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Orosz F, Vértessy BG. What's in a name? From "fluctuation fit" to "conformational selection": rediscovery of a concept. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2021; 43:88. [PMID: 34244885 PMCID: PMC8270835 DOI: 10.1007/s40656-021-00442-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 06/19/2021] [Indexed: 06/13/2023]
Abstract
Rediscoveries are not rare in biology. A recent example is the re-birth of the "fluctuation fit" concept developed by F. B. Straub and G. Szabolcsi in the sixties of the last century, under various names, the most popular of which is the "conformational selection". This theory offers an alternative to the "induced fit" concept by Koshland for the interpretation of the mechanism of protein-ligand interactions. A central question is whether the ligand induces a conformational change (as described by the induced fit model) or rather selects and stabilizes a complementary conformation from a pre-existing equilibrium of various states of the protein (according to the fluctuation fit/conformational selection model). Straub and Szabolcsi's role and the factors hindering the spread of the fluctuation fit theory are discussed in the context of the history of the Hungarian biology in the 1950s and 1960s.
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Affiliation(s)
- Ferenc Orosz
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest, 1117 Hungary
| | - Beáta G. Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest, 1117 Hungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, 1111 Hungary
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Whittington AC, Rokyta DR. Biophysical Spandrels form a Hot-Spot for Kosmotropic Mutations in Bacteriophage Thermal Adaptation. J Mol Evol 2018; 87:27-36. [PMID: 30564861 DOI: 10.1007/s00239-018-9882-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/15/2018] [Indexed: 12/18/2022]
Abstract
Temperature plays a dominating role in protein structure and function, and life has evolved myriad strategies to adapt proteins to environmental thermal stress. Cellular systems can utilize kosmotropic osmolytes, the products of complex biochemical pathways, to act as chemical chaperones. These extrinsic molecules, e.g., trehalose, alter local water structure to modulate the strength of the hydrophobic effect and increase protein stability. In contrast, simpler genetic systems must rely on intrinsic mutation to affect protein stability. In naturally occurring microvirid bacteriophages of the subfamily Bullavirinae, capsid stability is randomly distributed across the phylogeny, suggesting it is not phylogenetically linked and could be altered through adaptive mutation. We hypothesized that these phages could utilize an adaptive mechanism that mimics the stabilizing effects of the kosmotrope trehalose through mutation. Kinetic stability of wild-type ID8, a relative of ΦX174, displays a saturable response to trehalose. Thermal adaptation mutations in ID8 improve capsid stability and reduce responsiveness to trehalose suggesting the mutations move stability closer to the kosmotropic saturation point, mimicking the kosmotropic effect of trehalose. These mutations localize to and modulate the hydrophobicity of a cavern formation at the interface of phage coat and spike proteins-an evolutionary spandrel. Across a series of genetically distinct phages, responsiveness to trehalose correlates positively with cavern hydrophobicity suggesting that the level of hydrophobicity of the cavern may provide a biophysical gating mechanism constraining or permitting adaptation in a lineage-specific manner. Our results demonstrate that a single mutation can exploit pre-existing, non-adaptive structural features to mimic the adaptive effects of complex biochemical pathways.
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Affiliation(s)
- A Carl Whittington
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306, USA.
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306, USA
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Dittner M, Hartke B. Globally Optimal Catalytic Fields - Inverse Design of Abstract Embeddings for Maximum Reaction Rate Acceleration. J Chem Theory Comput 2018; 14:3547-3564. [PMID: 29883539 DOI: 10.1021/acs.jctc.8b00151] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The search for, and understanding of, good catalysts for chemical reactions is a central issue for chemists. Here, we present first steps toward developing a general computational framework to better support this task. This framework combines efficient, unbiased global optimization techniques with an abstract representation of the catalytic environment, to shrink the search space. To analyze the resulting catalytic embeddings, we employ dimensionality reduction and clustering techniques. This not only provides an inverse design approach to new catalytic embeddings but also illuminates the actual interactions behind catalytic effects. All this is illustrated here with a strictly electrostatic model for the environment and with two versions of a selected example reaction. We close with detailed discussions of future improvements of our framework.
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Affiliation(s)
- Mark Dittner
- Institute for Physical Chemistry , Christian-Albrechts-University Kiel , 24098 Kiel , Germany
| | - Bernd Hartke
- Institute for Physical Chemistry , Christian-Albrechts-University Kiel , 24098 Kiel , Germany
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Saavedra JM, Azócar MA, Rodríguez V, Ramírez-Sarmiento CA, Andrews BA, Asenjo JA, Parra LP. Relevance of Local Flexibility Near the Active Site for Enzymatic Catalysis: Biochemical Characterization and Engineering of Cellulase Cel5A FromBacillus agaradherans. Biotechnol J 2018; 13:e1700669. [DOI: 10.1002/biot.201700669] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/19/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Juan M. Saavedra
- Department of Chemical Engineering and Biotechnology; Centre for Biotechnology and Bioengineering (CeBiB); University of Chile; Santiago Chile
| | - Mauricio A. Azócar
- Department of Chemical Engineering and Biotechnology; Centre for Biotechnology and Bioengineering (CeBiB); University of Chile; Santiago Chile
| | - Vida Rodríguez
- Department of Chemical Engineering and Biotechnology; Centre for Biotechnology and Bioengineering (CeBiB); University of Chile; Santiago Chile
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering; Schools of Engineering,; Medicine and Biological Sciences; Pontificia Universidad Católica de Chile; Avenida Vicuña Mackenna 4860 Santiago 7820436 Chile
| | - Barbara A. Andrews
- Department of Chemical Engineering and Biotechnology; Centre for Biotechnology and Bioengineering (CeBiB); University of Chile; Santiago Chile
| | - Juan A. Asenjo
- Department of Chemical Engineering and Biotechnology; Centre for Biotechnology and Bioengineering (CeBiB); University of Chile; Santiago Chile
| | - Loreto P. Parra
- Institute for Biological and Medical Engineering; Schools of Engineering,; Medicine and Biological Sciences; Pontificia Universidad Católica de Chile; Avenida Vicuña Mackenna 4860 Santiago 7820436 Chile
- Department of Chemical and Bioprocesses Engineering; School of Engineering; Pontificia Universidad Católica de Chile; Santiago Chile
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Svetlichny G. The enzyme-substrate complex as a cat state: A toy quantum analog. Biosystems 2017; 162:157-167. [PMID: 29066365 DOI: 10.1016/j.biosystems.2017.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 10/08/2017] [Accepted: 10/13/2017] [Indexed: 11/30/2022]
Abstract
We introduce a quantum model system incorporating qualitative aspects of tunneling in enzyme action and analyze the possibilities of quantum superposition of several conformations of the enzyme-substrate complex. There is a potential barrier in each conformation which for simplicity's sake is assumed to be of zero width making the system explicitly solvable. Such a system exhibits generic features of quantum dynamics that should be present to some extent in real enzyme action. We find that depending on the parameters of the system, the rate of conversion of substrate to product can be either enhanced or suppressed in relation to the rates that can be achieved in fixed conformations. There are also solutions in which a component of the quantum state exists as a bound state, something that cannot happen in a fixed conformation. This may provide some measure of stability to the complex. Paradoxically enough, superposition of a finite barrier with an infinite barrier can also enhance the conversion of substrate to product in relation to the finite barrier alone. We suggest that binding to a superposition of conformations could be preferred in relation to binding to a fixed conformation, and analyze the conditions in living cells that could support enzyme action by conformations in superposition.
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Affiliation(s)
- George Svetlichny
- Departamento de Matemática, Pontifícia Universidade Católica, Rio de Janeiro, Brazil.
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Bardon C, Poly F, Piola F, Pancton M, Comte G, Meiffren G, Haichar FEZ. Mechanism of biological denitrification inhibition: procyanidins induce an allosteric transition of the membrane-bound nitrate reductase through membrane alteration. FEMS Microbiol Ecol 2016; 92:fiw034. [PMID: 26906096 DOI: 10.1093/femsec/fiw034] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2016] [Indexed: 12/14/2022] Open
Abstract
Recently, it has been shown that procyanidins from Fallopia spp. inhibit bacterial denitrification, a phenomenon called biological denitrification inhibition (BDI). However, the mechanisms involved in such a process remain unknown. Here, we investigate the mechanisms of BDI involving procyanidins, using the model strain Pseudomonas brassicacearum NFM 421. The aerobic and anaerobic (denitrification) respiration, cell permeability and cell viability of P. brassicacearum were determined as a function of procyanidin concentration. The effect of procyanidins on the bacterial membrane was observed using transmission electronic microscopy. Bacterial growth, denitrification, NO3- and NO2-reductase activity, and the expression of subunits of NO3- (encoded by the gene narG) and NO2-reductase (encoded by the gene nirS) under NO3 or NO2 were measured with and without procyanidins. Procyanidins inhibited the denitrification process without affecting aerobic respiration at low concentrations. Procyanidins also disturbed cell membranes without affecting cell viability. They specifically inhibited NO3- but not NO2-reductase.Pseudomonas brassicacearum responded to procyanidins by over-expression of the membrane-bound NO3-reductase subunit (encoded by the gene narG). Our results suggest that procyanidins can specifically inhibit membrane-bound NO3-reductase inducing enzymatic conformational changes through membrane disturbance and that P. brassicacearum responds by over-expressing membrane-bound NO3-reductase. Our results lead the way to a better understanding of BDI.
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Affiliation(s)
- Clément Bardon
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA USC 1364, F-69622 Villeurbanne Cedex, France Université de Lyon, UMR5023 LEHNA, Université Lyon 1, CNRS, ENTPE, F-69622 Villeurbanne Cedex, France
| | - Franck Poly
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA USC 1364, F-69622 Villeurbanne Cedex, France
| | - Florence Piola
- Université de Lyon, UMR5023 LEHNA, Université Lyon 1, CNRS, ENTPE, F-69622 Villeurbanne Cedex, France
| | - Muriel Pancton
- Université de Lyon, UMR5276 LGLTPE, Université Lyon 1, CNRS, ENTPE, F-69622 Villeurbanne Cedex, France
| | - Gilles Comte
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA USC 1364, F-69622 Villeurbanne Cedex, France
| | - Guillaume Meiffren
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA USC 1364, F-69622 Villeurbanne Cedex, France
| | - Feth el Zahar Haichar
- Université de Lyon, UMR 5557 LEM, Université Lyon 1, CNRS, INRA USC 1364, F-69622 Villeurbanne Cedex, France
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Affiliation(s)
- Alan C. Gibbs
- Janssen Pharmaceutical Research and Development, LLC, Welsh and McKean Road, Spring House, Pennsylvania 19477-0776, United States
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