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Chen H, Li Q, Wang J, Niu C, Zheng F, Liu C. Improving ribonucleic acid production in Saccharomyces pastorianus via in silico genome-scale metabolic network model. Biotechnol J 2023; 18:e2300240. [PMID: 37522392 DOI: 10.1002/biot.202300240] [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: 05/24/2023] [Revised: 07/12/2023] [Accepted: 07/30/2023] [Indexed: 08/01/2023]
Abstract
Ribonucleic acid (RNA) and its degradation products are important biomolecules widely used in the food and pharmaceutical industries for their flavoring and nutritional functions. In this study, we used a genome-scale metabolic network model (GSMM) to explore genetic targets for nucleic acid synthesis in a Saccharomyces pastorianus strain (G03). Yeast 8.5.0 was used as the base model, which accurately predicted G03's growth. Using OptForce, we found that overexpression of ARO8 and ATP1 among six different strategies increased the RNA content of G03 by 58.0% and 74.8%, respectively. We also identified new metabolic targets for improved RNA production using a modified GSMM called TissueModel, constructed using the GIMME transcriptome constraint tool to remove low-expressed reactions in the model. After running OptKnock, the RNA content of G03-△BNA1 and G03-△PMA1 increased by 44.6% and 39.8%, respectively, compared to G03. We suggest that ATP1, ARO8, BNA1, and PMA1 regulate cell fitness, which affects RNA content. This study is the first to identify strategies for RNA overproduction using GSMM and to report that regulation of ATP1, ARO8, BNA1, and PMA1 can increase RNA content in S. pastorianus. These findings also provide valuable knowledge on model reconstruction for S. pastorianus.
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Affiliation(s)
- Hao Chen
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, China
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, China
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jinjing Wang
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, China
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Chengtuo Niu
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, China
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Feiyun Zheng
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, China
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Chunfeng Liu
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, China
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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Jin D, Sun B, Zhao W, Ma J, Zhou Q, Han X, Mei Y, Fan Y, Pei Y. Thiamine-biosynthesis genes Bbpyr and Bbthi are required for conidial production and cell wall integrity of the entomopathogenic fungus Beauveria bassiana. J Invertebr Pathol 2021; 184:107639. [PMID: 34139258 DOI: 10.1016/j.jip.2021.107639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 01/29/2023]
Abstract
Beauveria bassiana is an important entomopathogenic fungus used to control a variety of insect pests. Conidia are the infective propagules of the fungus. However, some important factors that influence conidiation are still to be investigated. In this study, a mutant with decreased conidial production and hyphal growth was identified from a random T-DNA insertional library of B. bassiana. The corresponding gene (Bbthi) for this mutation encodes a putative thiazole synthase. Thiazole and pyrimidine are structural components of thiamine (vitamin B1), which is an essential nutrient for all forms of life. Disruption of Bbthi, Bbpyr, a putative pyrimidine synthetic gene, or both in B. bassiana results in a significant decrease of thiamine content. Loss of Bbthi and Bbpyr function significantly decreased the conidial production and hyphal growth, as well as disrupted the integrity of conidial cell wall. However, the defect of Bbpyr and Bbthi does not decrease the virulence of B. bassiana. Our results indicate the importance of thiamine biosynthesis in conidiation of B. bassiana, and provide useful information to produce conidia of entomopathogenic fungi for biocontrol of insect pests.
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Affiliation(s)
- Dan Jin
- Biotechnology Research Center, Southwest University, Chongqing, China
| | - Binda Sun
- Biotechnology Research Center, Southwest University, Chongqing, China; Institute of Medicine and Equipment for High Altitude Region, College of High Altitude Military Medicine, Army Medical University (Third Military Medical University), China
| | - Wenqi Zhao
- Biotechnology Research Center, Southwest University, Chongqing, China; Institute of Medicine and Equipment for High Altitude Region, College of High Altitude Military Medicine, Army Medical University (Third Military Medical University), China
| | - Jincheng Ma
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Qiuyue Zhou
- Biotechnology Research Center, Southwest University, Chongqing, China
| | - Xuemeng Han
- Biotechnology Research Center, Southwest University, Chongqing, China
| | - Yalin Mei
- Biotechnology Research Center, Southwest University, Chongqing, China
| | - Yanhua Fan
- Biotechnology Research Center, Southwest University, Chongqing, China
| | - Yan Pei
- Biotechnology Research Center, Southwest University, Chongqing, China.
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Peraman R, Sure SK, Dusthackeer VNA, Chilamakuru NB, Yiragamreddy PR, Pokuri C, Kutagulla VK, Chinni S. Insights on recent approaches in drug discovery strategies and untapped drug targets against drug resistance. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021; 7:56. [PMID: 33686369 PMCID: PMC7928709 DOI: 10.1186/s43094-021-00196-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/03/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Despite the various strategies undertaken in the clinical practice, the mortality rate due to antibiotic-resistant microbes has been markedly increasing worldwide. In addition to multidrug-resistant (MDR) microbes, the "ESKAPE" bacteria are also emerging. Of course, the infection caused by ESKAPE cannot be treated even with lethal doses of antibiotics. Now, the drug resistance is also more prevalent in antiviral, anticancer, antimalarial and antifungal chemotherapies. MAIN BODY To date, in the literature, the quantum of research reported on the discovery strategies for new antibiotics is remarkable but the milestone is still far away. Considering the need of the updated strategies and drug discovery approaches in the area of drug resistance among researchers, in this communication, we consolidated the insights pertaining to new drug development against drug-resistant microbes. It includes drug discovery void, gene paradox, transposon mutagenesis, vitamin biosynthesis inhibition, use of non-conventional media, host model, target through quorum sensing, genomic-chemical network, synthetic viability to targets, chemical versus biological space, combinational approach, photosensitization, antimicrobial peptides and transcriptome profiling. Furthermore, we optimally briefed about antievolution drugs, nanotheranostics and antimicrobial adjuvants and then followed by twelve selected new feasible drug targets for new drug design against drug resistance. Finally, we have also tabulated the chemical structures of potent molecules against antimicrobial resistance. CONCLUSION It is highly recommended to execute the anti-drug resistance research as integrated approach where both molecular and genetic research needs to be as integrative objective of drug discovery. This is time to accelerate new drug discovery research with advanced genetic approaches instead of conventional blind screening.
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Affiliation(s)
- Ramalingam Peraman
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research (RIPER)-Autonomous, Anantapur, Andhra Pradesh India
| | - Sathish Kumar Sure
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research (RIPER)-Autonomous, Anantapur, Andhra Pradesh India
| | - V. N. Azger Dusthackeer
- grid.417330.20000 0004 1767 6138ICMR-National Institute of Research in Tuberculosis, Chennai, Tamilnadu India
| | - Naresh Babu Chilamakuru
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research (RIPER)-Autonomous, Anantapur, Andhra Pradesh India
| | - Padmanabha Reddy Yiragamreddy
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research (RIPER)-Autonomous, Anantapur, Andhra Pradesh India
| | - Chiranjeevi Pokuri
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research (RIPER)-Autonomous, Anantapur, Andhra Pradesh India
| | - Vinay Kumar Kutagulla
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research (RIPER)-Autonomous, Anantapur, Andhra Pradesh India
| | - Santhivardhan Chinni
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research (RIPER)-Autonomous, Anantapur, Andhra Pradesh India
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Krishnan J, Lu L, Alam Nazki A. The interplay of spatial organization and biochemistry in building blocks of cellular signalling pathways. J R Soc Interface 2020; 17:20200251. [PMID: 32453980 PMCID: PMC7276544 DOI: 10.1098/rsif.2020.0251] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022] Open
Abstract
Biochemical pathways and networks are central to cellular information processing. While a broad range of studies have dissected multiple aspects of information processing in biochemical pathways, the effect of spatial organization remains much less understood. It is clear that space is central to intracellular organization, plays important roles in cellular information processing and has been exploited in evolution; additionally, it is being increasingly exploited in synthetic biology through the development of artificial compartments, in a variety of ways. In this paper, we dissect different aspects of the interplay between spatial organization and biochemical pathways, by focusing on basic building blocks of these pathways: covalent modification cycles and two-component systems, with enzymes which may be monofunctional or bifunctional. Our analysis of spatial organization is performed by examining a range of 'spatial designs': patterns of localization or non-localization of enzymes/substrates, theoretically and computationally. Using these well-characterized in silico systems, we analyse the following. (i) The effect of different types of spatial organization on the overall kinetics of modification, and the role of distinct modification mechanisms therein. (ii) How different information processing characteristics seen experimentally and studied from the viewpoint of kinetics are perturbed, or generated. (iii) How the activity of enzymes (bifunctional enzymes in particular) may be spatially manipulated, and the relationship between localization and activity. (iv) How transitions in spatial organization (encountered either through evolution or through the lifetime of cells, as seen in multiple model organisms) impacts the kinetic module (and pathway) behaviour, and how transitions in chemistry may be impacted by prior spatial organization. The basic insights which emerge are central to understanding the role of spatial organization in biochemical pathways in both bacteria and eukaryotes, and are of direct relevance to engineering spatial organization of pathways in bottom-up synthetic biology in cellular and cell-free systems.
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Affiliation(s)
- J. Krishnan
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
- Institute for Systems and Synthetic Biology, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Lingjun Lu
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Aiman Alam Nazki
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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Barra ALC, Dantas LDOC, Morão LG, Gutierrez RF, Polikarpov I, Wrenger C, Nascimento AS. Essential Metabolic Routes as a Way to ESKAPE From Antibiotic Resistance. Front Public Health 2020; 8:26. [PMID: 32257985 PMCID: PMC7093009 DOI: 10.3389/fpubh.2020.00026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/27/2020] [Indexed: 02/03/2023] Open
Abstract
Antibiotic resistance is a worldwide concern that requires a concerted action from physicians, patients, governmental agencies, and academia to prevent infections and the spread of resistance, track resistant bacteria, improve the use of current antibiotics, and develop new antibiotics. Despite the efforts spent so far, the current antibiotics in the market are restricted to only five general targets/pathways highlighting the need for basic research focusing on the discovery and evaluation of new potential targets. Here we interrogate two biosynthetic pathways as potentially druggable pathways in bacteria. The biosynthesis pathway for thiamine (vitamin B1), absent in humans, but found in many bacteria, including organisms in the group of the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter sp.) and the biosynthesis pathway for pyridoxal 5'-phosphate and its vitamers (vitamin B6), found in S. aureus. Using current genomic data, we discuss the possibilities of inhibition of enzymes in the pathway and review the current state of the art in the scientific literature.
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Affiliation(s)
| | | | - Luana Galvão Morão
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Raíssa F. Gutierrez
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Meir Z, Osherov N. Vitamin Biosynthesis as an Antifungal Target. J Fungi (Basel) 2018; 4:E72. [PMID: 29914189 PMCID: PMC6023522 DOI: 10.3390/jof4020072] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 12/18/2022] Open
Abstract
The large increase in the population of immunosuppressed patients, coupled with the limited efficacy of existing antifungals and rising resistance toward them, have dramatically highlighted the need to develop novel drugs for the treatment of invasive fungal infections. An attractive possibility is the identification of possible drug targets within essential fungal metabolic pathways not shared with humans. Here, we review the vitamin biosynthetic pathways (vitamins A⁻E, K) as candidates for the development of antifungals. We present a set of ranking criteria that identify the vitamin B2 (riboflavin), B5 (pantothenic acid), and B9 (folate) biosynthesis pathways as being particularly rich in new antifungal targets. We propose that recent scientific advances in the fields of drug design and fungal genomics have developed sufficiently to merit a renewed look at these pathways as promising sources for the development of novel classes of antifungals.
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Affiliation(s)
- Zohar Meir
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel.
| | - Nir Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel.
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Tani Y, Kimura K, Mihara H. Purification and properties of 4-methyl-5-hydroxyethylthiazole kinase from Escherichia coli. Biosci Biotechnol Biochem 2015; 80:514-7. [PMID: 26634770 DOI: 10.1080/09168451.2015.1104239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
4-Methyl-5-hydroxyethylthiazole kinase (ThiM) participates in thiamin biosynthesis as the key enzyme in its salvage pathway. We purified and characterized ThiM from Escherichia coli. It has broad substrate specificity toward various nucleotides and shows a preference for dATP as a phosphate donor over ATP. It is activated by divalent cations, and responds more strongly to Co(2+) than to Mg(2+).
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Affiliation(s)
- Yasushi Tani
- a Department of Biotechnology , College of Life Sciences, Ritsumeikan University , Kusatsu , Japan.,b Ritsumeikan Global Innovation Research Organization , Ritsumeikan University , Kusatsu , Japan
| | - Keisuke Kimura
- a Department of Biotechnology , College of Life Sciences, Ritsumeikan University , Kusatsu , Japan
| | - Hisaaki Mihara
- a Department of Biotechnology , College of Life Sciences, Ritsumeikan University , Kusatsu , Japan
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Fitzpatrick TB, Thore S. Complex behavior: from cannibalism to suicide in the vitamin B1 biosynthesis world. Curr Opin Struct Biol 2014; 29:34-43. [DOI: 10.1016/j.sbi.2014.08.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/27/2014] [Accepted: 08/28/2014] [Indexed: 10/24/2022]
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Abstract
Thiaminases, enzymes that cleave vitamin B1, are sporadically distributed among prokaryotes and eukaryotes. Thiaminase I enzymes catalyze the elimination of the thiazole ring moiety from thiamin through substitution of the methylene group with a nitrogenous base or sulfhydryl compound. In eukaryotic organisms, these enzymes are reported to have much higher molecular weights than their bacterial counterparts. A thiaminase I of the single-celled amoeboflagellate Naegleria gruberi is the only eukaryotic thiaminase I to have been cloned, sequenced, and expressed. Here, we present the crystal structure of N. gruberi thiaminase I to a resolution of 2.8 Å, solved by isomorphous replacement and pseudo-two-wavelength multiwavelength anomalous diffraction and refined to an R factor of 0.231 (Rfree, 0.265). This structure was used to solve the structure of the enzyme in complex with 3-deazathiamin, a noncleavable thiamin analog and enzyme inhibitor (2.7 Å; R, 0.233; Rfree, 0.267). These structures define the mode of thiamin binding to this class of thiaminases and indicate the involvement of Asp272 as the catalytic base. This enzyme is able to use thiamin as a substrate and is active with amines such as aniline and veratrylamine as well as sulfhydryl compounds such as l-cysteine and β-mercaptoethanol as cosubstrates. Despite significant differences in polypeptide sequence and length, we have shown that the N. gruberi thiaminase I is homologous in structure and activity to a previously characterized bacterial thiaminase I.
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Yazdani M, Zallot R, Tunc-Ozdemir M, de Crécy-Lagard V, Shintani DK, Hanson AD. Identification of the thiamin salvage enzyme thiazole kinase in Arabidopsis and maize. PHYTOCHEMISTRY 2013; 94:68-73. [PMID: 23816351 DOI: 10.1016/j.phytochem.2013.05.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/23/2013] [Accepted: 05/29/2013] [Indexed: 05/06/2023]
Abstract
The breakdown of thiamin (vitamin B1) and its phosphates releases a thiazole moiety, 4-methyl-5-(2-hydroxyethyl)thiazole (THZ), that microorganisms and plants are able to salvage for re-use in thiamin synthesis. The salvage process starts with the ATP-dependent phosphorylation of THZ, which in bacteria is mediated by ThiM. The Arabidopsis and maize genomes encode homologs of ThiM (At3g24030 and GRMZM2G094558, respectively). Plasmid-driven expression of either plant homolog restored the ability of THZ to rescue Escherichia coli thiM deletant strains, showing that the plant proteins have ThiM activity in vivo. Enzymatic assays with purified recombinant proteins confirmed the presence of THZ kinase activity. Furthermore, ablating the Arabidopsis At3g24030 gene in a thiazole synthesis mutant severely impaired rescue by THZ. Collectively, these results show that ThiM homologs are the main source of THZ kinase activity in plants and are consequently crucial for thiamin salvage.
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Affiliation(s)
- Mohammad Yazdani
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
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Bell JA, Ho KL, Farid R. Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:935-52. [PMID: 22868759 PMCID: PMC3413210 DOI: 10.1107/s0907444912017453] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 04/19/2012] [Indexed: 11/12/2022]
Abstract
All-atom models are essential for many applications in molecular modeling and computational chemistry. Nonbonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5-2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R(free) values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein-ligand interactions.
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Affiliation(s)
- Jeffrey A. Bell
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
| | - Kenneth L. Ho
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
| | - Ramy Farid
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
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French JB, Begley TP, Ealick SE. Structure of trifunctional THI20 from yeast. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:784-91. [PMID: 21904031 DOI: 10.1107/s0907444911024814] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 06/24/2011] [Indexed: 11/10/2022]
Abstract
In a recently characterized thiamin-salvage pathway, thiamin-degradation products are hydrolyzed by thiaminase II, yielding 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP). This compound is an intermediate in thiamin biosynthesis that, once phosphorylated by an HMP kinase, can be used to synthesize thiamin monophosphate. Here, the crystal structure of Saccharomyces cerevisiae THI20, a trifunctional enzyme containing an N-terminal HMP kinase/HMP-P kinase (ThiD-like) domain and a C-terminal thiaminase II (TenA-like) domain, is presented. Comparison to structures of the monofunctional enzymes reveals that while the ThiD-like dimer observed in THI20 resembles other ThiD structures, the TenA-like domain, which is tetrameric in all previously reported structures, forms a dimer. Similarly, the active site of the ThiD-like domain of THI20 is highly similar to other known ThiD enzymes, while the TenA-like active site shows unique features compared with previously structurally characterized TenAs. In addition, a survey of known TenA structures revealed two structural classes, both of which have distinct conserved features. The TenA domain of THI20 possesses some features of both classes, consistent with its ability to hydrolyze both thiamin and the thiamin-degradation product 2-methyl-4-amino-5-aminomethylpyrimidine.
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Affiliation(s)
- Jarrod B French
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA
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