1
|
Zhang X, Niu P, Liu H, Fang H. Production of pyrimidine nucleosides in microbial systems via metabolic engineering: Theoretical analysis research and prospects. Biotechnol Adv 2024; 75:108419. [PMID: 39053562 DOI: 10.1016/j.biotechadv.2024.108419] [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: 05/10/2024] [Revised: 06/26/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
Pyrimidine nucleosides, as intermediate materials of significant commercial value, find extensive applications in the pharmaceutical industry. However, the current production of pyrimidine nucleosides largely relies on chemical synthesis, creating environmental problems that do not align with sustainable development goals. Recent progress in systemic metabolic engineering and synthetic biology has enabled the synthesis of natural products like pyrimidine nucleosides through microbial fermentation, offering a more sustainable alternative. Nevertheless, the intricate and tightly regulated biosynthetic pathways involved in the microbial production of pyrimidine nucleosides pose a formidable challenge. This study focuses on metabolic engineering and synthetic biology strategies aimed at enhancing pyrimidine nucleoside production. These strategies include gene modification, transcriptional regulation, metabolic flux analysis, cofactor balance optimization, and transporter engineering. Finally, this research highlights the challenges involved in the further development of pyrimidine nucleoside-producing strains and offers potential solutions in order to provide theoretical guidance for future research endeavors in this field.
Collapse
Affiliation(s)
- Xiangjun Zhang
- School of Life Science, Ningxia University, Yinchuan, Ningxia 750021, China
| | - Pilian Niu
- School of Life Science, Ningxia University, Yinchuan, Ningxia 750021, China
| | - Huiyan Liu
- School of Food Science and Engineering, Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, Ningxia 750021, China.
| | - Haitian Fang
- School of Food Science and Engineering, Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, Ningxia 750021, China.
| |
Collapse
|
2
|
Zhang X, Liu L, Ma C, Zhang H, Liu H, Fang H. Improving the level of the cytidine biosynthesis in E. coli through atmospheric room temperature plasma mutagenesis and metabolic engineering. J Appl Microbiol 2024; 135:lxae133. [PMID: 38830792 DOI: 10.1093/jambio/lxae133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/09/2024] [Accepted: 06/01/2024] [Indexed: 06/05/2024]
Abstract
AIMS Cytidine, as an important commercial precursor in the chemical synthesis of antiviral and antitumor drugs, is in great demand in the market. Therefore, the purpose of this study is to build a microbial cell factory with high cytidine production. METHODS AND RESULTS A mutant E. coli NXBG-11-F34 with high tolerance to uridine monophosphate structural analogs and good genetic stability was obtained by atmospheric room temperature plasma (ARTP) mutagenesis combined with high-throughput screening. Then, the udk and rihA genes involved in cytidine catabolism were knocked out by CRISPR/Cas9 gene editing technology, and the recombinant strain E. coli NXBG-13 was constructed. The titer, yield, and productivity of cytidine fermented in a 5 l bioreactor were 15.7 g l-1, 0.164 g g-1, and 0.327 g l-1 h-1, respectively. Transcriptome analysis of the original strain and the recombinant strain E. coli NXBG-13 showed that the gene expression profiles of the two strains changed significantly, and the cytidine de novo pathway gene of the recombinant strain was up-regulated significantly. CONCLUSIONS ARTP mutagenesis combined with metabolic engineering is an effective method to construct cytidine-producing strains.
Collapse
Affiliation(s)
- Xiangjun Zhang
- School of Life Science, Ningxia University, Yinchuan 750021, China
| | - Lu Liu
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Cong Ma
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Haojie Zhang
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Huiyan Liu
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Haitian Fang
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| |
Collapse
|
3
|
Wagner AG, Stagnitta RT, Xu Z, Pezzullo JL, Kandel N, Giner JL, Covey DF, Wang C, Callahan BP. Nanomolar, Noncovalent Antagonism of Hedgehog Cholesterolysis: Exception to the "Irreversibility Rule" for Protein Autoprocessing Inhibition. Biochemistry 2022; 61:1022-1028. [PMID: 34941260 PMCID: PMC9382716 DOI: 10.1021/acs.biochem.1c00697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hedgehog (Hh) signaling ligands undergo carboxy terminal sterylation through specialized autoprocessing, called cholesterolysis. Sterylation is brought about intramolecularly in a single turnover by an adjacent enzymatic domain, called HhC, which is found in precursor Hh proteins only. Previous attempts to identify antagonists of the intramolecular activity of HhC have yielded inhibitors that bind HhC irreversibly through covalent mechanisms, as is common for protein autoprocessing inhibitors. Here, we report an exception to the "irreversibility rule" for autoprocessing inhibition. Using a fluorescence resonance energy transfer-based activity assay for HhC, we screened a focused library of sterol-like analogues for noncovalent inhibitors and identified and validated four structurally related molecules, which were then used for structure-activity relationship studies. The most effective derivative, tBT-HBT, inhibits HhC noncovalently with an IC50 of 300 nM. An allosteric binding site for tBT-HBT, encompassing residues from the two subdomains of HhC, is suggested by kinetic analysis, mutagenesis studies, and photoaffinity labeling. The inhibitors described here resemble a family of noncovalent, allosteric inducers of HhC paracatalysis which we have described previously. The inhibition and the induction appear to be mediated by a shared allosteric site on HhC.
Collapse
Affiliation(s)
- Andrew G Wagner
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Robert T Stagnitta
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Zihan Xu
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - John L Pezzullo
- Department of Chemistry, SUNY-ESF, Syracuse, New York 13210, United States
| | - Nabin Kandel
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
| | - José-Luis Giner
- Department of Chemistry, SUNY-ESF, Syracuse, New York 13210, United States
| | - Douglas F Covey
- Department of Developmental Biology, Taylor Family Institute for Innovative Psychiatric Research, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
| | - Brian P Callahan
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| |
Collapse
|
4
|
Subsets of Slow Dynamic Modes Reveal Global Information Sources as Allosteric Sites. J Mol Biol 2022; 434:167644. [DOI: 10.1016/j.jmb.2022.167644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 02/06/2023]
|
5
|
Lei Z, Wang N, Tan H, Zheng J, Jia Z. Conformational Plasticity of the Active Site Entrance in E. coli Aspartate Transcarbamoylase and Its Implication in Feedback Regulation. Int J Mol Sci 2020; 21:ijms21010320. [PMID: 31947715 PMCID: PMC6981877 DOI: 10.3390/ijms21010320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/21/2019] [Accepted: 12/23/2019] [Indexed: 11/21/2022] Open
Abstract
Aspartate transcarbamoylase (ATCase) has been studied for decades and Escherichia coli ATCase is referred as a “textbook example” for both feedback regulation and cooperativity. However, several critical questions about the catalytic and regulatory mechanisms of E. coli ATCase remain unanswered, especially about its remote feedback regulation. Herein, we determined a structure of E. coli ATCase in which a key residue located (Arg167) at the entrance of the active site adopted an uncommon open conformation, representing the first wild-type apo-form E. coli ATCase holoenzyme that features this state. Based on the structure and our results of enzymatic characterization, as well as molecular dynamic simulations, we provide new insights into the feedback regulation of E. coli ATCase. We speculate that the binding of pyrimidines or purines would affect the hydrogen bond network at the interface of the catalytic and regulatory subunit, which would further influence the stability of the open conformation of Arg167 and the enzymatic activity of ATCase. Our results not only revealed the importance of the previously unappreciated open conformation of Arg167 in the active site, but also helped to provide rationalization for the mechanism of the remote feedback regulation of ATCase.
Collapse
Affiliation(s)
- Zhen Lei
- College of Chemistry, Beijing Normal University, Beijing 100875, China; (Z.L.); (N.W.); (H.T.)
| | - Nan Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, China; (Z.L.); (N.W.); (H.T.)
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry and Molecular Biology, Xuzhou Medical University, Xuzhou 221004, China
| | - Hongwei Tan
- College of Chemistry, Beijing Normal University, Beijing 100875, China; (Z.L.); (N.W.); (H.T.)
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, Beijing 100875, China; (Z.L.); (N.W.); (H.T.)
- Correspondence: (J.Z.); (Z.J.); Tel.: +86-010-58806002 (J.Z.); +1-613-5336277 (Z.J.)
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L3N6, Canada
- Correspondence: (J.Z.); (Z.J.); Tel.: +86-010-58806002 (J.Z.); +1-613-5336277 (Z.J.)
| |
Collapse
|
6
|
Madej T, Marchler-Bauer A, Lanczycki C, Zhang D, Bryant SH. Biological Assembly Comparison with VAST. Methods Mol Biol 2020; 2112:175-186. [PMID: 32006286 DOI: 10.1007/978-1-0716-0270-6_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The VAST+ algorithm is an efficient, simple, and elegant solution to the problem of comparing the atomic structures of biological assemblies. Given two protein assemblies, it takes as input all the pairwise structural alignments of the component proteins. It then clusters the rotation matrices from the pairwise superpositions, with the clusters corresponding to subsets of the two assemblies that may be aligned and well superposed. It uses the Vector Alignment Search Tool (VAST) protein-protein comparison method for the input structural alignments, but other methods could be used, as well. From a chosen cluster, an "original" alignment for the assembly may be defined by simply combining the relevant input alignments. However, it is often useful to reduce/trim the original alignment, using a Monte Carlo refinement algorithm, which allows biologically relevant conformational differences to be more readily detected and observed. The method is easily extended to include RNA or DNA molecules. VAST+ results may be accessed via the URL https://www.ncbi.nlm.nih.gov/Structure , then entering a PDB accession or terms in the search box, and using the link [VAST+] in the upper right corner of the Structure Summary page.
Collapse
Affiliation(s)
- Thomas Madej
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
| | - Aron Marchler-Bauer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Christopher Lanczycki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Dachuan Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Stephen H Bryant
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
7
|
Regulation of Bacterial Gene Expression by Transcription Attenuation. Microbiol Mol Biol Rev 2019; 83:83/3/e00019-19. [PMID: 31270135 DOI: 10.1128/mmbr.00019-19] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A wide variety of mechanisms that control gene expression in bacteria are based on conditional transcription termination. Generally, in these mechanisms, a transcription terminator is located between a promoter and a downstream gene(s), and the efficiency of the terminator is controlled by a regulatory effector that can be a metabolite, protein, or RNA. The most common type of regulation involving conditional termination is transcription attenuation, in which the primary regulatory target is an essential element of a single terminator. The terminator can be either intrinsic or Rho dependent, with each presenting unique regulatory targets. Transcription attenuation mechanisms can be divided into five classes based primarily on the manner in which transcription termination is rendered conditional. This review summarizes each class of control mechanisms from a historical perspective, describes important examples in a physiological context and the current state of knowledge, highlights major advances, and discusses expectations of future discoveries.
Collapse
|
8
|
Sizemore AE, Karuza EA, Giusti C, Bassett DS. Knowledge gaps in the early growth of semantic feature networks. Nat Hum Behav 2018; 2:682-692. [PMID: 30333998 PMCID: PMC6186390 DOI: 10.1038/s41562-018-0422-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 07/25/2018] [Indexed: 12/20/2022]
Abstract
Understanding language learning, and more general knowledge acquisition, requires characterization of inherently qualitative structures. Recent work has applied network science to this task by creating semantic feature networks, in which words correspond to nodes and connections to shared features, then characterizing the structure of strongly inter-related groups of words. However, the importance of sparse portions of the semantic network - knowledge gaps - remains unexplored. Using applied topology we query the prevalence of knowledge gaps, which we propose manifest as cavities within the growing semantic feature network of toddlers. We detect topological cavities of multiple dimensions and find that despite word order variation, global organization remains similar. We also show that nodal network measures correlate with filling cavities better than basic lexical properties. Finally, we discuss the importance of semantic feature network topology in language learning and speculate that the progression through knowledge gaps may be a robust feature of knowledge acquisition.
Collapse
Affiliation(s)
- Ann E Sizemore
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Elisabeth A Karuza
- Department of Psychology, College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Chad Giusti
- Department of Mathematical Sciences, University of Delaware, Newark, DE, USA
| | - Danielle S Bassett
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Physics and Astronomy, College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Electrical and Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
9
|
Hodges M, Barahona M, Yaliraki SN. Allostery and cooperativity in multimeric proteins: bond-to-bond propensities in ATCase. Sci Rep 2018; 8:11079. [PMID: 30038211 PMCID: PMC6056424 DOI: 10.1038/s41598-018-27992-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/13/2018] [Indexed: 11/08/2022] Open
Abstract
Aspartate carbamoyltransferase (ATCase) is a large dodecameric enzyme with six active sites that exhibits allostery: its catalytic rate is modulated by the binding of various substrates at distal points from the active sites. A recently developed method, bond-to-bond propensity analysis, has proven capable of predicting allosteric sites in a wide range of proteins using an energy-weighted atomistic graph obtained from the protein structure and given knowledge only of the location of the active site. Bond-to-bond propensity establishes if energy fluctuations at given bonds have significant effects on any other bond in the protein, by considering their propagation through the protein graph. In this work, we use bond-to-bond propensity analysis to study different aspects of ATCase activity using three different protein structures and sources of fluctuations. First, we predict key residues and bonds involved in the transition between inactive (T) and active (R) states of ATCase by analysing allosteric substrate binding as a source of energy perturbations in the protein graph. Our computational results also indicate that the effect of multiple allosteric binding is non linear: a switching effect is observed after a particular number and arrangement of substrates is bound suggesting a form of long range communication between the distantly arranged allosteric sites. Second, cooperativity is explored by considering a bisubstrate analogue as the source of energy fluctuations at the active site, also leading to the identification of highly significant residues to the T ↔ R transition that enhance cooperativity across active sites. Finally, the inactive (T) structure is shown to exhibit a strong, non linear communication between the allosteric sites and the interface between catalytic subunits, rather than the active site. Bond-to-bond propensity thus offers an alternative route to explain allosteric and cooperative effects in terms of detailed atomistic changes to individual bonds within the protein, rather than through phenomenological, global thermodynamic arguments.
Collapse
Affiliation(s)
- Maxwell Hodges
- Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
- Institute of Chemical Biology, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
- Institute of Chemical Biology, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Sophia N Yaliraki
- Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom.
- Institute of Chemical Biology, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom.
| |
Collapse
|
10
|
Human SHMT inhibitors reveal defective glycine import as a targetable metabolic vulnerability of diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A 2017; 114:11404-11409. [PMID: 29073064 DOI: 10.1073/pnas.1706617114] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The enzyme serine hydroxymethyltransferse (SHMT) converts serine into glycine and a tetrahydrofolate-bound one-carbon unit. Folate one-carbon units support purine and thymidine synthesis, and thus cell growth. Mammals have both cytosolic SHMT1 and mitochondrial SHMT2, with the mitochondrial isozyme strongly up-regulated in cancer. Here we show genetically that dual SHMT1/2 knockout blocks HCT-116 colon cancer tumor xenograft formation. Building from a pyrazolopyran scaffold that inhibits plant SHMT, we identify small-molecule dual inhibitors of human SHMT1/2 (biochemical IC50 ∼ 10 nM). Metabolomics and isotope tracer studies demonstrate effective cellular target engagement. A cancer cell-line screen revealed that B-cell lines are particularly sensitive to SHMT inhibition. The one-carbon donor formate generally rescues cells from SHMT inhibition, but paradoxically increases the inhibitor's cytotoxicity in diffuse large B-cell lymphoma (DLBCL). We show that this effect is rooted in defective glycine uptake in DLBCL cell lines, rendering them uniquely dependent upon SHMT enzymatic activity to meet glycine demand. Thus, defective glycine import is a targetable metabolic deficiency of DLBCL.
Collapse
|
11
|
Abstract
X-ray scattering is uniquely suited to the study of disordered systems and thus has the potential to provide insight into dynamic processes where diffraction methods fail. In particular, while X-ray crystallography has been a staple of structural biology for more than half a century and will continue to remain so, a major limitation of this technique has been the lack of dynamic information. Solution X-ray scattering has become an invaluable tool in structural and mechanistic studies of biological macromolecules where large conformational changes are involved. Such systems include allosteric enzymes that play key roles in directing metabolic fluxes of biochemical pathways, as well as large, assembly-line type enzymes that synthesize secondary metabolites with pharmaceutical applications. Furthermore, crystallography has the potential to provide information on protein dynamics via the diffuse scattering patterns that are overlaid with Bragg diffraction. Historically, these patterns have been very difficult to interpret, but recent advances in X-ray detection have led to a renewed interest in diffuse scattering analysis as a way to probe correlated motions. Here, we will review X-ray scattering theory and highlight recent advances in scattering-based investigations of protein solutions and crystals, with a particular focus on complex enzymes.
Collapse
Affiliation(s)
- Steve P Meisburger
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - William C Thomas
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Maxwell B Watkins
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Nozomi Ando
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| |
Collapse
|
12
|
Fetler L, Vachette P. The Quaternary Structure of the R-State of Escherichia coli Aspartate Transcarbamoylase in Solution Is Different from That in the Crystal and Is Modified by Mg 2+·ATP Binding. Biochemistry 2017; 56:2860-2862. [PMID: 28535029 DOI: 10.1021/acs.biochem.7b00160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- L Fetler
- CERMES3, U. INSERM 988, CNRS UMR 8211, EHESS, Université Paris Descartes , BP 8, F-94801 Villejuif Cedex, France
| | - P Vachette
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Université Paris-Sud , F-91405 Orsay Cedex, France
| |
Collapse
|
13
|
Strain analysis of protein structures and low dimensionality of mechanical allosteric couplings. Proc Natl Acad Sci U S A 2016; 113:E5847-E5855. [PMID: 27655887 DOI: 10.1073/pnas.1609462113] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In many proteins, especially allosteric proteins that communicate regulatory states from allosteric to active sites, structural deformations are functionally important. To understand these deformations, dynamical experiments are ideal but challenging. Using static structural information, although more limited than dynamical analysis, is much more accessible. Underused for protein analysis, strain is the natural quantity for studying local deformations. We calculate strain tensor fields for proteins deformed by ligands or thermal fluctuations using crystal and NMR structure ensembles. Strains-primarily shears-show deformations around binding sites. These deformations can be induced solely by ligand binding at distant allosteric sites. Shears reveal quasi-2D paths of mechanical coupling between allosteric and active sites that may constitute a widespread mechanism of allostery. We argue that strain-particularly shear-is the most appropriate quantity for analysis of local protein deformations. This analysis can reveal mechanical and biological properties of many proteins.
Collapse
|
14
|
Abstract
The concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic processes, yet a simple and unified treatment of the effects of allostery in enzymes has been lacking. In this work, we take a step toward this goal by modeling allosteric enzymes and their interaction with two key molecular players-allosteric regulators and competitive inhibitors. We then apply this model to characterize existing data on enzyme activity, comment on how enzyme parameters (such as substrate binding affinity) can be experimentally tuned, and make novel predictions on how to control phenomena such as substrate inhibition.
Collapse
Affiliation(s)
- Tal Einav
- Department of Physics, California Institute of Technology , Pasadena, California 91125, United States
| | - Linas Mazutis
- Institute of Biotechnology, Vilnius University , Vilnius, 02241 Lithuania
| | - Rob Phillips
- Department of Applied Physics and Division of Biology, California Institute of Technology , Pasadena, California 91125, United States
| |
Collapse
|
15
|
Shi D, Allewell NM, Tuchman M. From Genome to Structure and Back Again: A Family Portrait of the Transcarbamylases. Int J Mol Sci 2015; 16:18836-64. [PMID: 26274952 PMCID: PMC4581275 DOI: 10.3390/ijms160818836] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 11/18/2022] Open
Abstract
Enzymes in the transcarbamylase family catalyze the transfer of a carbamyl group from carbamyl phosphate (CP) to an amino group of a second substrate. The two best-characterized members, aspartate transcarbamylase (ATCase) and ornithine transcarbamylase (OTCase), are present in most organisms from bacteria to humans. Recently, structures of four new transcarbamylase members, N-acetyl-l-ornithine transcarbamylase (AOTCase), N-succinyl-l-ornithine transcarbamylase (SOTCase), ygeW encoded transcarbamylase (YTCase) and putrescine transcarbamylase (PTCase) have also been determined. Crystal structures of these enzymes have shown that they have a common overall fold with a trimer as their basic biological unit. The monomer structures share a common CP binding site in their N-terminal domain, but have different second substrate binding sites in their C-terminal domain. The discovery of three new transcarbamylases, l-2,3-diaminopropionate transcarbamylase (DPTCase), l-2,4-diaminobutyrate transcarbamylase (DBTCase) and ureidoglycine transcarbamylase (UGTCase), demonstrates that our knowledge and understanding of the spectrum of the transcarbamylase family is still incomplete. In this review, we summarize studies on the structures and function of transcarbamylases demonstrating how structural information helps to define biological function and how small structural differences govern enzyme specificity. Such information is important for correctly annotating transcarbamylase sequences in the genome databases and for identifying new members of the transcarbamylase family.
Collapse
Affiliation(s)
- Dashuang Shi
- Center for Genetic Medicine Research, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA.
- Department of Integrative Systems Biology, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA.
| | - Norma M Allewell
- Department of Cell Biology and Molecular Genetics, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park, MD 20742, USA.
- Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park, MD 20742, USA.
| | - Mendel Tuchman
- Center for Genetic Medicine Research, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA.
- Department of Integrative Systems Biology, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA.
| |
Collapse
|
16
|
Balogun EO, Inaoka DK, Shiba T, Kido Y, Tsuge C, Nara T, Aoki T, Honma T, Tanaka A, Inoue M, Matsuoka S, Michels PAM, Kita K, Harada S. Molecular basis for the reverse reaction of African human trypanosomes glycerol kinase. Mol Microbiol 2014; 94:1315-29. [PMID: 25315291 DOI: 10.1111/mmi.12831] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2014] [Indexed: 11/26/2022]
Abstract
The glycerol kinase (GK) of African human trypanosomes is compartmentalized in their glycosomes. Unlike the host GK, which under physiological conditions catalyzes only the forward reaction (ATP-dependent glycerol phosphorylation), trypanosome GK can additionally catalyze the reverse reaction. In fact, owing to this unique reverse catalysis, GK is potentially essential for the parasites survival in the human host, hence a promising drug target. The mechanism of its reverse catalysis was unknown; therefore, it was not clear if this ability was purely due to its localization in the organelles or whether structure-based catalytic differences also contribute. To investigate this lack of information, the X-ray crystal structure of this protein was determined up to 1.90 Å resolution, in its unligated form and in complex with three natural ligands. These data, in conjunction with results from structure-guided mutagenesis suggests that the trypanosome GK is possibly a transiently autophosphorylating threonine kinase, with the catalytic site formed by non-conserved residues. Our results provide a series of structural peculiarities of this enzyme, and gives unexpected insight into the reverse catalysis mechanism. Together, they provide an encouraging molecular framework for the development of trypanosome GK-specific inhibitors, which may lead to the design of new and safer trypanocidal drug(s).
Collapse
Affiliation(s)
- Emmanuel Oluwadare Balogun
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Kyoto, 606-8585, Japan; Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan; Department of Biochemistry, Ahmadu Bello University, Zaria, 2222, Nigeria
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Kumar M, George SJ. Homotropic and heterotropic allosteric regulation of supramolecular chirality. Chem Sci 2014. [DOI: 10.1039/c4sc00813h] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Homotropic/heterotropic allosteric control over the handedness of dipicolylethylenediamine-functionalized perylene bisimide assemblies was obtained with chiral ATP and achiral PPi guests binding.
Collapse
Affiliation(s)
- Mohit Kumar
- Supramolecular Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
- Bangalore-560064, India
| | - Subi J. George
- Supramolecular Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
- Bangalore-560064, India
| |
Collapse
|