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein. Proc Natl Acad Sci U S A 2019; 116:6806-6811. [PMID: 30877249 DOI: 10.1073/pnas.1818744116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The successful de novo design of proteins can provide insights into the physical chemical basis of stability, the role of evolution in constraining amino acid sequences, and the production of customizable platforms for engineering applications. Previous guanidine hydrochloride (GdnHCl; an ionic denaturant) experiments of a designed, naturally occurring βα fold, Di-III_14, revealed a cooperative, two-state unfolding transition and a modest stability. Continuous-flow mixing experiments in our laboratory revealed a simple two-state reaction in the microsecond to millisecond time range and consistent with the thermodynamic results. In striking contrast, the protein remains folded up to 9.25 M in urea, a neutral denaturant, and hydrogen exchange (HDX) NMR analysis in water revealed the presence of numerous high-energy states that interconvert on a time scale greater than seconds. The complex protection pattern for HDX corresponds closely with a pair of electrostatic networks on the surface and an extensive network of hydrophobic side chains in the interior of the protein. Mutational analysis showed that electrostatic and hydrophobic networks contribute to the resistance to urea denaturation for the WT protein; remarkably, single charge reversals on the protein surface restore the expected urea sensitivity. The roughness of the energy surface reflects the densely packed hydrophobic core; the removal of only two methyl groups eliminates the high-energy states and creates a smooth surface. The design of a very stable βα fold containing electrostatic and hydrophobic networks has created a complex energy surface rarely observed in natural proteins.
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11
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Bigman LS, Levy Y. Stability Effects of Protein Mutations: The Role of Long-Range Contacts. J Phys Chem B 2018; 122:11450-11459. [DOI: 10.1021/acs.jpcb.8b07379] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lavi S. Bigman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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12
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Carlsson ACC, Scholfield MR, Rowe RK, Ford MC, Alexander AT, Mehl RA, Ho PS. Increasing Enzyme Stability and Activity through Hydrogen Bond-Enhanced Halogen Bonds. Biochemistry 2018; 57:4135-4147. [PMID: 29921126 PMCID: PMC6052408 DOI: 10.1021/acs.biochem.8b00603] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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The construction of more stable proteins
is important in biomolecular
engineering, particularly in the design of biologics-based therapeutics.
We show here that replacing the tyrosine at position 18 (Y18) of T4
lysozyme with the unnatural amino acid m-chlorotyrosine
(mClY) increases both the thermal stability
(increasing the melting temperature by ∼1 °C and the melting
enthalpy by 3 kcal/mol) and the enzymatic activity at elevated temperatures
(15% higher than that of the parent enzyme at 40 °C) of this
classic enzyme. The chlorine of mClY forms
a halogen bond (XB) to the carbonyl oxygen of the peptide bond at
glycine 28 (G28) in a tight loop near the active site. In this case,
the XB potential of the typically weak XB donor Cl is shown from quantum
chemical calculations to be significantly enhanced by polarization
via an intramolecular hydrogen bond (HB) from the adjacent hydroxyl
substituent of the tyrosyl side chain, resulting in a distinctive
synergistic HB-enhanced XB (or HeX-B for short) interaction. The larger
halogens (bromine and iodine) are not well accommodated within this
same loop and, consequently, do not exhibit the effects on protein
stability or function associated with the HeX-B interaction. Thus,
we have for the first time demonstrated that an XB can be engineered
to stabilize and increase the activity of an enzyme, with the increased
stabilizing potential of the HeX-B further extending the application
of halogenated amino acids in the design of more stable protein therapeutics.
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Affiliation(s)
- Anna-Carin C Carlsson
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Matthew R Scholfield
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Rhianon K Rowe
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Melissa Coates Ford
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Austin T Alexander
- Department of Biochemistry & Biophysics , Oregon State University , Corvallis , Oregon 97333 , United States
| | - Ryan A Mehl
- Department of Biochemistry & Biophysics , Oregon State University , Corvallis , Oregon 97333 , United States
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
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13
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Leavens MJ, Cherney MM, Finnegan ML, Bowler BE. Probing Denatured State Conformational Bias in a Three-Helix Bundle, UBA(2), Using a Cytochrome c Fusion Protein. Biochemistry 2018; 57:1711-1721. [PMID: 29480716 DOI: 10.1021/acs.biochem.8b00015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Previous work with the four-helix-bundle protein cytochrome c' from Rhodopseudomonas palustris using histidine-heme loop formation methods revealed fold-specific deviations from random coil behavior in its denatured state ensemble. To examine the generality of this finding, we extend this work to a three-helix-bundle polypeptide, the second ubiquitin-associated domain, UBA(2), of the human DNA excision repair protein. We use yeast iso-1-cytochrome c as a scaffold, fusing the UBA(2) domain at the N-terminus of iso-1-cytochrome c. We have engineered histidine into highly solvent accessible positions of UBA(2), creating six single histidine variants. Guanidine hydrochloride denaturation studies show that the UBA(2)-cytochrome c fusion protein unfolds in a three-state process with iso-1-cytochrome c unfolding first. Furthermore, engineered histidine residues in UBA(2) strongly destabilize the iso-1-cytochrome c domain. Equilibrium and kinetic histidine-heme loop formation measurements in the denatured state at 4 and 6 M guanidine hydrochloride show that loop stability decreases as the size of the histidine-heme loop increases, in accord with the Jacobson-Stockmayer equation. However, we observe that the His27-heme loop is both more stable than expected from the Jacobson-Stockmayer relationship and breaks more slowly than expected. These results show that the sequence near His27, which is in the reverse turn between helices 2 and 3 of UBA(2), is prone to persistent interactions in the denatured state. Therefore, consistent with our results for cytochrome c', this reverse turn sequence may help to establish the topology of this fold by biasing the conformational distribution of the denatured state.
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Affiliation(s)
- Moses J Leavens
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
| | - Melisa M Cherney
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
| | - Michaela L Finnegan
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
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14
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Zhou HX, Pang X. Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation. Chem Rev 2018; 118:1691-1741. [PMID: 29319301 DOI: 10.1021/acs.chemrev.7b00305] [Citation(s) in RCA: 454] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, we will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Our hope is to capture both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago , Chicago, Illinois 60607, United States.,Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
| | - Xiaodong Pang
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
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15
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Sawle L, Huihui J, Ghosh K. All-Atom Simulations Reveal Protein Charge Decoration in the Folded and Unfolded Ensemble Is Key in Thermophilic Adaptation. J Chem Theory Comput 2017; 13:5065-5075. [DOI: 10.1021/acs.jctc.7b00545] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lucas Sawle
- Department of Physics and
Astronomy, University of Denver, Denver, Colorado 80208, United States
| | - Jonathan Huihui
- Department of Physics and
Astronomy, University of Denver, Denver, Colorado 80208, United States
| | - Kingshuk Ghosh
- Department of Physics and
Astronomy, University of Denver, Denver, Colorado 80208, United States
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16
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Watson MD, Monroe J, Raleigh DP. Size-Dependent Relationships between Protein Stability and Thermal Unfolding Temperature Have Important Implications for Analysis of Protein Energetics and High-Throughput Assays of Protein–Ligand Interactions. J Phys Chem B 2017; 122:5278-5285. [DOI: 10.1021/acs.jpcb.7b05684] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Daniel P. Raleigh
- Research Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, United Kingdom
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17
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Makhatadze GI. Linking computation and experiments to study the role of charge-charge interactions in protein folding and stability. Phys Biol 2017; 14:013002. [PMID: 28169222 DOI: 10.1088/1478-3975/14/1/013002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the past two decades there has been an increase in appreciation for the role of surface charge-charge interactions in protein folding and stability. The perception shifted from the belief that charge-charge interactions are not important for protein folding and stability to the near quantitative understanding of how these interactions shape the folding energy landscape. This led to the ability of computational approaches to rationally redesign surface charge-charge interactions to modulate thermodynamic properties of proteins. Here we summarize our progress in understanding the role of charge-charge interactions for protein stability using examples drawn from my own laboratory and touch upon unanswered questions.
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Affiliation(s)
- George I Makhatadze
- Center for Biotechnology and Interdisciplinary Studies, and Department of Biological Sciences, Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180 USA
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18
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Solgi Z, Khalifeh K, Hosseinkhani S, Ranjbar B. Surface Arginine Saturation Effect on Unfolding Reaction of Firefly Luciferase: A Thermodynamic and Kinetic Perspective. Photochem Photobiol 2016; 92:688-93. [DOI: 10.1111/php.12614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/08/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Zahra Solgi
- Department of Biophysics; Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Khosrow Khalifeh
- Department of Biology; Faculty of Sciences; University of Zanjan; Zanjan Iran
| | - Saman Hosseinkhani
- Department of Biochemistry; Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Bijan Ranjbar
- Department of Biophysics; Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
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19
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Abstract
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We review how major cell behaviors,
such as bacterial growth laws,
are derived from the physical chemistry of the cell’s proteins.
On one hand, cell actions depend on the individual biological functionalities
of their many genes and proteins. On the other hand, the common physics
among proteins can be as important as the unique biology that distinguishes
them. For example, bacterial growth rates depend strongly on temperature.
This dependence can be explained by the folding stabilities across
a cell’s proteome. Such modeling explains how thermophilic
and mesophilic organisms differ, and how oxidative damage of highly
charged proteins can lead to unfolding and aggregation in aging cells.
Cells have characteristic time scales. For example, E. coli can duplicate as fast as 2–3 times per hour. These time scales
can be explained by protein dynamics (the rates of synthesis and degradation,
folding, and diffusional transport). It rationalizes how bacterial
growth is slowed down by added salt. In the same way that the behaviors
of inanimate materials can be expressed in terms of the statistical
distributions of atoms and molecules, some cell behaviors can be expressed
in terms of distributions of protein properties, giving insights into
the microscopic basis of growth laws in simple cells.
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Affiliation(s)
- Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver , Denver, Colorado 80209, United States
| | - Adam M R de Graff
- Laufer Center for Physical and Quantitative Biology and Departments of Chemistry and Physics and Astronomy, Stony Brook University , Stony Brook, New York 11794, United States
| | - Lucas Sawle
- Department of Physics and Astronomy, University of Denver , Denver, Colorado 80209, United States
| | - Ken A Dill
- Laufer Center for Physical and Quantitative Biology and Departments of Chemistry and Physics and Astronomy, Stony Brook University , Stony Brook, New York 11794, United States
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Tripathi S, Garcìa AE, Makhatadze GI. Alterations of Nonconserved Residues Affect Protein Stability and Folding Dynamics through Charge–Charge Interactions. J Phys Chem B 2015; 119:13103-12. [DOI: 10.1021/acs.jpcb.5b08527] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Swarnendu Tripathi
- Department
of Physics, University of Houston, Houston, Texas 77204, United States
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21
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Samuel PP, Smith LP, Phillips GN, Olson JS. Apoglobin Stability Is the Major Factor Governing both Cell-free and in Vivo Expression of Holomyoglobin. J Biol Chem 2015. [PMID: 26205820 DOI: 10.1074/jbc.m115.672204] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Expression levels in animal muscle tissues and in Escherichia coli vary widely for naturally occurring mammalian myoglobins (Mb). To explore this variation, we developed an in vitro transcription and wheat germ extract-based translation assay to examine quantitatively the factors that govern expression of holoMb. We constructed a library of naturally occurring Mbs from two terrestrial and four deep-diving aquatic mammals and three distal histidine mutants designed to enhance apoglobin stability but decrease hemin affinity. A strong linear correlation is observed between cell-free expression levels of holo-metMb variants and their corresponding apoglobin stabilities, which were measured independently by guanidine HCl-induced unfolding titrations using purified proteins. In contrast, there is little dependence of expression on hemin affinity. Our results confirm quantitatively that deep diving mammals have highly stable Mbs that express to higher levels in animal myocytes, E. coli, and the wheat germ cell-free system than Mbs from terrestrial mammals. Our theoretical analyses show that the rate of aggregation of unfolded apoMb is very large, and as a result, the key factor for high level expression of holoMb, and presumably other heme proteins, is an ultra high fraction of folded, native apoglobin that is capable of rapidly binding hemin. This fraction is determined by the overall equilibrium folding constant and not hemin affinity. These results also demonstrate that the cell-free transcription/translation system can be used as a high throughput platform to screen for apoglobin stability without the need to generate large amounts of protein for in vitro unfolding measurements.
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Affiliation(s)
| | | | - George N Phillips
- From BioSciences at Rice and Department of Chemistry, Rice University, Houston, Texas 77005
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22
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The route to protein aggregate superstructures: Particulates and amyloid-like spherulites. FEBS Lett 2015; 589:2448-63. [DOI: 10.1016/j.febslet.2015.07.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/02/2015] [Accepted: 07/06/2015] [Indexed: 12/15/2022]
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23
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Oellermann M, Strugnell JM, Lieb B, Mark FC. Positive selection in octopus haemocyanin indicates functional links to temperature adaptation. BMC Evol Biol 2015; 15:133. [PMID: 26142723 PMCID: PMC4491423 DOI: 10.1186/s12862-015-0411-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 06/04/2015] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Octopods have successfully colonised the world's oceans from the tropics to the poles. Yet, successful persistence in these habitats has required adaptations of their advanced physiological apparatus to compensate impaired oxygen supply. Their oxygen transporter haemocyanin plays a major role in cold tolerance and accordingly has undergone functional modifications to sustain oxygen release at sub-zero temperatures. However, it remains unknown how molecular properties evolved to explain the observed functional adaptations. We thus aimed to assess whether natural selection affected molecular and structural properties of haemocyanin that explains temperature adaptation in octopods. RESULTS Analysis of 239 partial sequences of the haemocyanin functional units (FU) f and g of 28 octopod species of polar, temperate, subtropical and tropical origin revealed natural selection was acting primarily on charge properties of surface residues. Polar octopods contained haemocyanins with higher net surface charge due to decreased glutamic acid content and higher numbers of basic amino acids. Within the analysed partial sequences, positive selection was present at site 2545, positioned between the active copper binding centre and the FU g surface. At this site, methionine was the dominant amino acid in polar octopods and leucine was dominant in tropical octopods. Sites directly involved in oxygen binding or quaternary interactions were highly conserved within the analysed sequence. CONCLUSIONS This study has provided the first insight into molecular and structural mechanisms that have enabled octopods to sustain oxygen supply from polar to tropical conditions. Our findings imply modulation of oxygen binding via charge-charge interaction at the protein surface, which stabilize quaternary interactions among functional units to reduce detrimental effects of high pH on venous oxygen release. Of the observed partial haemocyanin sequence, residue 2545 formed a close link between the FU g surface and the active centre, suggesting a role as allosteric binding site. The prevalence of methionine at this site in polar octopods, implies regulation of oxygen affinity via increased sensitivity to allosteric metal binding. High sequence conservation of sites directly involved in oxygen binding indicates that functional modifications of octopod haemocyanin rather occur via more subtle mechanisms, as observed in this study.
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Affiliation(s)
- Michael Oellermann
- Integrative Ecophysiology, Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany.
| | - Jan M Strugnell
- Department of Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC, 3086, Australia.
| | - Bernhard Lieb
- Institute of Zoology, Johannes Gutenberg-Universität, Müllerweg 6, 55099, Mainz, Germany.
| | - Felix C Mark
- Integrative Ecophysiology, Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany.
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24
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Thermodynamical Studies of an Example Peptide Containing Metaaminobenzoic Acid (MABA) that Promotes Bends in Proteins. J SOLUTION CHEM 2015. [DOI: 10.1007/s10953-015-0307-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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25
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Dudek MJ. A detailed representation of electrostatic energy in prediction of sequence and pH dependence of protein stability. Proteins 2014; 82:2497-511. [DOI: 10.1002/prot.24613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/11/2014] [Accepted: 05/15/2014] [Indexed: 11/05/2022]
Affiliation(s)
- Michael J. Dudek
- Protabit LLC; 250 S Oak Knoll Ave. #211 Pasadena California 91101
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26
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Nick Pace C, Scholtz JM, Grimsley GR. Forces stabilizing proteins. FEBS Lett 2014; 588:2177-84. [PMID: 24846139 DOI: 10.1016/j.febslet.2014.05.006] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 04/30/2014] [Accepted: 05/05/2014] [Indexed: 11/30/2022]
Abstract
The goal of this article is to summarize what has been learned about the major forces stabilizing proteins since the late 1980s when site-directed mutagenesis became possible. The following conclusions are derived from experimental studies of hydrophobic and hydrogen bonding variants. (1) Based on studies of 138 hydrophobic interaction variants in 11 proteins, burying a -CH2- group on folding contributes 1.1±0.5 kcal/mol to protein stability. (2) The burial of non-polar side chains contributes to protein stability in two ways: first, a term that depends on the removal of the side chains from water and, more importantly, the enhanced London dispersion forces that result from the tight packing in the protein interior. (3) Based on studies of 151 hydrogen bonding variants in 15 proteins, forming a hydrogen bond on folding contributes 1.1±0.8 kcal/mol to protein stability. (4) The contribution of hydrogen bonds to protein stability is strongly context dependent. (5) Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. (6) Polar group burial can make a favorable contribution to protein stability even if the polar group is not hydrogen bonded. (7) Hydrophobic interactions and hydrogen bonds both make large contributions to protein stability.
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Affiliation(s)
- C Nick Pace
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States; Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, United States.
| | - J Martin Scholtz
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States; Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, United States
| | - Gerald R Grimsley
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, United States
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27
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Pey AL, Majtan T, Kraus JP. The role of surface electrostatics on the stability, function and regulation of human cystathionine β-synthase, a complex multidomain and oligomeric protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1453-62. [PMID: 24780582 DOI: 10.1016/j.bbapap.2014.04.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/06/2014] [Accepted: 04/21/2014] [Indexed: 11/25/2022]
Abstract
Human cystathionine β-synthase (hCBS) is a key enzyme of sulfur amino acid metabolism, controlling the commitment of homocysteine to the transsulfuration pathway and antioxidant defense. Mutations in hCBS cause inherited homocystinuria (HCU), a rare inborn error of metabolism characterized by accumulation of toxic homocysteine in blood and urine. hCBS is a complex multidomain and oligomeric protein whose activity and stability are independently regulated by the binding of S-adenosyl-methionine (SAM) to two different types of sites at its C-terminal regulatory domain. Here we study the role of surface electrostatics on the complex regulation and stability of hCBS using biophysical and biochemical procedures. We show that the kinetic stability of the catalytic and regulatory domains is significantly affected by the modulation of surface electrostatics through noticeable structural and energetic changes along their denaturation pathways. We also show that surface electrostatics strongly affect SAM binding properties to those sites responsible for either enzyme activation or kinetic stabilization. Our results provide new insight into the regulation of hCBS activity and stability in vivo with implications for understanding HCU as a conformational disease. We also lend experimental support to the role of electrostatic interactions in the recently proposed binding modes of SAM leading to hCBS activation and kinetic stabilization.
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Affiliation(s)
- Angel L Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071 Granada, Spain.
| | - Tomas Majtan
- Department of Pediatrics, University of Colorado, School of Medicine, Aurora, CO 80045, USA
| | - Jan P Kraus
- Department of Pediatrics, University of Colorado, School of Medicine, Aurora, CO 80045, USA
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28
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An in silico method for designing thermostable variant of a dimeric mesophilic protein based on its 3D structure. J Mol Graph Model 2013; 42:92-103. [PMID: 23584153 DOI: 10.1016/j.jmgm.2013.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 02/25/2013] [Accepted: 02/27/2013] [Indexed: 11/21/2022]
Abstract
Designing proteins with enhanced thermostability has been a major interest of protein engineering because of its potential industrial applications. Here, we have presented a computational method for designing dimeric thermostable protein based on rational mutations on a mesophilic protein. Experimental and structural data indicate that the surface stability of a protein is a major factor controlling denaturation of a protein and ion-pairs are most efficient in enhancing the stability of the surfaces of the monomers and the interface between them. Our mutation based strategy is to first identify several polar or charged residues on the protein surface, interacting weakly with the rest of the protein and then replacing the side-chains of suitable neighboring residues to increase the interaction between these two residues. In stabilizing the interface, mutation is done in the interface for forming an ion pairs between the monomers. Application of this design strategy to a homo-dimeric protein and a hetero-dimeric protein as examples has produced excellent results. In both the cases the designed mutated proteins including the individual monomers and the interfaces were found to be considerably more stable than the respective mesophilic proteins as judged by self-energies and residue-wise interaction patterns. This method is easily applicable to any multi-meric proteins.
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29
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Tretyakova T, Shushanyan M, Partskhaladze T, Makharadze M, van Eldik R, Khoshtariya DE. Simplicity within the complexity: bilateral impact of DMSO on the functional and unfolding patterns of α-chymotrypsin. Biophys Chem 2013; 175-176:17-27. [PMID: 23524288 DOI: 10.1016/j.bpc.2013.02.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 02/05/2013] [Accepted: 02/09/2013] [Indexed: 10/27/2022]
Abstract
New understanding of the fundamental links between protein stability, conformational flexibility and function, can be gained through synergic studies on their catalytic and folding/unfolding properties under the influence of stabilizing/destabilizing additives. We explored an impact of dimethyl sulfoxide (DMSO), the moderate effector of multilateral action, on the kinetic (functional) and thermodynamic (thermal unfolding) patterns of a hydrolytic enzyme, α-chymotrypsin (α-CT), over a wide range of additive concentrations, 0-70% (v/v). Both the calorimetric and kinetic data exhibited rich behavior pointing to the complex interplay of global/local stability (and flexibility) patterns. The complex action of DMSO is explained through the negative and positive preferential solvation motifs that prevail for the extreme opposite, native-like and unfolded states, respectively, implying essential stabilization of compact domains by enhancement of interfacial water networks and destabilization of a flexible active site by direct binding of DMSO to the unoccupied specific positions intended for elongated polypeptide substrates.
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Affiliation(s)
- Tatyana Tretyakova
- Institute for Biophysics and Bionanosciences at the Department of Physics, I. Javakhishvili Tbilisi State University, I. Chavchavadze Ave. 3, 0128 Tbilisi, Georgia
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30
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Basu S, Sen S. Do Homologous Thermophilic–Mesophilic Proteins Exhibit Similar Structures and Dynamics at Optimal Growth Temperatures? A Molecular Dynamics Simulation Study. J Chem Inf Model 2013; 53:423-34. [DOI: 10.1021/ci300474h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sohini Basu
- Molecular modeling Section, Biolab, Chembiotek, TCG Lifesciences Ltd., Bengal Intelligent Park, Tower-B 2nd Floor, Block-EP & GP, Sector-V, Salt Lake Electronic Complex, Calcutta-700091, India
| | - Srikanta Sen
- Molecular modeling Section, Biolab, Chembiotek, TCG Lifesciences Ltd., Bengal Intelligent Park, Tower-B 2nd Floor, Block-EP & GP, Sector-V, Salt Lake Electronic Complex, Calcutta-700091, India
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31
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Kim NA, An IB, Lee SY, Park ES, Jeong SH. Optimization of protein solution by a novel experimental design method using thermodynamic properties. Arch Pharm Res 2012; 35:1609-19. [DOI: 10.1007/s12272-012-0912-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Revised: 06/14/2012] [Accepted: 06/29/2012] [Indexed: 10/27/2022]
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32
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Veit S, Takeda K, Tsunoyama Y, Rexroth D, Rögner M, Miki K. Structure of a thermophilic cyanobacterial b6f-type Rieske protein. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1400-8. [PMID: 22993094 DOI: 10.1107/s0907444912034129] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 07/31/2012] [Indexed: 11/10/2022]
Abstract
The `Rieske protein' PetC is one of the key subunits of the cytochrome b(6)f complex. Its Rieske-type [2Fe-2S] cluster participates in the photosynthetic electron-transport chain. Overexpression and careful structure analysis at 2.0 Å resolution of the extrinsic soluble domain of PetC from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 enabled in-depth spectroscopic and structural characterization and suggested novel structural features. In particular, both the protein structure and the positions of the internal water molecules unexpectedly showed a higher similarity to eukaryotic PetCs than to other prokaryotic PetCs. The structure also revealed a deep pocket on the PetC surface which is oriented towards the membrane surface in the whole complex. Its surface properties suggest a binding site for a hydrophobic compound and the complete conservation of the pocket-forming residues in all known PetC sequences indicates the functional importance of this pocket in the cytochrome b(6)f complex.
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Affiliation(s)
- Sebastian Veit
- Plant Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany
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33
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Mechanism of the Bell-Shaped Profile of Ribonuclease A activity: Molecular Dynamic Approach. Protein J 2012; 31:573-9. [DOI: 10.1007/s10930-012-9435-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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34
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Mullins EA, Starks CM, Francois JA, Sael L, Kihara D, Kappock TJ. Formyl-coenzyme A (CoA):oxalate CoA-transferase from the acidophile Acetobacter aceti has a distinctive electrostatic surface and inherent acid stability. Protein Sci 2012; 21:686-96. [PMID: 22374910 DOI: 10.1002/pro.2054] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 01/26/2012] [Accepted: 02/20/2012] [Indexed: 11/09/2022]
Abstract
Bacterial formyl-CoA:oxalate CoA-transferase (FCOCT) and oxalyl-CoA decarboxylase work in tandem to perform a proton-consuming decarboxylation that has been suggested to have a role in generalized acid resistance. FCOCT is the product of uctB in the acidophilic acetic acid bacterium Acetobacter aceti. As expected for an acid-resistance factor, UctB remains folded at the low pH values encountered in the A. aceti cytoplasm. A comparison of crystal structures of FCOCTs and related proteins revealed few features in UctB that would distinguish it from nonacidophilic proteins and thereby account for its acid stability properties, other than a strikingly featureless electrostatic surface. The apparently neutral surface is a result of a "speckled" charge decoration, in which charged surface residues are surrounded by compensating charges but do not form salt bridges. A quantitative comparison among orthologs identified a pattern of residue substitution in UctB that may be a consequence of selection for protein stability by constant exposure to acetic acid. We suggest that this surface charge pattern, which is a distinctive feature of A. aceti proteins, creates a stabilizing electrostatic network without stiffening the protein or compromising protein-solvent interactions.
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Affiliation(s)
- Elwood A Mullins
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
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35
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Electrostatic contribution of surface charge residues to the stability of a thermophilic protein: benchmarking experimental and predicted pKa values. PLoS One 2012; 7:e30296. [PMID: 22279578 PMCID: PMC3261180 DOI: 10.1371/journal.pone.0030296] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 12/13/2011] [Indexed: 11/20/2022] Open
Abstract
Optimization of the surface charges is a promising strategy for increasing thermostability of proteins. Electrostatic contribution of ionizable groups to the protein stability can be estimated from the differences between the pKa values in the folded and unfolded states of a protein. Using this pKa-shift approach, we experimentally measured the electrostatic contribution of all aspartate and glutamate residues to the stability of a thermophilic ribosomal protein L30e from Thermococcus celer. The pKa values in the unfolded state were found to be similar to model compound pKas. The pKa values in both the folded and unfolded states obtained at 298 and 333 K were similar, suggesting that electrostatic contribution of ionizable groups to the protein stability were insensitive to temperature changes. The experimental pKa values for the L30e protein in the folded state were used as a benchmark to test the robustness of pKa prediction by various computational methods such as H++, MCCE, MEAD, pKD, PropKa, and UHBD. Although the predicted pKa values were affected by crystal contacts that may alter the side-chain conformation of surface charged residues, most computational methods performed well, with correlation coefficients between experimental and calculated pKa values ranging from 0.49 to 0.91 (p<0.01). The changes in protein stability derived from the experimental pKa-shift approach correlate well (r = 0.81) with those obtained from stability measurements of charge-to-alanine substituted variants of the L30e protein. Our results demonstrate that the knowledge of the pKa values in the folded state provides sufficient rationale for the redesign of protein surface charges leading to improved protein stability.
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36
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Makowska J, Uber D, Chmurzyński L. Thermodynamics of the Protonation Equilibria of Two Fragments of N-Terminal β-Hairpin of FPB28 WW Domain. J Phys Chem B 2011; 116:653-9. [DOI: 10.1021/jp209844v] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joanna Makowska
- Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
| | - Dorota Uber
- Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
| | - Lech Chmurzyński
- Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
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37
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Mortazavi M, Hosseinkhani S. Design of thermostable luciferases through arginine saturation in solvent-exposed loops. Protein Eng Des Sel 2011; 24:893-903. [PMID: 22068960 DOI: 10.1093/protein/gzr051] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In most bioluminescence systems the oxidation of luciferin and production of light is catalyzed by luciferases. Protein engineering studies have shown that thermostable proteins from thermophilic organisms have a higher frequency of Arg, especially in exposed states. To further clarify the arginine saturation effect on thermostability of firefly luciferase, some of hydrophobic solvent-exposed residues in Lampyris turkestanicus luciferase are changed to arginine. All of these residues are located at the surface loops of L.turkestanicus luciferase. Starting with a luciferase mutant (E³⁵⁴Q/Arg³⁵⁶), single mutation (-Q³⁵R, -I¹⁸²R, -I²³²R and -L(300)R), double mutation (-Q³⁵R/I²³²R) and triple mutation (-Q³⁵R/I²³²R/I¹⁸²R) are added. Bioluminescence emission spectra indicate that substitution of Arg by these residues, do not effect on the maximum wavelength of emission spectrum. It should be noted, introduction of double mutation (-Q³⁵R/I²³²R) and triple mutation (-Q³⁵R/I²³²R/I¹⁸²R) were kept specific activity of firefly luciferase. By addition of positively charged residue, some specific mutations (-I²³²R, -Q³⁵R/I²³²R and -Q³⁵R/I²³²R/I¹⁸²R) showed that optimum temperature of activity was increased to 40°C which are 12 and 15°C higher than E³⁵⁴Q/Arg³⁵⁶ and wild-type luciferases, respectively. Also, after 40 min incubation of enzymes at 40°C, the relative remaining activity of wild type was only 5%, whereas for -I²³²R, -Q³⁵R/I²³²R and -Q³⁵R/I²³²R/I¹⁸²R was 60, 80 and 80% of original activity, respectively.
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Affiliation(s)
- Mojtaba Mortazavi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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38
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Meng W, Raleigh DP. Analysis of electrostatic interactions in the denatured state ensemble of the N-terminal domain of L9 under native conditions. Proteins 2011; 79:3500-10. [PMID: 21915914 DOI: 10.1002/prot.23145] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 07/05/2011] [Accepted: 07/15/2011] [Indexed: 11/06/2022]
Abstract
The pH dependence of protein stability is defined by the difference in the number of protons bound to the folded state and to the denatured state ensemble (DSE) as a function of pH. In many cases, the protonation behavior can be described as the sum of a set of independently titrating residues; in this case, the pH dependence of stability reflects differences in folded and DSE pK(a)'s. pH dependent stability studies have shown that there are energetically important interactions involving charged residues in the DSE of the N-terminal domain of L9 (NTL9), which affect significantly the stability of the protein. The DSE of wild type NTL9 cannot be directly characterized under native conditions because of its high stability. A destabilized double mutant of NTL9, V3AI4A, significantly populates the folded state and the DSE in the absence of denaturant. The two states are in slow exchange on the nuclear magnetic resonance time scale, and diffusion measurements indicate that the DSE is compact. The DSE pK(a)'s of all of the acidic residues were directly determined. The DSE pK(a) of Asp8 and Asp23 are depressed relative to model compounds values. Use of the mutant DSE pK(a)'s together with known native state pK(a)'s leads to a significantly improved agreement between the measured pH dependent stability and that predicted by the Tanford-Wyman linkage relationship. An analysis of the literature suggests that DSE interactions involving charged residues are relatively common and should be considered in discussions of protein stability.
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Affiliation(s)
- Wenli Meng
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, USA
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39
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Warshel A, Dryga A. Simulating electrostatic energies in proteins: perspectives and some recent studies of pKas, redox, and other crucial functional properties. Proteins 2011; 79:3469-84. [PMID: 21910139 DOI: 10.1002/prot.23125] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 05/09/2011] [Accepted: 06/09/2011] [Indexed: 01/30/2023]
Abstract
Electrostatic energies provide what is arguably the most effective tool for structure-function correlation of biological molecules. Here, we provide an overview of the current state-of-the-art simulations of electrostatic energies in macromolecules, emphasizing the microscopic perspective but also relating it to macroscopic approaches. We comment on the convergence issue and other problems of the microscopic models and the ways of keeping the microscopic physics while moving to semi-macroscopic directions. We discuss the nature of the protein dielectric "constants" reiterating our long-standing point that the dielectric "constants" in semi-macroscopic models depend on the definition and the specific treatment. The advances and the challenges in the field are illustrated considering different functional properties including pK(a)'s, redox potentials, ion and proton channels, enzyme catalysis, ligand binding, and protein stability. We emphasize the microscopic overcharging approach for studying pK(a) 's of internal groups in proteins and give a demonstration of power of this approach. We also emphasize recent advances in coarse grained models with a physically based electrostatic treatment and provide some examples including further directions in treating voltage activated ion channels.
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Affiliation(s)
- Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, USA.
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40
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pH-Dependent Conformational Transitions in Conalbumin (Ovotransferrin), a Metalloproteinase from Hen Egg White. Cell Biochem Biophys 2011; 61:551-60. [DOI: 10.1007/s12013-011-9237-x] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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41
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Pace CN, Fu H, Fryar KL, Landua J, Trevino SR, Shirley BA, Hendricks MM, Iimura S, Gajiwala K, Scholtz JM, Grimsley GR. Contribution of hydrophobic interactions to protein stability. J Mol Biol 2011; 408:514-28. [PMID: 21377472 DOI: 10.1016/j.jmb.2011.02.053] [Citation(s) in RCA: 254] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/21/2011] [Accepted: 02/23/2011] [Indexed: 11/29/2022]
Abstract
Our goal was to gain a better understanding of the contribution of hydrophobic interactions to protein stability. We measured the change in conformational stability, Δ(ΔG), for hydrophobic mutants of four proteins: villin headpiece subdomain (VHP) with 36 residues, a surface protein from Borrelia burgdorferi (VlsE) with 341 residues, and two proteins previously studied in our laboratory, ribonucleases Sa and T1. We compared our results with those of previous studies and reached the following conclusions: (1) Hydrophobic interactions contribute less to the stability of a small protein, VHP (0.6±0.3 kcal/mol per -CH(2)- group), than to the stability of a large protein, VlsE (1.6±0.3 kcal/mol per -CH(2)- group). (2) Hydrophobic interactions make the major contribution to the stability of VHP (40 kcal/mol) and the major contributors are (in kilocalories per mole) Phe18 (3.9), Met13 (3.1), Phe7 (2.9), Phe11 (2.7), and Leu21 (2.7). (3) Based on the Δ(ΔG) values for 148 hydrophobic mutants in 13 proteins, burying a -CH(2)- group on folding contributes, on average, 1.1±0.5 kcal/mol to protein stability. (4) The experimental Δ(ΔG) values for aliphatic side chains (Ala, Val, Ile, and Leu) are in good agreement with their ΔG(tr) values from water to cyclohexane. (5) For 22 proteins with 36 to 534 residues, hydrophobic interactions contribute 60±4% and hydrogen bonds contribute 40±4% to protein stability. (6) Conformational entropy contributes about 2.4 kcal/mol per residue to protein instability. The globular conformation of proteins is stabilized predominantly by hydrophobic interactions.
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Affiliation(s)
- C Nick Pace
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.
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Lam SY, Yeung RCY, Yu TH, Sze KH, Wong KB. A rigidifying salt-bridge favors the activity of thermophilic enzyme at high temperatures at the expense of low-temperature activity. PLoS Biol 2011; 9:e1001027. [PMID: 21423654 PMCID: PMC3057955 DOI: 10.1371/journal.pbio.1001027] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 02/01/2011] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Thermophilic enzymes are often less active than their mesophilic homologues at low temperatures. One hypothesis to explain this observation is that the extra stabilizing interactions increase the rigidity of thermophilic enzymes and hence reduce their activity. Here we employed a thermophilic acylphosphatase from Pyrococcus horikoshii and its homologous mesophilic acylphosphatase from human as a model to study how local rigidity of an active-site residue affects the enzymatic activity. METHODS AND FINDINGS Acylphosphatases have a unique structural feature that its conserved active-site arginine residue forms a salt-bridge with the C-terminal carboxyl group only in thermophilic acylphosphatases, but not in mesophilic acylphosphatases. We perturbed the local rigidity of this active-site residue by removing the salt-bridge in the thermophilic acylphosphatase and by introducing the salt-bridge in the mesophilic homologue. The mutagenesis design was confirmed by x-ray crystallography. Removing the salt-bridge in the thermophilic enzyme lowered the activation energy that decreased the activation enthalpy and entropy. Conversely, the introduction of the salt-bridge to the mesophilic homologue increased the activation energy and resulted in increases in both activation enthalpy and entropy. Revealed by molecular dynamics simulations, the unrestrained arginine residue can populate more rotamer conformations, and the loss of this conformational freedom upon the formation of transition state justified the observed reduction in activation entropy. CONCLUSIONS Our results support the conclusion that restricting the active-site flexibility entropically favors the enzymatic activity at high temperatures. However, the accompanying enthalpy-entropy compensation leads to a stronger temperature-dependency of the enzymatic activity, which explains the less active nature of the thermophilic enzymes at low temperatures.
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Affiliation(s)
- Sonia Y. Lam
- School of Life Sciences, Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Rachel C. Y. Yeung
- School of Life Sciences, Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Tsz-Ha Yu
- School of Life Sciences, Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Kong-Hung Sze
- Department of Chemistry, University of Hong Kong, Hong Kong SAR, China
| | - Kam-Bo Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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43
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Cockburn DW, Clarke AJ. Modulating the pH-activity profile of cellulase A from Cellulomonas fimi by replacement of surface residues. Protein Eng Des Sel 2011; 24:429-37. [DOI: 10.1093/protein/gzr004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Chakravorty D, Parameswaran S, Dubey VK, Patra S. In silico characterization of thermostable lipases. Extremophiles 2010; 15:89-103. [PMID: 21153672 DOI: 10.1007/s00792-010-0337-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 11/15/2010] [Indexed: 11/28/2022]
Abstract
Thermostable lipases are of high priority for industrial applications as they are endowed with the capability of carrying out diversified reactions at elevated temperatures. Extremophiles are their potential source. Sequence and structure annotation of thermostable lipases can elucidate evolution of lipases from their mesophilic counterparts with enhanced thermostability hence better industrial potential. Sequence analysis highlighted the conserved residues in bacterial and fungal thermostable lipases. Higher frequency of AXXXA motif and poly Ala residues in lid domain of thermostable Bacillus lipases were distinguishing characteristics. Comparison of amino acid composition among thermostable and mesostable lipases brought into light the role of neutral, charged and aromatic amino acid residues in enhancement of thermostability. Structural annotation of thermostable lipases with that of mesostable lipases revealed some striking features which are increment of gamma turns in thermostable lipases; being first time reported in our paper, longer beta strands, lesser beta-branched residues in helices, increase in charged-neutral hydrogen bonding pair, hydrophobic-hydrophobic contact and differences in the N-cap and C-cap residues of the α helices. Conclusively, it can be stated that subtle changes in the arrangement of amino acid residues in the tertiary structure of lipases contributes to enhanced thermostability.
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Affiliation(s)
- Debamitra Chakravorty
- Department of Biotechnology, Indian Institute of Technology, Guwahati 781039, Assam, India
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45
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Finnegan ML, Bowler BE. Propensities of aromatic amino acids versus leucine and proline to induce residual structure in the denatured-state ensemble of iso-1-cytochrome c. J Mol Biol 2010; 403:495-504. [PMID: 20850458 DOI: 10.1016/j.jmb.2010.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2010] [Revised: 08/31/2010] [Accepted: 09/02/2010] [Indexed: 11/30/2022]
Abstract
Histidine-heme loop formation in the denatured state of a protein is a sensitive means for probing residual structure under unfolding conditions. In this study, we use a host-guest approach to investigate the relative tendencies of different amino acids to promote residual structure under denaturing conditions. The host for this work is a 6-amino-acid insert of five alanines, followed by a lysine engineered immediately following a unique histidine near the N-terminus of yeast iso-1-cytochrome c. We substitute the fourth alanine in this sequence HAAAXAK (with X=Trp, Phe, Tyr, and Leu). The effects of proline are tested with substitutions at positions 1 and 5 in the insert (HPAAAAK and HAAAAPK, respectively). Thermodynamic studies on His-heme loop formation in 3 M guanidine hydrochloride reveal significant stabilization of residual structure by aromatic amino acids, particularly Trp and Phe, and minimal stabilization of residual structure by Leu. Prolines slightly disfavor His-heme loop formation, presumably due to enhanced chain stiffness. Kinetic studies reveal that much of the change in His-heme loop stability for the aromatic amino acids is caused by a slowdown in the rate of His-heme loop breakage, indicating that residual structure is preferentially stabilized in the closed-loop form of the denatured state.
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Affiliation(s)
- Michaela L Finnegan
- Department of Chemistry and Biochemistry, Biochemistry Program and Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
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46
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Fu H, Grimsley G, Scholtz JM, Pace CN. Increasing protein stability: importance of DeltaC(p) and the denatured state. Protein Sci 2010; 19:1044-52. [PMID: 20340133 DOI: 10.1002/pro.381] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Increasing the conformational stability of proteins is an important goal for both basic research and industrial applications. In vitro selection has been used successfully to increase protein stability, but more often site-directed mutagenesis is used to optimize the various forces that contribute to protein stability. In previous studies, we showed that improving electrostatic interactions on the protein surface and improving the beta-turn sequences were good general strategies for increasing protein stability, and used them to increase the stability of RNase Sa. By incorporating seven of these mutations in RNase Sa, we increased the stability by 5.3 kcal/mol. Adding one more mutation, D79F, gave a total increase in stability of 7.7 kcal/mol, and a melting temperature 28 degrees C higher than the wild-type enzyme. Surprisingly, the D79F mutation lowers the change in heat capacity for folding, DeltaC(p), by 0.6 kcal/mol/K. This suggests that this mutation stabilizes structure in the denatured state ensemble. We made other mutants that give some insight into the structure present in the denatured state. Finally, the thermodynamics of folding of these stabilized variants of RNase Sa are compared with those observed for proteins from thermophiles.
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Affiliation(s)
- Hailong Fu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
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47
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Sreedhara A, Flengsrud R, Prakash V, Krowarsch D, Langsrud T, Kaul P, Devold TG, Vegarud GE. A comparison of effects of pH on the thermal stability and conformation of caprine and bovine lactoferrin. Int Dairy J 2010. [DOI: 10.1016/j.idairyj.2010.02.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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48
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Scirè A, Marabotti A, Staiano M, Iozzino L, Luchansky MS, Der BS, Dattelbaum JD, Tanfani F, D'Auria S. Amino acid transport in thermophiles: characterization of an arginine-binding protein in Thermotoga maritima. 2. Molecular organization and structural stability. MOLECULAR BIOSYSTEMS 2010; 6:687-98. [PMID: 20237647 DOI: 10.1039/b922092e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
ABC transport systems provide selective passage of metabolites across cell membranes and typically require the presence of a soluble binding protein with high specificity to a specific ligand. In addition to their primary role in nutrient gathering, the binding proteins associated with bacterial transport systems have been studied for their potential to serve as design scaffolds for the development of fluorescent protein biosensors. In this work, we used Fourier transform infrared spectroscopy and molecular dynamics simulations to investigate the physicochemical properties of a hyperthermophilic binding protein from Thermotoga maritima. We demonstrated preferential binding for the polar amino acid arginine and experimentally monitored the significant stabilization achieved upon binding of ligand to protein. The effect of temperature, pH, and detergent was also studied to provide a more complete picture of the protein dynamics. A protein structure model was obtained and molecular dynamic experiments were performed to investigate and couple the spectroscopic observations with specific secondary structural elements. The data determined the presence of a buried beta-sheet providing significant stability to the protein under all conditions investigated. The specific amino acid residues responsible for arginine binding were also identified. Our data on dynamics and stability will contribute to our understanding of bacterial binding protein family members and their potential biotechnological applications.
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Affiliation(s)
- Andrea Scirè
- Department of Biochemistry, Biology, and Genetics, Università Politecnica delle Marche, Ancona, Italy
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Fu H, Grimsley GR, Razvi A, Scholtz JM, Pace CN. Increasing protein stability by improving beta-turns. Proteins 2010; 77:491-8. [PMID: 19626709 DOI: 10.1002/prot.22509] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Our goal was to gain a better understanding of how protein stability can be increased by improving beta-turns. We studied 22 beta-turns in nine proteins with 66-370 residues by replacing other residues with proline and glycine and measuring the stability. These two residues are statistically preferred in some beta-turn positions. We studied: Cold shock protein B (CspB), Histidine-containing phosphocarrier protein, Ubiquitin, Ribonucleases Sa2, Sa3, T1, and HI, Tryptophan synthetase alpha-subunit, and Maltose binding protein. Of the 15 single proline mutations, 11 increased stability (Average = 0.8 +/- 0.3; Range = 0.3-1.5 kcal/mol), and the stabilizing effect of double proline mutants was additive. On the basis of this and our previous work, we conclude that proteins can generally be stabilized by replacing nonproline residues with proline residues at the i + 1 position of Type I and II beta-turns and at the i position in Type II beta-turns. Other turn positions can sometimes be used if the phi angle is near -60 degrees for the residue replaced. It is important that the side chain of the residue replaced is less than 50% buried. Identical substitutions in beta-turns in related proteins give similar results. Proline substitutions increase stability mainly by decreasing the entropy of the denatured state. In contrast, the large, diverse group of proteins considered here had almost no residues in beta-turns that could be replaced by Gly to increase protein stability. Improving beta-turns by substituting Pro residues is a generally useful way of increasing protein stability.
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Affiliation(s)
- Hailong Fu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
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50
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Azia A, Levy Y. Nonnative Electrostatic Interactions Can Modulate Protein Folding: Molecular Dynamics with a Grain of Salt. J Mol Biol 2009; 393:527-42. [DOI: 10.1016/j.jmb.2009.08.010] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 08/01/2009] [Accepted: 08/06/2009] [Indexed: 11/28/2022]
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