1
|
Naletova I, Schmalhausen E, Tomasello B, Pozdyshev D, Attanasio F, Muronetz V. The role of sperm-specific glyceraldehyde-3-phosphate dehydrogenase in the development of pathologies-from asthenozoospermia to carcinogenesis. Front Mol Biosci 2023; 10:1256963. [PMID: 37711387 PMCID: PMC10499166 DOI: 10.3389/fmolb.2023.1256963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 08/21/2023] [Indexed: 09/16/2023] Open
Abstract
The review considers various aspects of the influence of the glycolytic enzyme, sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDS) on the energy metabolism of spermatozoa and on the occurrence of several pathologies both in spermatozoa and in other cells. GAPDS is a unique enzyme normally found only in mammalian spermatozoa. GAPDS provides movement of the sperm flagellum through the ATP formation in glycolytic reactions. Oxidation of cysteine residues in GAPDS results in inactivation of the enzyme and decreases sperm motility. In particular, reduced sperm motility in diabetes can be associated with GAPDS oxidation by superoxide anion produced during glycation reactions. Mutations in GAPDS gene lead in the loss of motility, and in some cases, disrupts the formation of the structural elements of the sperm flagellum, in which the enzyme incorporates during spermiogenesis. GAPDS activation can be used to increase the spermatozoa fertility, and inhibitors of this enzyme are being tried as contraceptives. A truncated GAPDS lacking the N-terminal fragment of 72 amino acids that attaches the enzyme to the sperm flagellum was found in melanoma cell lines and then in specimens of melanoma and other tumors. Simultaneous production of the somatic form of GAPDH and sperm-specific GAPDS in cancer cells leads to a reorganization of their energy metabolism, which is accompanied by a change in the efficiency of metastasis of certain forms of cancer. Issues related to the use of GAPDS for the diagnosis of cancer, as well as the possibility of regulating the activity of this enzyme to prevent metastasis, are discussed.
Collapse
Affiliation(s)
- Irina Naletova
- Institute of Crystallography, National Council of Research, Catania, Italy
| | - Elena Schmalhausen
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Barbara Tomasello
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
| | - Denis Pozdyshev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Vladimir Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Butlerov Chemical Institute, Kazan Federal University, Kazan, Russia
| |
Collapse
|
2
|
Jarnot P, Ziemska-Legiecka J, Grynberg M, Gruca A. Insights from analyses of low complexity regions with canonical methods for protein sequence comparison. Brief Bioinform 2022; 23:bbac299. [PMID: 35914952 PMCID: PMC9487646 DOI: 10.1093/bib/bbac299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 11/28/2022] Open
Abstract
Low complexity regions are fragments of protein sequences composed of only a few types of amino acids. These regions frequently occur in proteins and can play an important role in their functions. However, scientists are mainly focused on regions characterized by high diversity of amino acid composition. Similarity between regions of protein sequences frequently reflect functional similarity between them. In this article, we discuss strengths and weaknesses of the similarity analysis of low complexity regions using BLAST, HHblits and CD-HIT. These methods are considered to be the gold standard in protein similarity analysis and were designed for comparison of high complexity regions. However, we lack specialized methods that could be used to compare the similarity of low complexity regions. Therefore, we investigated the existing methods in order to understand how they can be applied to compare such regions. Our results are supported by exploratory study, discussion of amino acid composition and biological roles of selected examples. We show that existing methods need improvements to efficiently search for similar low complexity regions. We suggest features that have to be re-designed specifically for comparing low complexity regions: scoring matrix, multiple sequence alignment, e-value, local alignment and clustering based on a set of representative sequences. Results of this analysis can either be used to improve existing methods or to create new methods for the similarity analysis of low complexity regions.
Collapse
Affiliation(s)
- Patryk Jarnot
- Department of Computer Networks and Systems, Silesian University of Technology, Akademicka 2A, 44-100, Gliwice, Poland
| | - Joanna Ziemska-Legiecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Aleksandra Gruca
- Department of Computer Networks and Systems, Silesian University of Technology, Akademicka 2A, 44-100, Gliwice, Poland
| |
Collapse
|
3
|
Muronetz VI, Melnikova AK, Saso L, Schmalhausen EV. Influence of Oxidative Stress on Catalytic and Non-glycolytic Functions of Glyceraldehyde-3-phosphate Dehydrogenase. Curr Med Chem 2020; 27:2040-2058. [PMID: 29848267 DOI: 10.2174/0929867325666180530101057] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) is a unique enzyme that, besides its main function in glycolysis (catalysis of glyceraldehyde-3-phosphate oxidation), possesses a number of non-glycolytic activities. The present review summarizes information on the role of oxidative stress in the regulation of the enzymatic activity as well as non-glycolytic functions of GAPDH. METHODS Based on the analysis of literature data and the results obtained in our research group, mechanisms of the regulation of GAPDH functions through the oxidation of the sulfhydryl groups in the active site of the enzyme have been suggested. RESULTS Mechanism of GAPDH oxidation includes consecutive oxidation of the catalytic Cysteine (Cys150) into sulfenic, sulfinic, and sulfonic acid derivatives, resulting in the complete inactivation of the enzyme. The cysteine sulfenic acid reacts with reduced glutathione (GSH) to form a mixed disulfide (S-glutathionylated GAPDH) that further reacts with Cys154 yielding the disulfide bond in the active site of the enzyme. In contrast to the sulfinic and sulfonic acids, the mixed disulfide and the intramolecular disulfide bond are reversible oxidation products that can be reduced in the presence of GSH or thioredoxin. CONCLUSION Oxidation of sulfhydryl groups in the active site of GAPDH is unavoidable due to the enhanced reactivity of Cys150. The irreversible oxidation of Cys150 is prevented by Sglutathionylation and disulfide bonding with Cys154. The oxidation/reduction of the sulfhydryl groups in the active site of GAPDH can be used for regulation of glycolysis and numerous side activities of this enzyme including the induction of apoptosis.
Collapse
Affiliation(s)
- Vladimir I Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Aleksandra K Melnikova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer"Sapienza, University of Rome, Rome, Italy
| | - Elena V Schmalhausen
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| |
Collapse
|
4
|
Kudryavtseva SS, Stroylova YY, Kurochkina LP, Muronetz VI. The chaperonin TRiC is blocked by native and glycated prion protein. Arch Biochem Biophys 2020; 683:108319. [PMID: 32101762 DOI: 10.1016/j.abb.2020.108319] [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: 10/29/2019] [Revised: 02/18/2020] [Accepted: 02/21/2020] [Indexed: 01/08/2023]
Abstract
Eukaryotic double-ring chaperonin TRiC is an ATP-dependent protein-folding machine. Most of its substrates are known to form large ordered structures from multiple polypeptide chains. Since these structures are similar to fibrillar and oligomeric forms of amyloidogenic proteins, we hypothesized that TRiC may play a role in the development of neurodegenerative diseases of amyloid nature including prion diseases. Enzyme-linked immunosorbent assay showed that monomeric, oligomeric and fibrillar forms of prion protein (PrP) bind strongly to chaperonin TRiC, whereas glycation reduces the prion protein affinity for chaperonin. Nevertheless, dynamic light scattering, electron microscopy and thioflavin T fluorescence confirmed that all studied forms of PrP undergo an amyloid transformation after interaction with chaperonin, but different forms of prion protein are capable of having different effects on the functional state of TRiC. For example, prion protein monomers completely block its ability to reactivate the chaperonin's natural substrate - sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDS). At the same time, PrP oligomers and fibrils only partially prevent the reactivation of GAPDS upon the action of TRiC. The monomeric forms of prion protein glycated by methylglyoxal do not inhibit, but only slow down the chaperone-dependent reactivation of GAPDS. Thus, the interaction of amyloidogenic proteins with chaperonins could cause cell malfunction.
Collapse
Affiliation(s)
- S S Kudryavtseva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Y Y Stroylova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - L P Kurochkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - V I Muronetz
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| |
Collapse
|
5
|
Muronetz VI, Melnikova AK, Barinova KV, Schmalhausen EV. Inhibitors of Glyceraldehyde 3-Phosphate Dehydrogenase and Unexpected Effects of Its Reduced Activity. BIOCHEMISTRY (MOSCOW) 2019; 84:1268-1279. [PMID: 31760917 DOI: 10.1134/s0006297919110051] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The review describes the use of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) inhibitors to study the enzyme and to suppress its activity in various cell types. The main problem of selective GAPDH inhibition is a highly conserved nature of the enzyme active site and, especially, Cys150 environment important for the catalytic action of cysteine sulfhydryl group. Numerous attempts to find specific inhibitors of sperm GAPDH and enzymes from Trypanosoma sp. and Mycobacterium tuberculosis that would not inhibit GAPDH of somatic mammalian cells have failed, which has pushed researchers to search for new ways to solve this problem. The sections of the review are devoted to the studies of GAPDH inactivation by reactive oxygen species, glutathione, and glycating agents. The final section discusses possible effects of GAPDH inhibition and inactivation on glycolysis and related metabolic pathways (pentose phosphate pathway, uncoupling of the glycolytic oxidation and phosphorylation, etc.).
Collapse
Affiliation(s)
- V I Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia. .,Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234, Russia
| | - A K Melnikova
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234, Russia
| | - K V Barinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - E V Schmalhausen
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| |
Collapse
|
6
|
Effect of GAPDS overexpression on high glucose-induced oxidative damage. Biochem Biophys Res Commun 2018; 500:191-195. [PMID: 29626473 DOI: 10.1016/j.bbrc.2018.04.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 04/03/2018] [Indexed: 11/24/2022]
Abstract
The occurrence of infertility in diabetic patients is attributed to oxidative damage of peroxidized products. High glucose-induced mitochondrial oxidative stress and glycolytic enzyme inactivation is considered to be an important mediator for sperm dysfunction. In this study, we successfully constructed TM3-GAPDS stable strain and investigated the role of sperm specific glyceraldehyde-3-phosphate dehydrogenase (GAPDS) on high glucose-induced apoptosis in TM3 cells. High glucose decreased the protein expression of SOD2 and catalase, while the level of intracellular ROS and the apoptosis - related protein increased in TM3 cells. Furthermore, high glucose-induced oxidative stress and apoptosis were reversed by GAPDS overexpression or antioxidant treatment. In conclusion, our data suggest that GAPDS overexpression antagonize high glucose-induced apoptosis by controlling ROS accumulation in TM3 cells.
Collapse
|
7
|
Barinova K, Eldarov M, Khomyakova E, Muronetz V, Schmalhausen E. Isolation of recombinant human untagged glyceraldehyde-3-phosphate dehydrogenase from E. coli producer strain. Protein Expr Purif 2017. [DOI: 10.1016/j.pep.2017.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
8
|
Danshina PV, Qu W, Temple BR, Rojas RJ, Miley MJ, Machius M, Betts L, O'Brien DA. Structural analyses to identify selective inhibitors of glyceraldehyde 3-phosphate dehydrogenase-S, a sperm-specific glycolytic enzyme. Mol Hum Reprod 2016; 22:410-26. [PMID: 26921398 PMCID: PMC4884916 DOI: 10.1093/molehr/gaw016] [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: 01/15/2016] [Revised: 02/11/2016] [Accepted: 02/22/2016] [Indexed: 12/21/2022] Open
Abstract
STUDY HYPOTHESIS Detailed structural comparisons of sperm-specific glyceraldehyde 3-phosphate dehydrogenase, spermatogenic (GAPDHS) and the somatic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) isozyme should facilitate the identification of selective GAPDHS inhibitors for contraceptive development. STUDY FINDING This study identified a small-molecule GAPDHS inhibitor with micromolar potency and >10-fold selectivity that exerts the expected inhibitory effects on sperm glycolysis and motility. WHAT IS KNOWN ALREADY Glycolytic ATP production is required for sperm motility and male fertility in many mammalian species. Selective inhibition of GAPDHS, one of the glycolytic isozymes with restricted expression during spermatogenesis, is a potential strategy for the development of a non-hormonal contraceptive that directly blocks sperm function. STUDY DESIGN, SAMPLES/MATERIALS, METHODS Homology modeling and x-ray crystallography were used to identify structural features that are conserved in GAPDHS orthologs in mouse and human sperm, but distinct from the GAPDH orthologs present in somatic tissues. We identified three binding pockets surrounding the substrate and cofactor in these isozymes and conducted a virtual screen to identify small-molecule compounds predicted to bind more tightly to GAPDHS than to GAPDH. Following the production of recombinant human and mouse GAPDHS, candidate compounds were tested in dose-response enzyme assays to identify inhibitors that blocked the activity of GAPDHS more effectively than GAPDH. The effects of a selective inhibitor on the motility of mouse and human sperm were monitored by computer-assisted sperm analysis, and sperm lactate production was measured to assess inhibition of glycolysis in the target cell. MAIN RESULTS AND THE ROLE OF CHANCE Our studies produced the first apoenzyme crystal structures for human and mouse GAPDHS and a 1.73 Å crystal structure for NAD(+)-bound human GAPDHS, facilitating the identification of unique structural features of this sperm isozyme. In dose-response assays T0501_7749 inhibited human GAPDHS with an IC50 of 1.2 μM compared with an IC50 of 38.5 μM for the somatic isozyme. This compound caused significant reductions in mouse sperm lactate production (P= 0.017 for 100 μM T0501_7749 versus control) and in the percentage of motile mouse and human sperm (P values from <0.05 to <0.0001, depending on incubation conditions). LIMITATIONS, REASONS FOR CAUTION The chemical properties of T0501_7749, including limited solubility and nonspecific protein binding, are not optimal for drug development. WIDER IMPLICATIONS OF THE FINDINGS This study provides proof-of-principle evidence that GAPDHS can be selectively inhibited, causing significant reductions in sperm glycolysis and motility. These results highlight the utility of structure-based drug design and support further exploration of GAPDHS, and perhaps other sperm-specific isozymes in the glycolytic pathway, as contraceptive targets. LARGE SCALE DATA None. Coordinates and data files for three GAPDHS crystal structures were deposited in the RCSB Protein Data Bank (http://www.rcsb.org). STUDY FUNDING AND COMPETING INTERESTS This work was supported by grants from the National Institutes of Health (NIH), USA, including U01 HD060481 and cooperative agreement U54 HD35041 as part of the Specialized Cooperative Centers Program in Reproduction and Infertility Research from the Eunice Kennedy Shriver National Institute of Child Health and Human Development, and TW/HD00627 from the NIH Fogarty International Center. Additional support was provided by subproject CIG-05-109 from CICCR, a program of CONRAD, Eastern Virginia Medical School, USA. There are no conflicts of interest.
Collapse
Affiliation(s)
- Polina V Danshina
- Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Weidong Qu
- Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA Present address: Key Laboratory of Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Brenda R Temple
- R.L. Juliano Structural Bioinformatics Core Facility, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Rafael J Rojas
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA Present address: Dart NeuroScience, LLC, San Diego, CA 92131, USA
| | - Michael J Miley
- Macromolecular X-Ray Crystallography Core Facility, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Mischa Machius
- Macromolecular X-Ray Crystallography Core Facility, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA Present address: 230 Jamestown Road, Pittsboro, NC 27312, USA
| | - Laurie Betts
- Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Deborah A O'Brien
- Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| |
Collapse
|
9
|
Kim SJ, Joo JE, Jeon SD, Hyeon JE, Kim SW, Um YS, Han SO. Enhanced thermostability of mesophilic endoglucanase Z with a high catalytic activity at active temperatures. Int J Biol Macromol 2016; 86:269-76. [DOI: 10.1016/j.ijbiomac.2016.01.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/16/2016] [Accepted: 01/20/2016] [Indexed: 12/18/2022]
|
10
|
Enhancement of the thermostability of Streptomyces kathirae SC-1 tyrosinase by rational design and empirical mutation. Enzyme Microb Technol 2015; 77:54-60. [DOI: 10.1016/j.enzmictec.2015.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/20/2015] [Accepted: 06/08/2015] [Indexed: 11/17/2022]
|
11
|
Structural basis for the NAD binding cooperativity and catalytic characteristics of sperm-specific glyceraldehyde-3-phosphate dehydrogenase. Biochimie 2015; 115:28-34. [PMID: 25936797 DOI: 10.1016/j.biochi.2015.04.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 04/21/2015] [Indexed: 11/22/2022]
Abstract
Catalytic properties of enzymes used in biotechnology can be improved by eliminating those regulatory mechanisms that are not absolutely required for their functioning. We exploited mammalian glyceraldehyde-3-phosphate dehydrogenase as a model protein and examined the structural basis of the NAD(+) cooperative binding exhibited by its homologous isoenzymes: the somatic enzyme (GAPD) and the recombinant sperm-specific enzyme (dN-GAPDS). Moreover, we obtained a mutant dN-GAPDS, which misses the cooperativity, but exhibits a twofold increase in the specific activity instead (92 and 45 μmol NADH/min per mg protein for the mutant and the wild type proteins, respectively). Such an effect was caused by the disruption of the interdomain salt bridge D311-H124, which is located close to the active site of the enzyme. The thermal stability of the mutant protein also increased compared to the wild type form (heat absorption peak values were 70.4 and 68.6 °C, respectively). We expect our findings to be of importance for the purposes of biotechnological applications.
Collapse
|
12
|
Makshakova ON, Semenyuk PI, Kuravsky ML, Ermakova EA, Zuev YF, Muronetz VI. Structural basis for regulation of stability and activity in glyceraldehyde-3-phosphate dehydrogenases. Differential scanning calorimetry and molecular dynamics. J Struct Biol 2015; 190:224-35. [PMID: 25869789 DOI: 10.1016/j.jsb.2015.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/30/2015] [Accepted: 04/07/2015] [Indexed: 11/19/2022]
Abstract
Tissue specific isoforms of human glyceraldehyde-3-phosphate dehydrogenase, somatic (GAPD) and sperm-specific (GAPDS), have been reported to display different levels of both stability and catalytic activity. Here we apply MD simulations to investigate molecular basis of this phenomenon. The protein is a tetramer where each subunit consists of two domains - catalytic and NAD-binding one. We demonstrated key residues responsible for intersubunit and interdomain interactions. Effect of several residues was studied by point mutations. Overall we considered three mutations (Glu96Gln, Glu244Gln and Asp311Asn) disrupting GAPDS-specific salt bridges. Comparison of calculated interaction energies with calorimetric enthalpies confirmed that intersubunit interactions were responsible for enhanced thermostability of GAPDS whereas interdomain interactions had indirect influence on intersubunit contacts. Mutation Asp311Asn was around 10Å far from the active center and corresponded to the closest natural substitution in the isoenzymes. MD simulations revealed that this residue had slight interaction with catalytic residues but influenced the hydrogen bond net and dynamics in active site. These effects can be responsible for a strong influence of this residue on catalytic activity. Overall, our results provide new insight into glyceraldehyde-3-phosphate dehydrogenase structure-function relationships and can be used for the engineering of mutant proteins with modified properties and for development of new inhibitors with indirect influence on the catalytic site.
Collapse
Affiliation(s)
- Olga N Makshakova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia.
| | - Pavel I Semenyuk
- Belozersky Institute of Physico-Chemical Biology of Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail L Kuravsky
- Belozersky Institute of Physico-Chemical Biology of Lomonosov Moscow State University, Moscow, Russia
| | - Elena A Ermakova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia
| | - Yuriy F Zuev
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia
| | - Vladimir I Muronetz
- Belozersky Institute of Physico-Chemical Biology of Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
13
|
Suplatov D, Voevodin V, Švedas V. Robust enzyme design: bioinformatic tools for improved protein stability. Biotechnol J 2014; 10:344-55. [PMID: 25524647 DOI: 10.1002/biot.201400150] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/30/2014] [Accepted: 11/04/2014] [Indexed: 01/22/2023]
Abstract
The ability of proteins and enzymes to maintain a functionally active conformation under adverse environmental conditions is an important feature of biocatalysts, vaccines, and biopharmaceutical proteins. From an evolutionary perspective, robust stability of proteins improves their biological fitness and allows for further optimization. Viewed from an industrial perspective, enzyme stability is crucial for the practical application of enzymes under the required reaction conditions. In this review, we analyze bioinformatic-driven strategies that are used to predict structural changes that can be applied to wild type proteins in order to produce more stable variants. The most commonly employed techniques can be classified into stochastic approaches, empirical or systematic rational design strategies, and design of chimeric proteins. We conclude that bioinformatic analysis can be efficiently used to study large protein superfamilies systematically as well as to predict particular structural changes which increase enzyme stability. Evolution has created a diversity of protein properties that are encoded in genomic sequences and structural data. Bioinformatics has the power to uncover this evolutionary code and provide a reproducible selection of hotspots - key residues to be mutated in order to produce more stable and functionally diverse proteins and enzymes. Further development of systematic bioinformatic procedures is needed to organize and analyze sequences and structures of proteins within large superfamilies and to link them to function, as well as to provide knowledge-based predictions for experimental evaluation.
Collapse
Affiliation(s)
- Dmitry Suplatov
- Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | | | | |
Collapse
|