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Jenney FE, Wang H, George SJ, Xiong J, Guo Y, Gee LB, Marizcurrena JJ, Castro-Sowinski S, Staskiewicz A, Yoda Y, Hu MY, Tamasaku K, Nagasawa N, Li L, Matsuura H, Doukov T, Cramer SP. Temperature-dependent iron motion in extremophile rubredoxins - no need for 'corresponding states'. Sci Rep 2024; 14:12197. [PMID: 38806591 PMCID: PMC11133467 DOI: 10.1038/s41598-024-62261-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Extremophile organisms are known that can metabolize at temperatures down to - 25 °C (psychrophiles) and up to 122 °C (hyperthermophiles). Understanding viability under extreme conditions is relevant for human health, biotechnological applications, and our search for life elsewhere in the universe. Information about the stability and dynamics of proteins under environmental extremes is an important factor in this regard. Here we compare the dynamics of small Fe-S proteins - rubredoxins - from psychrophilic and hyperthermophilic microorganisms, using three different nuclear techniques as well as molecular dynamics calculations to quantify motion at the Fe site. The theory of 'corresponding states' posits that homologous proteins from different extremophiles have comparable flexibilities at the optimum growth temperatures of their respective organisms. Although 'corresponding states' would predict greater flexibility for rubredoxins that operate at low temperatures, we find that from 4 to 300 K, the dynamics of the Fe sites in these homologous proteins are essentially equivalent.
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Affiliation(s)
- Francis E Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA, 30024, USA
| | | | | | - Jin Xiong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Leland B Gee
- LCLS, SLAC National Laboratory, Stanford, CA, 94025, USA
| | | | | | - Anna Staskiewicz
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA, 30024, USA
| | - Yoshitaka Yoda
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo, 679-5198, Japan
| | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439, USA
| | | | - Nobumoto Nagasawa
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo, 679-5198, Japan
| | - Lei Li
- Synchrotron Radiation Research Center, Hyogo, 679-5165, Japan
| | | | - Tzanko Doukov
- SSRL, SLAC National Laboratory, Stanford, CA, 94025, USA
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2
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Karshikoff A, Nilsson L, Ladenstein R. Rigidity versus flexibility: the dilemma of understanding protein thermal stability. FEBS J 2015; 282:3899-917. [PMID: 26074325 DOI: 10.1111/febs.13343] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/17/2015] [Accepted: 06/09/2015] [Indexed: 01/19/2023]
Abstract
The role of fluctuations in protein thermostability has recently received considerable attention. In the current literature a dualistic picture can be found: thermostability seems to be associated with enhanced rigidity of the protein scaffold in parallel with the reduction of flexible parts of the structure. In contradiction to such arguments it has been shown by experimental studies and computer simulation that thermal tolerance of a protein is not necessarily correlated with the suppression of internal fluctuations and mobility. Both concepts, rigidity and flexibility, are derived from mechanical engineering and represent temporally insensitive features describing static properties, neglecting that relative motion at certain time scales is possible in structurally stable regions of a protein. This suggests that a strict separation of rigid and flexible parts of a protein molecule does not describe the reality correctly. In this work the concepts of mobility/flexibility versus rigidity will be critically reconsidered by taking into account molecular dynamics calculations of heat capacity and conformational entropy, salt bridge networks, electrostatic interactions in folded and unfolded states, and the emerging picture of protein thermostability in view of recently developed network theories. Last, but not least, the influence of high temperature on the active site and activity of enzymes will be considered.
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Affiliation(s)
- Andrey Karshikoff
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Rudolf Ladenstein
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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3
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Pezeshgi Modarres H, Dorokhov BD, Popov VO, Ravin NV, Skryabin KG, Dal Peraro M. Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp. 1519. Biochemistry 2015; 54:3076-85. [DOI: 10.1021/bi501227b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hassan Pezeshgi Modarres
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland
| | - Boris D. Dorokhov
- Centre
“Bioengineering”, Russian Academy of Sciences, Moscow 117312, Russia
| | - Vladimir O. Popov
- Bach
Institute of Biochemistry, Russian Academy of Sciences, Moscow 119071, Russia
- RSC “Kurchatov Institute”, Moscow 123182, Russia
| | - Nikolai V. Ravin
- Centre
“Bioengineering”, Russian Academy of Sciences, Moscow 117312, Russia
| | - Konstantin G. Skryabin
- Centre
“Bioengineering”, Russian Academy of Sciences, Moscow 117312, Russia
- RSC “Kurchatov Institute”, Moscow 123182, Russia
| | - Matteo Dal Peraro
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland
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4
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Gamiz-Hernandez AP, Kieseritzky G, Ishikita H, Knapp EW. Rubredoxin Function: Redox Behavior from Electrostatics. J Chem Theory Comput 2011; 7:742-52. [DOI: 10.1021/ct100476h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ana Patricia Gamiz-Hernandez
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Fabeckstrasse 36a, D-14195, Berlin, Germany
| | - Gernot Kieseritzky
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Fabeckstrasse 36a, D-14195, Berlin, Germany
| | - Hiroshi Ishikita
- Career-Path Promotion Unit for Young Life Scientists, Kyoto University, 202 Building E, Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - E. W. Knapp
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Fabeckstrasse 36a, D-14195, Berlin, Germany
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5
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Grottesi A, Ceruso MA, Colosimo A, Di Nola A. Molecular dynamics study of a hyperthermophilic and a mesophilic rubredoxin. Proteins 2002; 46:287-94. [PMID: 11835504 DOI: 10.1002/prot.10045] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In recent years, increased interest in the origin of protein thermal stability has gained attention both for its possible role in understanding the forces governing the folding of a protein and for the design of new highly stable engineered biocatalysts. To study the origin of thermostability, we have performed molecular dynamics simulations of two rubredoxins, from the mesophile Clostridium pasteurianum and from the hyperthermophile Pyrococcus furiosus. The simulations were carried out at two temperatures, 300 and 373 K, for each molecule. The length of the simulations was within the range of 6-7.2 ns. The rubredoxin from the hyperthermophilic organism was more flexible than its mesophilic counterpart at both temperatures; however, the overall flexibility of both molecules at their optimal growth temperature was the same, despite 59% sequence homology. The conformational space sampled by both molecules was larger at 300 K than at 373 K. The essential dynamics analysis showed that the principal overall motions of the two molecules are significantly different. On the contrary, each molecule showed similar directions of motion at both temperatures.
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Affiliation(s)
- Alessandro Grottesi
- Department of Biochemical Sciences, University of Rome, La Sapienza, Rome, Italy.
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6
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Affiliation(s)
- F E Jenney
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
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7
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Lazaridis T, Lee I, Karplus M. Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin. Protein Sci 1997; 6:2589-605. [PMID: 9416608 PMCID: PMC2143628 DOI: 10.1002/pro.5560061211] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Molecular dynamics simulations in solution are performed for a rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus (RdPf) and one from the mesophilic organism Desulfovibrio vulgaris (RdDv). The two proteins are simulated at four temperatures: 300 K, 373 K, 473 K (two sets), and 500 K; the various simulations extended from 200 ps to 1,020 ps. At room temperature, the two proteins are stable, remain close to the crystal structure, and exhibit similar dynamic behavior; the RMS residue fluctuations are slightly smaller in the hyperthermophilic protein. An analysis of the average energy contributions in the two proteins is made; the results suggest that the intraprotein energy stabilizes RdPf relative to RdDv. At 373 K, the mesophilic protein unfolds rapidly (it begins to unfold at 300 ps), whereas the hyperthermophilic does not unfold over the simulation of 600 ps. This is in accord with the expected stability of the two proteins. At 473 K, where both proteins are expected to be unstable, unfolding behavior is observed within 200 ps and the mesophilic protein unfolds faster than the hyperthermophilic one. At 500 K, both proteins unfold; the hyperthermophilic protein does so faster than the mesophilic protein. The unfolding behavior for the two proteins is found to be very similar. Although the exact order of events differs from one trajectory to another, both proteins unfold first by opening of the loop region to expose the hydrophobic core. This is followed by unzipping of the beta-sheet. The results obtained in the simulation are discussed in terms of the factors involved in flexibility and thermostability.
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Affiliation(s)
- T Lazaridis
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massacusetts 02138, USA
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8
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Wampler JE, Neuhaus EB. A model for the unusual kinetics of thermal denaturation of rubredoxin. JOURNAL OF PROTEIN CHEMISTRY 1997; 16:721-32. [PMID: 9330230 DOI: 10.1023/a:1026362605769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The thermal denaturation of the simple, redox-active iron protein rubredoxin is characterized by a slow, irreversible decay of the characteristic red color of the iron center at elevated temperatures in the presence of oxygen at pH 7.8. The denaturation rate is essentially constant and the time period for complete bleaching is nearly independent of protein concentration. These two characteristics of the kinetics can be fit by a simple self-catalyzed kinetics model consisting of the combination of a first-order decay and catalysis by some product of that decay, i.e., dP/dt = k1[A] + (k2[P][A])/(K(m) + [A]), where A is native rubredoxin, P, is unspecified product, k1 is a first-order rate constant, and k2 and K(m) are the catalytic constants. In order for the second term to be of this simple form over the full course of a decay, the model must include the condition that the reaction is effectively irreversible. This model has properties which suggest other biological roles in regulation (changes in k1 or k2 can dramatically modulate the kinetics), in timing (titer-independent fixed reaction time), and in self-activation reactions. At one extreme (k1 >> k2) the kinetics becomes exponential, but at the other extreme (k2 >> k1) they show a dramatic and rapid terminal increase after a lag period. Some obvious possible roles in the kinetics of programmed cell death, prion disease, and protease autoactivation are discussed.
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Affiliation(s)
- J E Wampler
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens 30602, USA.
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9
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Jiang X, Bishop EJ, Farid RS. A de Novo Designed Protein with Properties That Characterize Natural Hyperthermophilic Proteins. J Am Chem Soc 1997. [DOI: 10.1021/ja963319l] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xin Jiang
- Department of Chemistry Rutgers, The State University of New Jersey Newark, New Jersey 07102
| | - Edmund J. Bishop
- Department of Chemistry Rutgers, The State University of New Jersey Newark, New Jersey 07102
| | - Ramy S. Farid
- Department of Chemistry Rutgers, The State University of New Jersey Newark, New Jersey 07102
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10
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Jung DH, Kang NS, Jhon MS. Site-Directed Mutation Study on Hyperthermostability of Rubredoxin from Pyrococcus furiosus Using Molecular Dynamics Simulations in Solution. J Phys Chem A 1997. [DOI: 10.1021/jp9617940] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dong Hyun Jung
- Department of Chemistry and Center for Molecular Science, Korea Advanced Institute of Science and Technology, 373-1 Kusung-dong Yusung-gu, Taejon 305-701, Korea
| | - Nam Sook Kang
- Department of Chemistry and Center for Molecular Science, Korea Advanced Institute of Science and Technology, 373-1 Kusung-dong Yusung-gu, Taejon 305-701, Korea
| | - Mu Shik Jhon
- Department of Chemistry and Center for Molecular Science, Korea Advanced Institute of Science and Technology, 373-1 Kusung-dong Yusung-gu, Taejon 305-701, Korea
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11
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Abstract
A database has been compiled documenting the peptide conformations and geometries from 70 diverse proteins refined at 1.75 A or better. Analysis of the well-ordered residues within the database shows phi, psi-distributions that have more fine structure than is generally observed. Also, clear evidence is presented that the peptide covalent geometry depends on conformation, with the interpeptide N-C alpha-C bond angle varying by nearly +/-5 degrees from its standard value. The observed deviations from standard peptide geometry are greatest near the edges of well-populated regions, consistent with strain occurring in these conformations. Minimization of such hidden strain could be an important factor in thermostability of proteins. These empirical data describing how equilibrium peptide geometry varies as a function of conformation confirm and extend quantum mechanics calculations, and have predictive value that will aid both theoretical and experimental analyses of protein structure.
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Affiliation(s)
- P A Karplus
- Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, USA.
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12
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Adams MW, Kletzin A. Oxidoreductase-type enzymes and redox proteins involved in fermentative metabolisms of hyperthermophilic Archaea. ADVANCES IN PROTEIN CHEMISTRY 1996; 48:101-80. [PMID: 8791625 DOI: 10.1016/s0065-3233(08)60362-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- M W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens 30602, USA
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13
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Abstract
Enzymes from hyperthermophilic microorganisms are characteristically thermostable and thermoactive at extremely high temperatures. Information about the basis for the structure and function of these novel proteins is beginning to emerge. However, there are very few generalizations that can be drawn at this point that can be derived from the limited number of studies that have focused on biocatalysis and thermostability at extremely high temperatures.
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Affiliation(s)
- M W Adams
- Department of Biochemistry, University of Georgia, Athens 30602-7229
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14
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Abstract
The methods of computational chemistry and molecular modeling are becoming more and more accessible to biochemists with the advent of fast, inexpensive graphics workstations and well-tested computer programs. The state of the art in small molecules allows chemists to use these programs as "black boxes" and be confident of the results at an amazingly high level of precision. This is not the case, however, for biological macro-molecules at this time. Therefore, it is necessary before using the programs listed in Section I that we familiarize ourselves with their theoretical basis and limitations. It is also important that they be used in the context of the accumulated literature on their use. The survey given in this chapter is intended as an introduction to these tools and as a source for initiating the discovery process with the literature cited.
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Affiliation(s)
- J E Wampler
- Department of Biochemistry, University of Georgia, Athens 30602
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15
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Wampler JE, Bradley EA, Stewart DE, Adams MW. Modeling the structure of Pyrococcus furiosus rubredoxin by homology to other X-ray structures. Protein Sci 1993; 2:640-9. [PMID: 8518735 PMCID: PMC2142362 DOI: 10.1002/pro.5560020414] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The three-dimensional structure of rubredoxin from the hyperthermophilic archaebacterium, Pyrococcus furiosus, has been modeled from the X-ray crystal structures of three homologous proteins from Clostridium pasteurianum, Desulfovibrio gigas, and Desulfovibrio vulgaris. All three homology models are similar. When comparing the positions of all heavy atoms and essential hydrogen atoms to the recently solved crystal structure (Day, M. W., et al., 1992, Protein Sci. 1, 1494-1507) of the same protein, the homology model differ from the X-ray structure by 2.09 A root mean square (RMS). The X-ray and the zinc-substituted NMR structures (Blake, P. R., et al., 1992b, Protein Sci. 1, 1508-1521) show a similar level of difference (2.05 A RMS). On average, the homology models are closer to the X-ray structure than to the NMR structures (2.09 vs. 2.42 A RMS).
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Affiliation(s)
- J E Wampler
- Department of Biochemistry, University of Georgia, Athens 30602
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