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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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Norrild RK, Johansson KE, O’Shea C, Morth JP, Lindorff-Larsen K, Winther JR. Increasing protein stability by inferring substitution effects from high-throughput experiments. CELL REPORTS METHODS 2022; 2:100333. [PMID: 36452862 PMCID: PMC9701609 DOI: 10.1016/j.crmeth.2022.100333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/22/2022] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
We apply a computational model, global multi-mutant analysis (GMMA), to inform on effects of most amino acid substitutions from a randomly mutated gene library. Using a high mutation frequency, the method can determine mutations that increase the stability of even very stable proteins for which conventional selection systems have reached their limit. As a demonstration of this, we screened a mutant library of a highly stable and computationally redesigned model protein using an in vivo genetic sensor for folding and assigned a stability effect to 374 of 912 possible single amino acid substitutions. Combining the top 9 substitutions increased the unfolding energy 47 to 69 kJ/mol in a single engineering step. Crystal structures of stabilized variants showed small perturbations in helices 1 and 2, which rendered them closer in structure to the redesign template. This case study illustrates the capability of the method, which is applicable to any screen for protein function.
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Affiliation(s)
- Rasmus Krogh Norrild
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Kristoffer Enøe Johansson
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Charlotte O’Shea
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Jens Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Jakob Rahr Winther
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
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3
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Chen Q, Yang X, Meng Q, Zhao L, Yuan Y, Chi W, He L, Shi K, Liu S. Integrative multiomics analysis of the acid stress response of Oenococcus oeni mutants at different growth stages. Food Microbiol 2021; 102:103905. [PMID: 34809937 DOI: 10.1016/j.fm.2021.103905] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Acid stress is one of the most important environmental stresses that adversely affect the growth of lactic acid bacteria (LAB), such as Oenococcus oeni which was isolated from grape-berries and mainly used in wine fermentation. The aim of this paper is to comprehensively characterize the mechanisms of acid stress regulation in O. oeni and to provide a viable theoretical basis for breed and improvement of existing LAB. METHOD First, six O. oeni mutants with acid-sensitive (strains b2, a1, c2) and acid-tolerant (strains b1, a3, c1) phenotypes were screened from three wild-type O. oeni, and then their genome (sequencing), transcriptome and metabolome (LC-MS/MS) were examined. RESULTS A total of 459 genes were identified with one or more intragenic single nucleotide polymorphisms (SNPs) in these mutants, and were extensively involved in metabolism and cellular functions with a high mutation rates in purine (46%) and pyrimidine (48%) metabolic pathways. There were 210 mutated genes that cause significant changes in expression levels. In addition, 446 differentially accumulated metabolites were detected, and they were consistently detected at relatively high levels in the acid-tolerant O. oeni mutant. The levels of intracellular differentially expressed genes and differential metabolites changed with increasing culture time. CONCLUSION The integrative pathways analysis showed that the intracellular response associated with acid regulation differed significantly between acid-sensitive and acid-tolerant O. oeni mutants, and also changed at different growth stages.
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Affiliation(s)
- Qiling Chen
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Xiangke Yang
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; Henan University of Animal Husbandry and Economy, Zhenzhou, Henan, China
| | - Qiang Meng
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Lili Zhao
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuxin Yuan
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Wei Chi
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ling He
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Kan Shi
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station of, Northwest A&F University, Yongning, Ningxia, 750104, China.
| | - Shuwen Liu
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station of, Northwest A&F University, Yongning, Ningxia, 750104, China.
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Bjerre B, Nissen J, Madsen M, Fahrig-Kamarauskaitė J, Norrild RK, Holm PC, Nordentoft MK, O'Shea C, Willemoës M, Johansson KE, Winther JR. Improving folding properties of computationally designed proteins. Protein Eng Des Sel 2019; 32:145-151. [PMID: 31553452 DOI: 10.1093/protein/gzz025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 11/12/2022] Open
Abstract
While the field of computational protein design has witnessed amazing progression in recent years, folding properties still constitute a significant barrier towards designing new and larger proteins. In order to assess and improve folding properties of designed proteins, we have developed a genetics-based folding assay and selection system based on the essential enzyme, orotate phosphoribosyl transferase from Escherichia coli. This system allows for both screening of candidate designs with good folding properties and genetic selection of improved designs. Thus, we identified single amino acid substitutions in two failed designs that rescued poorly folding and unstable proteins. Furthermore, when these substitutions were transferred into a well-structured design featuring a complex folding profile, the resulting protein exhibited native-like cooperative folding with significantly improved stability. In protein design, a single amino acid can make the difference between folding and misfolding, and this approach provides a useful new platform to identify and improve candidate designs.
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Affiliation(s)
- Benjamin Bjerre
- The Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University for Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Jakob Nissen
- The Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University for Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Mikkel Madsen
- The Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University for Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Jūratė Fahrig-Kamarauskaitė
- The Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University for Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Rasmus K Norrild
- The Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University for Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Peter C Holm
- The Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University for Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Mathilde K Nordentoft
- The Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University for Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Charlotte O'Shea
- The Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University for Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Martin Willemoës
- The Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University for Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Kristoffer E Johansson
- The Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University for Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Jakob R Winther
- The Linderstrøm-Lang Centre for Protein Science, Section for Biomolecular Sciences, Department of Biology, University for Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
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Johansson KE, Tidemand Johansen N, Christensen S, Horowitz S, Bardwell JC, Olsen JG, Willemoës M, Lindorff-Larsen K, Ferkinghoff-Borg J, Hamelryck T, Winther JR. Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template. J Mol Biol 2016; 428:4361-4377. [PMID: 27659562 PMCID: PMC5242314 DOI: 10.1016/j.jmb.2016.09.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 09/08/2016] [Accepted: 09/14/2016] [Indexed: 01/26/2023]
Abstract
Despite the development of powerful computational tools, the full-sequence design of proteins still remains a challenging task. To investigate the limits and capabilities of computational tools, we conducted a study of the ability of the program Rosetta to predict sequences that recreate the authentic fold of thioredoxin. Focusing on the influence of conformational details in the template structures, we based our study on 8 experimentally determined template structures and generated 120 designs from each. For experimental evaluation, we chose six sequences from each of the eight templates by objective criteria. The 48 selected sequences were evaluated based on their progressive ability to (1) produce soluble protein in Escherichia coli and (2) yield stable monomeric protein, and (3) on the ability of the stable, soluble proteins to adopt the target fold. Of the 48 designs, we were able to synthesize 32, 20 of which resulted in soluble protein. Of these, only two were sufficiently stable to be purified. An X-ray crystal structure was solved for one of the designs, revealing a close resemblance to the target structure. We found a significant difference among the eight template structures to realize the above three criteria despite their high structural similarity. Thus, in order to improve the success rate of computational full-sequence design methods, we recommend that multiple template structures are used. Furthermore, this study shows that special care should be taken when optimizing the geometry of a structure prior to computational design when using a method that is based on rigid conformations.
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Affiliation(s)
- Kristoffer E. Johansson
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen DK-2200, Denmark
| | - Nicolai Tidemand Johansen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen DK-2200, Denmark
| | - Signe Christensen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen DK-2200, Denmark
| | - Scott Horowitz
- Howard Hughes Medical Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - James C.A. Bardwell
- Howard Hughes Medical Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Johan G. Olsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen DK-2200, Denmark
| | - Martin Willemoës
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen DK-2200, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen DK-2200, Denmark
| | - Jesper Ferkinghoff-Borg
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen DK-2200, Denmark
| | - Thomas Hamelryck
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen DK-2200, Denmark
| | - Jakob R. Winther
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen DK-2200, Denmark
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Hermansen RA, Mannakee BK, Knecht W, Liberles DA, Gutenkunst RN. Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast. BMC Evol Biol 2015; 15:232. [PMID: 26511837 PMCID: PMC4625875 DOI: 10.1186/s12862-015-0515-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/20/2015] [Indexed: 12/05/2022] Open
Abstract
Background Selection on proteins is typically measured with the assumption that each protein acts independently. However, selection more likely acts at higher levels of biological organization, requiring an integrative view of protein function. Here, we built a kinetic model for de novo pyrimidine biosynthesis in the yeast Saccharomyces cerevisiae to relate pathway function to selective pressures on individual protein-encoding genes. Results Gene families across yeast were constructed for each member of the pathway and the ratio of nonsynonymous to synonymous nucleotide substitution rates (dN/dS) was estimated for each enzyme from S. cerevisiae and closely related species. We found a positive relationship between the influence that each enzyme has on pathway function and its selective constraint. Conclusions We expect this trend to be locally present for enzymes that have pathway control, but over longer evolutionary timescales we expect that mutation-selection balance may change the enzymes that have pathway control. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0515-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Russell A Hermansen
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA. .,Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
| | - Brian K Mannakee
- Division of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, 85721, USA.
| | - Wolfgang Knecht
- Department of Biology and Lund Protein Production Platform, Lund University, 22362, Lund, Sweden.
| | - David A Liberles
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA. .,Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
| | - Ryan N Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA.
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Jensen KF, Hansen MR, Jensen KS, Christoffersen S, Poulsen JCN, Mølgaard A, Kadziola A. Adenine phosphoribosyltransferase from Sulfolobus solfataricus is an enzyme with unusual kinetic properties and a crystal structure that suggests it evolved from a 6-oxopurine phosphoribosyltransferase. Biochemistry 2015; 54:2323-34. [PMID: 25790177 DOI: 10.1021/bi501334m] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The adenine phosphoribosyltransferase (APRTase) encoded by the open reading frame SSO2342 of Sulfolobus solfataricus P2 was subjected to crystallographic, kinetic, and ligand binding analyses. The enzyme forms dimers in solution and in the crystals, and binds one molecule of the reactants 5-phosphoribosyl-α-1-pyrophosphate (PRPP) and adenine or the product adenosine monophosphate (AMP) or the inhibitor adenosine diphosphate (ADP) in each active site. The individual subunit adopts an overall structure that resembles a 6-oxopurine phosphoribosyltransferase (PRTase) more than known APRTases implying that APRT functionality in Crenarchaeotae has its evolutionary origin in this family of PRTases. Only the N-terminal two-thirds of the polypeptide chain folds as a traditional type I PRTase with a five-stranded β-sheet surrounded by helices. The C-terminal third adopts an unusual three-helix bundle structure that together with the nucleobase-binding loop undergoes a conformational change upon binding of adenine and phosphate resulting in a slight contraction of the active site. The inhibitor ADP binds like the product AMP with both the α- and β-phosphates occupying the 5'-phosphoribosyl binding site. The enzyme shows activity over a wide pH range, and the kinetic and ligand binding properties depend on both pH and the presence/absence of phosphate in the buffers. A slow hydrolysis of PRPP to ribose 5-phosphate and pyrophosphate, catalyzed by the enzyme, may be facilitated by elements in the C-terminal three-helix bundle part of the protein.
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Affiliation(s)
- Kaj Frank Jensen
- †University of Copenhagen, Department of Biology, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Michael Riis Hansen
- †University of Copenhagen, Department of Biology, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Kristine Steen Jensen
- †University of Copenhagen, Department of Biology, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Stig Christoffersen
- ‡University of Copenhagen, Department of Chemistry, Center of Crystallographic Studies, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Jens-Christian Navarro Poulsen
- ‡University of Copenhagen, Department of Chemistry, Center of Crystallographic Studies, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Anne Mølgaard
- ‡University of Copenhagen, Department of Chemistry, Center of Crystallographic Studies, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Anders Kadziola
- ‡University of Copenhagen, Department of Chemistry, Center of Crystallographic Studies, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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