1
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Siraj S, Yameen D, Bhati S, Athar T, Khan S, Bhattacharya J, Islam A, Haque MM. Sugar osmolyte inhibits and attenuates the fibrillogenesis in RNase A: An in vitro and in silico characterizations. Int J Biol Macromol 2023; 253:127378. [PMID: 37839601 DOI: 10.1016/j.ijbiomac.2023.127378] [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: 06/27/2023] [Revised: 09/07/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023]
Abstract
Mechanisms of protein aggregation are of immense interest in therapeutic biology and neurodegenerative medicine. Biochemical processes within the living cell occur in a highly crowded environment. The phenomenon of macromolecular crowding affects the diffusional and conformational dynamics of proteins and modulates their folding. Macromolecular crowding is reported to cause protein aggregation in some cases, so it is a cause of concern as it leads to a plethora of neurodegenerative disorders and systemic amyloidosis. To divulge the mechanism of aggregation, it is imperative to study aggregation in well-characterized model proteins in the presence of macromolecular crowder. One such protein is ribonuclease A (RNase A), which deciphers neurotoxic function in humans; therefore we decided to explore the amyloid fibrillogenesis of this thermodynamically stable protein. To elucidate the impact of crowder, dextran-70 and its monomer glucose on the aggregation profile of RNase-A various techniques such as Absorbance, Fluorescence, Fourier Transforms Infrared, Dynamic Light Scattering and circular Dichroism spectroscopies along with imaging techniques like Atomic Force Microscopy and Transmission Electron Microscopy were employed. Thermal aggregation and fibrillation were further promoted by dextran-70 while glucose counteracted the effect of the crowding agent in a concentration-dependent manner. This study shows that glucose provides stability to the protein and prevents fibrillation. Intending to combat aggregation, which is the hallmark of numerous late-onset neurological disorders and systemic amyloidosis, this investigation unveils that naturally occurring osmolytes or other co-solutes can be further exploited in novel drug design strategies.
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Affiliation(s)
- Seerat Siraj
- Molecular Enzymology Laboratory, Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Daraksha Yameen
- Molecular Enzymology Laboratory, Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Shivani Bhati
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Teeba Athar
- Molecular Enzymology Laboratory, Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Salman Khan
- Translational Research Laboratory, Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | | | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
| | - Mohammad Mahfuzul Haque
- Molecular Enzymology Laboratory, Department of Biotechnology, Jamia Millia Islamia, New Delhi, India.
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2
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Huang T, Snell KC, Kalia N, Gardezi S, Guo L, Harris ME. Kinetic analysis of RNA cleavage by coronavirus Nsp15 endonuclease: Evidence for acid base catalysis and substrate dependent metal ion activation. J Biol Chem 2023:104787. [PMID: 37149147 PMCID: PMC10158045 DOI: 10.1016/j.jbc.2023.104787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/08/2023] Open
Abstract
Understanding the functional properties of SARS-CoV-2 nonstructural proteins is essential for defining their roles in the viral life cycle, developing improved therapeutics and diagnostics, and countering future variants. Coronavirus nonstructural protein Nsp15 is a hexameric U-specific endonuclease whose functions, substrate specificity, mechanism, and dynamics have not been fully defined. Previous studies report SARS-CoV-2 Nsp15 requires Mn2+ ions for optimal activity; however, the effects of divalent ions on Nsp15 reaction kinetics have not been investigated in detail. Here, we analyzed the single and multiple turnover kinetics for model single-stranded RNA substrates. Our data confirm that divalent ions are dispensable for catalysis and show that Mn2+ activates Nsp15 cleavage of two different ssRNA oligonucleotide substrates, but not a dinucleotide. Furthermore, biphasic kinetics of ssRNA substrates demonstrates that Mn2+ stabilizes alternative enzyme states that have faster substrate cleavage on the enzyme. However, we did not detect Mn2+-induced conformational changes using CD and fluorescence spectroscopy. The pH-rate profiles in the presence and absence of Mn2+ are consistent with active site ionizable groups with similar pKas of ca. 4.8-5.2. We found the Rp stereoisomer phosphorothioate modification at the scissile phosphate had minimal effect on catalysis, which supports a mechanism involving an anionic transition state. In contrast, the Sp stereoisomer is inactive due to weak binding, consistent with models that position the non-bridging phosphoryl oxygen deep in the active site. Together, these kinetic data demonstrate that Nsp15 employs a conventional acid-base catalytic mechanism passing through an anionic transition state, and that divalent ion activation is substrate-dependent.
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Affiliation(s)
- Tong Huang
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Kimberly C Snell
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Nidhi Kalia
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Shahbaz Gardezi
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Lily Guo
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, FL 32611.
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3
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Franco LFM, Pessoa Filho PDA. Mathematical Description of the Enzymatic Activity of Proteins with Ionizable Groups Exhibiting Deviations from the Henderson-Hasselbalch Equation. Appl Biochem Biotechnol 2021; 194:1221-1234. [PMID: 34652586 DOI: 10.1007/s12010-021-03700-y] [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: 07/01/2021] [Accepted: 10/04/2021] [Indexed: 11/24/2022]
Abstract
The ionization equilibrium implied in the calculation of the specific activity is classically described through the Henderson-Hasselbalch equation. An extension for the description of anomalous ionization profiles using the Hill equation is presented in this communication. The proposed framework was applied to the description of the specific enzymatic activity curve as a function of pH of five enzymes presenting different ionization states in their active site. The developed equation improves the description of relative enzymatic curves that deviate from the bell curve predicted by the application of the Henderson-Hasselbalch equation, regardless of the ionization scheme related to the active site.
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Affiliation(s)
| | - Pedro de Alcantara Pessoa Filho
- Department of Chemical Engineering, Engineering School, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Bl. 20, Sao Paulo, SP, 05508-000, Brazil.
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4
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Mushegian A, Sorokina I, Eroshkin A, Dlakić M. An ancient evolutionary connection between Ribonuclease A and EndoU families. RNA (NEW YORK, N.Y.) 2020; 26:803-813. [PMID: 32284351 PMCID: PMC7297114 DOI: 10.1261/rna.074385.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
The ribonuclease A family of proteins is well studied from the biochemical and biophysical points of view, but its evolutionary origins are obscure, as no sequences homologous to this family have been reported outside of vertebrates. Recently, the spatial structure of the ribonuclease domain from a bacterial polymorphic toxin was shown to be closely similar to the structure of vertebrate ribonuclease A. The absence of sequence similarity between the two structures prompted a speculation of convergent evolution of bacterial and vertebrate ribonuclease A-like enzymes. We show that bacterial and homologous archaeal polymorphic toxin ribonucleases with a known or predicted ribonuclease A-like fold are distant homologs of the ribonucleases from the EndoU family, found in all domains of cellular life and in viruses. We also detected a homolog of vertebrate ribonucleases A in the transcriptome assembly of the sea urchin Mesocentrotus franciscanus These observations argue for the common ancestry of prokaryotic ribonuclease A-like and ubiquitous EndoU-like ribonucleases, and suggest a better-grounded scenario for the origin of animal ribonucleases A, which could have emerged in the deuterostome lineage, either by an extensive modification of a copy of an EndoU gene, or, more likely, by a horizontal acquisition of a prokaryotic immunity-mediating ribonuclease gene.
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Affiliation(s)
- Arcady Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, Virginia 22314, USA
| | | | | | - Mensur Dlakić
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
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5
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Chernikov IV, Vlassov VV, Chernolovskaya EL. Current Development of siRNA Bioconjugates: From Research to the Clinic. Front Pharmacol 2019; 10:444. [PMID: 31105570 PMCID: PMC6498891 DOI: 10.3389/fphar.2019.00444] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
Small interfering RNAs (siRNAs) acting via RNA interference mechanisms are able to recognize a homologous mRNA sequence in the cell and induce its degradation. The main problems in the development of siRNA-based drugs for therapeutic use are the low efficiency of siRNA delivery to target cells and the degradation of siRNAs by nucleases in biological fluids. Various approaches have been proposed to solve the problem of siRNA delivery in vivo (e.g., viruses, cationic lipids, polymers, nanoparticles), but all have limitations for therapeutic use. One of the most promising approaches to solve the problem of siRNA delivery to target cells is bioconjugation; i.e., the covalent connection of siRNAs with biogenic molecules (lipophilic molecules, antibodies, aptamers, ligands, peptides, or polymers). Bioconjugates are "ideal nanoparticles" since they do not need a positive charge to form complexes, are less toxic, and are less effectively recognized by components of the immune system because of their small size. This review is focused on strategies and principles for constructing siRNA bioconjugates for in vivo use.
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Affiliation(s)
- Ivan V Chernikov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentin V Vlassov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena L Chernolovskaya
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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6
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Michalska K, Quan Nhan D, Willett JLE, Stols LM, Eschenfeldt WH, Jones AM, Nguyen JY, Koskiniemi S, Low DA, Goulding CW, Joachimiak A, Hayes CS. Functional plasticity of antibacterial EndoU toxins. Mol Microbiol 2018; 109:509-527. [PMID: 29923643 PMCID: PMC6173971 DOI: 10.1111/mmi.14007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2018] [Indexed: 01/05/2023]
Abstract
Bacteria use several different secretion systems to deliver toxic EndoU ribonucleases into neighboring cells. Here, we present the first structure of a prokaryotic EndoU toxin in complex with its cognate immunity protein. The contact-dependent growth inhibition toxin CdiA-CTSTECO31 from Escherichia coli STEC_O31 adopts the eukaryotic EndoU fold and shares greatest structural homology with the nuclease domain of coronavirus Nsp15. The toxin contains a canonical His-His-Lys catalytic triad in the same arrangement as eukaryotic EndoU domains, but lacks the uridylate-specific ribonuclease activity that characterizes the superfamily. Comparative sequence analysis indicates that bacterial EndoU domains segregate into at least three major clades based on structural variations in the N-terminal subdomain. Representative EndoU nucleases from clades I and II degrade tRNA molecules with little specificity. In contrast, CdiA-CTSTECO31 and other clade III toxins are specific anticodon nucleases that cleave tRNAGlu between nucleotides C37 and m2 A38. These findings suggest that the EndoU fold is a versatile scaffold for the evolution of novel substrate specificities. Such functional plasticity may account for the widespread use of EndoU effectors by diverse inter-bacterial toxin delivery systems.
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Affiliation(s)
- Karolina Michalska
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL, USA.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Dinh Quan Nhan
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Julia L E Willett
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Lucy M Stols
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL, USA
| | - William H Eschenfeldt
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL, USA
| | - Allison M Jones
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Josephine Y Nguyen
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - David A Low
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
| | - Celia W Goulding
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, USA.,Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL, USA.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
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7
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Xie J, Chen Z, Zhang X, Chen H, Guan W. Identification of an RNase that preferentially cleaves A/G nucleotides. Sci Rep 2017; 7:45207. [PMID: 28322335 PMCID: PMC5359670 DOI: 10.1038/srep45207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/20/2017] [Indexed: 02/02/2023] Open
Abstract
Ribonucleases play an important role in the RNA metabolism which is critical for the localization, stability and function of mature RNA transcripts. More and more ribonucleases were discovered in recent years with the progress of technology. In the present study, we found that the uncharacterized C19orf43, a novel interacting protein of human telomerase RNA (hTR), digested T7 transcribed RNA, total cellular RNA and RNA oligos but not DNA. Thus we named this new RNase as hTRIR (human telomerase RNA interacting RNase). Genetic analysis showed that hTRIR is conserved among eukaryotic species and widely expressed in different cell lines. The RNase activity of hTRIR works in a broad temperature and pH range while divalent cations are not required. The conserved C-terminus of C19orf43 is necessary for its activity. Finally, we found that hTRIR cleaves all four unpaired RNA nucleotides from 5′ end or 3′ end with higher efficiency for purine bases, which suggested that hTRIR is an exoribonuclease. Taken together, our study showed the first evidence of the novel function of hTRIR in vitro, which provides clue to study the regulatory mechanism of hTR homeostasis in vivo.
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Affiliation(s)
- Jumin Xie
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Zhen Chen
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Xueyan Zhang
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Honghe Chen
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Wuxiang Guan
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
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8
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Harris ME, Piccirilli JA, York DM. Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1801-8. [PMID: 25936517 DOI: 10.1016/j.bbapap.2015.04.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 01/21/2023]
Abstract
The well-studied mechanism of ribonuclease A is believed to involve concerted general acid-base catalysis by two histidine residues, His12 and His119. The basic features of this mechanism are often cited to explain rate enhancement by both protein and RNA enzymes that catalyze RNA 2'-O-transphosphorylation. Recent kinetic isotope effect analyses and computational studies are providing a more chemically detailed description of the mechanism of RNase A and the rate limiting transition state. Overall, the results support an asynchronous mechanism for both solution and ribonuclease catalyzed reactions in which breakdown of a transient dianoinic phosphorane intermediate by 5'OP bond cleavage is rate limiting. Relative to non-enzymatic reactions catalyzed by specific base, a smaller KIE on the 5'O leaving group and a less negative βLG are observed for RNase A catalysis. Quantum mechanical calculations consistent with these data support a model in which electrostatic and H-bonding interactions with the non-bridging oxygens and proton transfer from His119 render departure of the 5'O less advanced and stabilize charge buildup in the transition state. Both experiment and computation indicate advanced 2'OP bond formation in the rate limiting transition state. However, this feature makes it difficult to resolve the chemical steps involved in 2'O activation. Thus, modeling the transition state for RNase A catalysis underscores those elements of its chemical mechanism that are well resolved, as well as highlighting those where ambiguity remains. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment.
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Affiliation(s)
- Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44118, United States.
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, United States; Department of Chemistry, University of Chicago, Chicago, IL 60637, United States
| | - Darrin M York
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, United States; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, United States
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9
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A simplified electrostatic model for hydrolase catalysis. Int J Biol Macromol 2015; 78:257-65. [PMID: 25881958 DOI: 10.1016/j.ijbiomac.2015.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 11/23/2022]
Abstract
Toward the development of an electrostatic model for enzyme catalysis, the active site of the enzyme is represented by a cavity whose surface (and beyond) is populated by electric charges as determined by pH and the enzyme's structure. The electric field in the cavity is obtained from electrostatics and a suitable computer program. The key chemical bond in the substrate, at its ends, has partial charges with opposite signs determined from published force-field parameters. The electric field attracts one end of the bond and repels the other, causing bond tension. If that tension exceeds the attractive force between the atoms, the bond breaks; the enzyme is then a successful catalyst. To illustrate this very simple model, based on numerous assumptions, some results are presented for three hydrolases: hen-egg white lysozyme, bovine trypsin and bovine ribonuclease. Attention is given to the effect of pH.
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10
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Leal NA, Kim HJ, Hoshika S, Kim MJ, Carrigan MA, Benner SA. Transcription, reverse transcription, and analysis of RNA containing artificial genetic components. ACS Synth Biol 2015; 4:407-13. [PMID: 25137127 DOI: 10.1021/sb500268n] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Expanding the synthetic biology of artificially expanded genetic information systems (AEGIS) requires tools to make and analyze RNA molecules having added nucleotide "letters". We report here the development of T7 RNA polymerase and reverse transcriptase to catalyze transcription and reverse transcription of xNA (DNA or RNA) having two complementary AEGIS nucleobases, 6-amino-5-nitropyridin-2-one (trivially, Z) and 2-aminoimidazo[1,2a]-1,3,5-triazin-4(8H)-one (trivially, P). We also report MALDI mass spectrometry and HPLC-based analyses for oligomeric GACUZP six-letter RNA and the use of ribonuclease (RNase) A and T1 RNase as enzymatic tools for the sequence-specific degradation of GACUZP RNA. We then applied these tools to analyze the GACUZP and GACTZP products of polymerases and reverse transcriptases (respectively) made from DNA and RNA templates. In addition to advancing this 6-letter AEGIS toward the biosynthesis of proteins containing additional amino acids, these experiments provided new insights into the biophysics of DNA.
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Affiliation(s)
- Nicole A. Leal
- Foundation
for
Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Hyo-Joong Kim
- Foundation
for
Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Shuichi Hoshika
- Foundation
for
Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Myong-Jung Kim
- Foundation
for
Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Matthew A. Carrigan
- Department
of Natural Sciences, Santa Fe College, 3000 NW 83rd Street L209, Gainesville, Florida 32606, United States
| | - Steven A. Benner
- Foundation
for
Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
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11
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Fried SD, Boxer SG. Evaluation of the energetics of the concerted acid-base mechanism in enzymatic catalysis: the case of ketosteroid isomerase. J Phys Chem B 2012; 116:690-7. [PMID: 22148842 PMCID: PMC3257410 DOI: 10.1021/jp210544w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Structures of enzymes invariably reveal the proximity of acidic and basic residues to reactive sites on the substrate, so it is natural and common to suggest that enzymes employ concerted mechanisms to catalyze their difficult reactions. Ketosteroid isomerase (KSI) has served as a paradigm of enzymatic proton transfer chemistry, and its catalytic effect has previously been attributed to concerted proton transfer. We employ a specific inhibitor that contains an IR probe that reports directly and quantitatively on the ionization state of the ligand when bound in the active site of KSI. Measurement of the fractional ionization provides a missing link in a thermodynamic cycle that can discriminate the free energy advantage of a concerted versus nonconcerted mechanism. It is found that the maximum thermodynamic advantage that KSI could capture from a concerted mechanism (ΔΔG° = 0.5 kcal mol(-1)) is quite small.
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Affiliation(s)
- Stephen D. Fried
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080
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12
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Cuchillo CM, Nogués MV, Raines RT. Bovine pancreatic ribonuclease: fifty years of the first enzymatic reaction mechanism. Biochemistry 2011; 50:7835-41. [PMID: 21838247 DOI: 10.1021/bi201075b] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fifty years ago, the group of Tony Mathias and Bob Rabin at University College London deduced the first mechanism for catalysis by an enzyme, ribonuclease [Findlay, D., Herries, D. G., Mathias, A. P., Rabin, B. R., and Ross, C. A. (1961) Nature 190, 781-784]. Here, we celebrate this historic accomplishment by surveying knowledge of enzymology and protein science at that time, facts that led to the formulation of the mechanism, criticisms and alternative mechanisms, data that supported the proposed mechanism, and some of the refinements that have since provided a more precise picture of catalysis of RNA cleavage by ribonucleases. The Mathias and Rabin mechanism has appeared in numerous textbooks, monographs, and reviews and continues to have a profound impact on biochemistry.
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Affiliation(s)
- Claudi M Cuchillo
- Departament de Bioquímica i Biologia Molecular, Unitat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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13
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van Batenburg O, Raap J, Kerling K, Havinga E. Studies on polypeptides XVIII Solid-phase synthesis of RNase S-peptide analogues with high S-protein activating ability; replacement of histidine-12 by L-homohistidine. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19760951108] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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14
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Marchiori F, Borin G, Moroder L. Studies on ribonuclease S': the role of lysine-7 for activation of S-protein. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 2009; 6:419-34. [PMID: 4376128 DOI: 10.1111/j.1399-3011.1974.tb02403.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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15
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Borin G, Toniolo C, Moroder L, Marchiori F, Rocchi R, Scoffone E. Synthesis of peptide analogs of the N-terminal eicosapeptide sequence of ribonuclease A. XV. Synthesis and guanidination of(Orn 10 ,Orn 12 )S-peptide. INTERNATIONAL JOURNAL OF PROTEIN RESEARCH 2009; 4:37-45. [PMID: 5016602 DOI: 10.1111/j.1399-3011.1972.tb03396.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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16
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Lee JE, Bae E, Bingman CA, Phillips GN, Raines RT. Structural basis for catalysis by onconase. J Mol Biol 2007; 375:165-77. [PMID: 18001769 DOI: 10.1016/j.jmb.2007.09.089] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2007] [Accepted: 09/20/2007] [Indexed: 11/18/2022]
Abstract
Onconase (ONC) is a homolog of bovine pancreatic ribonuclease (RNase A) from the frog Rana pipiens. ONC displays antitumoral activity and is in advanced clinical trials for the treatment of cancer. Here, we report the first atomic structures of ONC-nucleic acid complexes: a T89N/E91A ONC-5'-AMP complex at 1.65 A resolution and a wild-type ONC-d(AUGA) complex at 1.90 A resolution. The latter structure and site-directed mutagenesis were used to reveal the atomic basis for substrate recognition and turnover by ONC. The residues in ONC that are proximal to the scissile phosphodiester bond (His10, Lys31, and His97) and uracil nucleobase (Thr35, Asp67, and Phe98) are conserved from RNase A and serve to generate a similar bell-shaped pH versus k(cat)/K(M) profile for RNA cleavage. Glu91 of ONC forms two hydrogen bonds with the guanine nucleobase in d(AUGA), and Thr89 is in close proximity to that nucleobase. Installing a neutral or cationic residue at position 91 or an asparagine residue at position 89 virtually eliminated the 10(2)-fold guanine:adenine preference of ONC. A variant that combined such substitutions, T89N/E91A ONC, actually preferred adenine over guanine. In contrast, installing an arginine residue at position 91 increased the guanine preference and afforded an ONC variant with the highest known k(cat)/K(M) value. These data indicate that ONC discriminates between guanine and adenine by using Coulombic interactions and a network of hydrogen bonds. The structure of the ONC-d(AUGA) complex was also used to probe other aspects of catalysis. For example, the T5R substitution, designed to create a favorable Coulombic interaction between ONC and a phosphoryl group in RNA, increased ribonucleolytic activity by twofold. No variant, however, was more toxic to human cancer cells than wild-type ONC. Together, these findings provide a cynosure for understanding catalysis of RNA cleavage in a system of high medicinal relevance.
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Affiliation(s)
- J Eugene Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
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17
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Cleland WW. Determining the chemical mechanisms of enzyme-catalyzed reactions by kinetic studies. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 45:273-387. [PMID: 21524 DOI: 10.1002/9780470122907.ch4] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Cai L, Cao A, Lai L. An isothermal titration calorimetric method to determine the kinetic parameters of enzyme catalytic reaction by employing the product inhibition as probe. Anal Biochem 2001; 299:19-23. [PMID: 11726179 DOI: 10.1006/abio.2001.5397] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An isothermal titration calorimetric (ITC) method was developed to measure the kinetic parameters of ribonuclease A catalytic hydrolysis of cytidine 2',3'-cyclic monophosphate. Employing the inhibition of product as a probe, the K(m), K(i), k(c), and DeltaH(m) can be determined by two simple calorimetric measurements. First, the substrate was titrated into the cell containing high concentration of enzyme. The molar reaction heat was calculated from the titration peak area divided by substrate moles per titration, and the initial catalytic reaction rate in the presence of various concentrations of product can be calculated from the peak height and the molar reaction heat. From Michaelis-Menten function in the presence of inhibitors, the relationship between K(m) and K(i) can be obtained. Then, the dissociation constant, which is equal to K(i), was measured by a regular ITC experiment. Thus, K(m) and k(c) can be calculated. The method developed here can be applied in other enzyme catalytic systems with inhibitive products.
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Affiliation(s)
- L Cai
- Institute of Physical Chemistry, College of Chemistry and Molecular Engineering, State Key Laboratory for Structural Chemistry of Stable and Unstable Species, Peking University, Beijing 100871, China
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19
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Ushijima K, Shirakawa M, Kagoshima K, Park WS, Miyano-Kurosaki N, Takaku H. Anti-HIV-1 activity of an antisense phosphorothioate oligonucleotide bearing imidazole and primary amine groups. Bioorg Med Chem 2001; 9:2165-9. [PMID: 11504653 DOI: 10.1016/s0968-0896(01)00126-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We have previously shown that RNA cleaving reagents with imidazole and primary amine groups on the 5'-end of antisense oligodeoxyribonucleotides could site-specifically cleave CpA as the target sequence of the substrate tRNA in vitro. In this study, a RNA cleaving reagent, composed of imidazole and primary amine groups on an antisense phosphorothioate oligonucleotide (Im-anti-s-ODN), was synthesized and evaluated for anti-HIV-1 activity in MT-4 cells. The sequence of the Im-anti-s-ODN was designed to be complementary to the HIV-1 gag-mRNA and to bind adjacent to the CpA cleavage site position. Im-anti-s-ODN encapsulated with the transfection reagent, DMRIE-C, had higher anti-HIV-1 activity than the unmodified antisense phosphorothioate oligonucleotide (anti-s-ODN) at a 2 microM concentration. Furthermore, the Im-anti-ODN encapsulated with DMRIE-C conferred sequence-specific inhibition.
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Affiliation(s)
- K Ushijima
- Department of Industrial Chemistry, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Japan
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20
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Rupert PB, Ferré-D'Amaré AR. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature 2001; 410:780-6. [PMID: 11298439 DOI: 10.1038/35071009] [Citation(s) in RCA: 358] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The hairpin ribozyme catalyses sequence-specific cleavage of RNA. The active site of this natural RNA results from the docking of two irregular helices: stems A and B. One strand of stem A harbours the scissile bond. The 2.4 A resolution structure of a hairpin ribozyme-inhibitor complex reveals that the ribozyme aligns the 2'-OH nucleophile and the 5'-oxo leaving group by twisting apart the nucleotides that flank the scissile phosphate. The base of the nucleotide preceding the cleavage site is stacked within stem A; the next nucleotide, a conserved guanine, is extruded from stem A and accommodated by a highly complementary pocket in the minor groove of stem B. Metal ions are absent from the active site. The bases of four conserved purines are positioned potentially to serve as acid-base catalysts. This is the first structure determination of a fully assembled ribozyme active site that catalyses a phosphodiester cleavage without recourse to metal ions.
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Affiliation(s)
- P B Rupert
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA
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21
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Griffith EC, Su Z, Niwayama S, Ramsay CA, Chang YH, Liu JO. Molecular recognition of angiogenesis inhibitors fumagillin and ovalicin by methionine aminopeptidase 2. Proc Natl Acad Sci U S A 1998; 95:15183-8. [PMID: 9860943 PMCID: PMC28017 DOI: 10.1073/pnas.95.26.15183] [Citation(s) in RCA: 189] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Angiogenesis inhibitors are a novel class of promising therapeutic agents for treating cancer and other human diseases. Fumagillin and ovalicin compose a class of structurally related natural products that potently inhibit angiogenesis by blocking endothelial cell proliferation. A synthetic analog of fumagillin, TNP-470, is currently undergoing clinical trials for treatment of a variety of cancers. A common target for fumagillin and ovalicin recently was identified as the type 2 methionine aminopeptidase (MetAP2). These natural products bind MetAP2 covalently, inhibiting its enzymatic activity. The specificity of this binding is underscored by the lack of inhibition of the closely related type 1 enzyme, MetAP1. The molecular basis of the high affinity and specificity of these inhibitors for MetAP2 has remained undiscovered. To determine the structural elements of these inhibitors and MetAP2 that are involved in this interaction, we synthesized fumagillin analogs in which each of the potentially reactive epoxide groups was removed either individually or in combination. We found that the ring epoxide in fumagillin is involved in the covalent modification of MetAP2, whereas the side chain epoxide group is dispensable. By using a fumagillin analog tagged with fluorescein, His-231 in MetAP2 was identified as the residue that is covalently modified by fumagillin. Site-directed mutagenesis of His-231 demonstrated its importance for the catalytic activity of MetAP2 and confirmed that the same residue is covalently modified by fumagillin. These results, in agreement with a recent structural study, suggest that fumagillin and ovalicin inhibit MetAP2 by irreversible blockage of the active site.
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Affiliation(s)
- E C Griffith
- Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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22
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Sowa GA, Hengge AC, Cleland WW. 18O Isotope Effects Support a Concerted Mechanism for Ribonuclease A. J Am Chem Soc 1997. [DOI: 10.1021/ja963974t] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gwendolyn A. Sowa
- Institute for Enzyme Research and Department of Biochemistry, University of WisconsinMadison Madison, Wisconsin 53705
| | - Alvan C. Hengge
- Institute for Enzyme Research and Department of Biochemistry, University of WisconsinMadison Madison, Wisconsin 53705
| | - W. W. Cleland
- Institute for Enzyme Research and Department of Biochemistry, University of WisconsinMadison Madison, Wisconsin 53705
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23
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Toiron C, González C, Bruix M, Rico M. Three-dimensional structure of the complexes of ribonuclease A with 2',5'-CpA and 3',5'-d(CpA) in aqueous solution, as obtained by NMR and restrained molecular dynamics. Protein Sci 1996; 5:1633-47. [PMID: 8844852 PMCID: PMC2143484 DOI: 10.1002/pro.5560050817] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The three-dimensional structure of the complexes of ribonuclease A with cytidyl-2',5'-adenosine (2',5'-CpA) and deoxycytidyl-3',5'-deoxyadenosine [3',5'-d(CpA)] in aqueous solution has been determined by 1H NMR methods in combination with restrained molecular dynamics calculations. Twenty-three intermolecular NOE cross-corrections for the 3',5'-d(CpA) complex and 19 for the 2',5'-CpA, together with about 1,000 intramolecular NOEs assigned for each complex, were translated into distance constraints and used in the calculation. No significant changes in the global structure of the enzyme occur upon complex formation. The side chains of His 12, Thr 45, His 119, and the amide backbone group of Phe 120 are involved directly in the binding of the ligands at the active site. The conformation of the two bases is anti in the two complexes, but differs from the crystal structure in the conformation of the two sugar rings in 3',5'-d(CpA), shown to be in the S-type region, as deduced from an analysis of couplings between the ribose protons. His 119 is found in the two complexes in only one conformation, corresponding to position A in the free protein. Side chains of Asn 67, Gln 69, Asn 71, and Glu 111 from transient hydrogen bonds with the adenine base, showing the existence of a pronounced flexibility of these enzyme side chains at the binding site of the downstream adenine. All other general features on the structures coincide clearly with those observed in the crystal state.
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Affiliation(s)
- C Toiron
- Instituto de Estructura de la Materia, CSIC, Madrid, Spain
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24
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Zegers I, Maes D, Dao-Thi MH, Poortmans F, Palmer R, Wyns L. The structures of RNase A complexed with 3'-CMP and d(CpA): active site conformation and conserved water molecules. Protein Sci 1994; 3:2322-39. [PMID: 7756988 PMCID: PMC2142771 DOI: 10.1002/pro.5560031217] [Citation(s) in RCA: 140] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The interactions of RNase A with cytidine 3'-monophosphate (3'-CMP) and deoxycytidyl-3',5'-deoxyadenosine (d(CpA)) were analyzed by X-ray crystallography. The 3'-CMP complex and the native structure were determined from trigonal crystals, and the d(CpA) complex from monoclinic crystals. The differences between the overall structures are concentrated in loop regions and are relatively small. The protein-inhibitor contacts are interpreted in terms of the catalytic mechanism. The general base His 12 interacts with the 2' oxygen, as does the electrostatic catalyst Lys 41. The general acid His 119 has 2 conformations (A and B) in the native structure and is found in, respectively, the A and the B conformation in the d(CpA) and the 3'-CMP complex. From the present structures and from a comparison with RNase T1, we propose that His 119 is active in the A conformation. The structure of the d(CpA) complex permits a detailed analysis of the downstream binding site, which includes His 119 and Asn 71. The comparison of the present RNase A structures with an inhibitor complex of RNase T1 shows that there are important similarities in the active sites of these 2 enzymes, despite the absence of any sequence homology. The water molecules were analyzed in order to identify conserved water sites. Seventeen water sites were found to be conserved in RNase A structures from 5 different space groups. It is proposed that 7 of those water molecules play a role in the binding of the N-terminal helix to the rest of the protein and in the stabilization of the active site.
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Affiliation(s)
- I Zegers
- Institute of Molecular Biology, Vrije Universiteit Brussel, St. Genesius Rode, Belgium
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25
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Fontecilla-Camps J, de Llorens R, le Du M, Cuchillo C. Crystal structure of ribonuclease A.d(ApTpApApG) complex. Direct evidence for extended substrate recognition. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)31836-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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26
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de Mel VS, Doscher MS, Martin PD, Edwards BF. The occupancy of two distinct conformations by active-site histidine-119 in crystals of ribonuclease is modulated by pH. FEBS Lett 1994; 349:155-60. [PMID: 8045294 DOI: 10.1016/0014-5793(94)00664-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Structures of a semisynthetic RNase have been obtained to a resolution of 2.0 A at pH values of 5.2, 6.5, 7.5, and 8.8, respectively. The principle structural transformation occurring over this pH range is the conversion of the side chain of active site residue His-119 from one conformation (chi 1 = -43 degrees to -57 degrees) at low pH to another (chi 1 = +159 degrees to +168 degrees) at higher pH values. On the basis of this observation, a model is proposed that reconciles the disparate pK values for His-119 in the enzyme-substrate complex that have been deduced from kinetic studies and from proton NMR measurements in the presence of pseudosubstrates.
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Affiliation(s)
- V S de Mel
- Department of Biochemistry, Wayne State University School of Medicine, Detroit, MI 48201
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27
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Veenstra TD, Lee L. NMR study of the positions of His-12 and His-119 in the ribonuclease A-uridine vanadate complex. Biophys J 1994; 67:331-5. [PMID: 7919003 PMCID: PMC1225363 DOI: 10.1016/s0006-3495(94)80485-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The binding of uridine vanadate to ribonuclease A has been investigated by one- and two-dimensional 1H NMR. The homonuclear Nuclear Overhauser and exchange spectroscopy spectrum of the uridine vanadate/RNase A complex exhibits cross peaks between both the C5H and C6H protons of uridine vanadate and the H epsilon 1 proton of His-12 of ribonuclease A. These cross peaks suggest that the H epsilon 1 proton of His-12 is in the vicinity of the uracil base of uridine vanadate, as observed in the crystallographic structure of the uridine vanadate/RNase A complex. However, no cross peaks are observed between the C5H and C6H protons of uridine vanadate and the H epsilon 1 proton of His-119 of ribonuclease A, although they were predicted based upon the distances calculated from coordinates of the crystallographic structure of the complex. These results suggest that there is a significant difference between the positioning of the His-119 side chain in the solution and in the crystallographic structures.
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Affiliation(s)
- T D Veenstra
- Department of Chemistry and Biochemistry, University of Windsor, Ontario, Canada
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28
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deMel VS, Martin PD, Doscher MS, Edwards BF. Structural changes that accompany the reduced catalytic efficiency of two semisynthetic ribonuclease analogs. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)48486-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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29
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Correlation of Crystal Data and Charge Density with the Reactivity and Activity of Molecules: Towards a Description of Elementary Steps in Enzyme Reactions. ACTA ACUST UNITED AC 1991. [DOI: 10.1007/978-1-4615-3700-7_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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30
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Martin PD, Doscher MS, Edwards BF. The refined crystal structure of a fully active semisynthetic ribonuclease at 1.8-A resolution. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)47678-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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31
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Eftink M, Biltonen R. Chapter 7 Pancreatic ribonuclease A: the most studied endoribonuclease. ACTA ACUST UNITED AC 1987. [DOI: 10.1016/s0167-7306(09)60021-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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32
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Nishikawa S, Morioka H, Fuchimura K, Tanaka T, Uesugi S, Ohtsuka E, Ikehara M. Modification of Glu 58, an amino acid of the active center of ribonuclease T1, to Gln and Asp. Biochem Biophys Res Commun 1986; 138:789-94. [PMID: 2874806 DOI: 10.1016/s0006-291x(86)80566-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Glu 58 is one of the amino acids which participates in its catalytic action of ribonuclease T1. We mutated this residue to Gln 58 or Asp 58 by genetic engineering using chemically synthesized genes. The mutant enzymes were expressed in E. coli as fused proteins and purified to homogeniety on SDS-PAGE after cleavage with cyanogen bromide. Their activities in hydrolyzing pGpC were reduced to 10% in the Asp 58 mutant and about 1% in the Gln 58 mutant compared to that of the wild-type enzyme. These results suggest that Glu 58 is important but not essential for catalysis of ribonuclease T1.
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33
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Borah B, Chen CW, Egan W, Miller M, Wlodawer A, Cohen JS. Nuclear magnetic resonance and neutron diffraction studies of the complex of ribonuclease A with uridine vanadate, a transition-state analogue. Biochemistry 1985; 24:2058-67. [PMID: 4016100 DOI: 10.1021/bi00329a038] [Citation(s) in RCA: 129] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The complex of ribonuclease A (RNase A) with uridine vanadate (U-V), a transition-state analogue, has been studied with 51V and proton NMR spectroscopy in solution and by neutron diffraction in the crystalline state. Upon the addition of aliquots of U-V at pH 6.6, the C epsilon-H resonances of the two active-site histidine residues 119 and 12 decrease in intensity while four new resonances appear. Above pH 8 and below pH 5, these four resonances decrease in intensity as the complex dissociates. These four resonances are assigned to His-119 and His-12 in protonated and unprotonated forms in the RNase-U-V complex. These resonances do not titrate or change in relative area in the pH range 5-8, indicating a slow protonation process, and the extent of protonation remains constant with ca. 58% of His-12 and ca. 26% of His-119 being protonated. The results of diffraction studies show that both His-12 and His-119 occupy well-defined positions in the RNase-U-V complex and that both are protonated. However, while the classic interpretation of the mechanism of action of RNase based on the proposal of Findlay et al. [Findlay, D., Herries, D. G., Mathias, A. P., Rabin, B. R., & Ross, C. A. (1962) Biochem. J. 85, 152-153] requires both His-12 and His-119 to be in axial positions relative to the pentacoordinate transition state, in the diffraction structure His-12 is found to be in an equatorial position, while Lys-41 is close to an axial position. Hydrogen exchange data show that the mobility and accessibility of amides in the RNase-U-V complex do not significantly differ from what was observed in the native enzyme. The results of both proton NMR in solution and neutron diffraction in the crystal are compared and interpreted in terms of the mechanism of action of RNase.
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34
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Douzou P, Petsko GA. Proteins at Work: “Stop-Action” Pictures at Subzero Temperatures. ADVANCES IN PROTEIN CHEMISTRY 1984. [DOI: 10.1016/s0065-3233(08)60299-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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35
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36
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37
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Photodynamic studies on acid ribonuclease from pea cotyledons. ACTA ACUST UNITED AC 1981. [DOI: 10.1007/bf01948353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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38
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Biosca JA, Cuchillo CM. Thermodynamic studies on the hydrolysis of cytidine 2':3'-phosphate by bovine pancreatic ribonuclease A. A possible effect of the change of the structure of water. Biochem J 1980; 189:655-7. [PMID: 7213352 PMCID: PMC1162049 DOI: 10.1042/bj1890655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The temperature-dependence of the ribonuclease A-catalysed hydrolysis of cytidine 2':3'-phosphate was studied in the range of temperatures 0--40 degrees C. A break at 4 degrees C was found both in the Arrhenius and the van't Hoff plots. It is likely that the transition observed is due to the change in the structure of water.
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39
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Santoro J, Juretschke HP, Rüterjans H. 13C NMR investigations on Npi-[13C1]carboxymethyl-histidine-119 ribonuclease. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 537:304-9. [PMID: 31923 DOI: 10.1016/0005-2795(78)90513-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ribonuclease A derivative Npi-[13C1]carboxymethyl-histine-119 ribonuclease prepared by using [13C1]bromoacetate as alkylating reagent has been investigated with high resolution 13C NMR spectroscopy. In the 13C NMR spectra two carbon resonances of relatively high intensity appear which can be assigned to carboxyl groups attached to His-119 and Met-30, their intensity ratio being 10 : 1. The pH dependence of the carbon resonance of the carboxy-methyl group bound to the Npi of His-119 differs in the absence and presence of Cyd-2'-P, thus indicating that the catalytically inactive derivative does bind nucleotides. A mechanism of the alkylation reaction at pH 5.6 is proposed in which the epsilon-amino group of Lys-41 acts as the binding site for the carboxyl group of bromoacetate pushing the bromomethylene group towards the Npi of His-119 or the Ntau of His-12.
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40
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41
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Schneider F. Histidine in enzyme active centers. ANGEWANDTE CHEMIE (INTERNATIONAL ED. IN ENGLISH) 1978; 17:583-92. [PMID: 101098 DOI: 10.1002/anie.197805831] [Citation(s) in RCA: 90] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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42
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van Batenburg OD, Voskuyl-Holtkamp I, Schattenkerk C, Hoes K, Kerling KE, Havinga E. The role of the imidazolyl nitrogen atoms of histidine-12 in ribonuclease S. Biochem J 1977; 163:385-7. [PMID: 869932 PMCID: PMC1164708 DOI: 10.1042/bj1630385] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
S-peptide (residues 1--14) analogues in which the active histidine-12 residue is replaced by Npi-methyl-L-histidine, Ntau-methyl-L-histidine and beta-(pyrid-3-yl)-L-alanine were synthesized and tested for their capacity to bind to S-protein and to activate it. The results show that both imidazolyl nitrogen atoms are required for optimal catalytic functioning, Ntau being essential to the catalytic reaction itself, Npi playing a role in keeping the imidazole ring in the correct position.
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43
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44
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Haar W, Maurer W, Rüterjans H. Proton-magnetic-resonance studies of complexes of pancreatic ribonuclease A with pyrimidine and purine nucleotides. EUROPEAN JOURNAL OF BIOCHEMISTRY 1974; 44:201-11. [PMID: 4853930 DOI: 10.1111/j.1432-1033.1974.tb03474.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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45
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Affinity Labeling of the Active Center of l-Aspartate-β-decarboxylase with β-Chloro-l-alanine. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42913-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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46
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Abstract
Diethyl pyrocarbonate inactivates muscle pyruvate kinase with the substitution of 3-4 histidine residues per subunit. Phosphoenolpyruvate, ATP and ADP to a lesser extent, and Mg(2+) and pyruvate to a small extent, protect against inactivation.
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47
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Walz FG. Kinetic and equilibrium studies on the interaction of ribonuclease A and 2'1-deoxyuridine 3'-phosphate. Biochemistry 1971; 10:2156-62. [PMID: 5562835 DOI: 10.1021/bi00787a031] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
49
|
|
50
|
Krishnaswamy M, Kenkare UW. The Effect of pH, Temperature, and Organic Solvents on the Kinetic Parameters of Escherichia coli Alkaline Phosphatase. J Biol Chem 1970. [DOI: 10.1016/s0021-9258(18)62941-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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