1
|
Neelam, Singh H. 1H, 15N and 13C resonance assignments of S2A mutant of human carbonic anhydrase II. BIOMOLECULAR NMR ASSIGNMENTS 2024; 18:45-49. [PMID: 38520652 DOI: 10.1007/s12104-024-10166-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/22/2024] [Indexed: 03/25/2024]
Abstract
In preparation for a detailed exploration of the structural and functional aspects of the Ser2Ala mutant of human carbonic anhydrase II, we present here almost complete sequence-specific resonance assignments for 1H, 15N, and 13C. The mutation of serine to alanine at position 2, located in the N-terminal region of the enzyme, significantly alters the hydrophilic nature of the site, rendering it hydrophobic. Consequently, there is an underlying assumption that this mutation would repel water from the site. However, intriguingly, comparative analysis of the mutant structure with the wild type reveals minimal discernible differences. These assignments serve as the basis for in-depth studies on histidine dynamics, protonation states, and its intricate role in protein-water interactions and catalysis.
Collapse
Affiliation(s)
- Neelam
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Berhampur, Odisha, 760010, India
| | - Himanshu Singh
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Berhampur, Odisha, 760010, India.
| |
Collapse
|
2
|
Shitov DA, Krutin DV, Tupikina EY. Mutual influence of non-covalent interactions formed by imidazole: A systematic quantum-chemical study. J Comput Chem 2024; 45:1046-1060. [PMID: 38216334 DOI: 10.1002/jcc.27309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/14/2024]
Abstract
Imidazole is a five-membered heterocycle that is part of a number of biologically important molecules such as the amino acid histidine and the hormone histamine. Imidazole has a unique ability to participate in a variety of non-covalent interactions involving the NH group, the pyridine-like nitrogen atom or the π-system. For many biologically active compounds containing the imidazole moiety, its participation in formation of hydrogen bond NH⋯O/N and following proton transfer is the key step of mechanism of their action. In this work a systematic study of the mutual influence of various paired combinations of non-covalent interactions (e.g., hydrogen bonds and π-interactions) involving the imidazole moiety was performed by means of quantum chemistry (PW6B95-GD3/def2-QZVPD) for a series of model systems constructed based on analysis of available x-ray data. It is shown that for considered complexes formation of additional non-covalent interactions can only enhance the proton-donating ability of imidazole. At the same time, its proton-accepting ability can be both enhanced and weakened, depending on what additional interactions are added to a given system. The mutual influence of non-covalent interactions involving imidazole can be classified as weak geometric and strong energetic cooperativity-a small change in the length of non-covalent interaction formed by imidazole can strongly influence its strength. The latter can be used to develop methods for controlling the rate and selectivity of chemical reactions involving the imidazole fragment in larger systems. It is shown that the strong mutual influence of non-covalent interactions involving imidazole is due to the unique ability of the imidazole ring to effectively redistribute electron density in non-covalently bound systems with its participation.
Collapse
Affiliation(s)
- Daniil A Shitov
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Danil V Krutin
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Elena Yu Tupikina
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| |
Collapse
|
3
|
Gong K, Meng Y, Zare RN, Xie J. Molecular Mechanism for Converting Carbon Dioxide Surrounding Water Microdroplets Containing 1,2,3-Triazole to Formic Acid. J Am Chem Soc 2024; 146:8576-8584. [PMID: 38488449 DOI: 10.1021/jacs.4c00529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Spraying water microdroplets containing 1,2,3-triazole (Tz) has been found to effectively convert gas-phase carbon dioxide (CO2), but not predissolved CO2, into formic acid (FA). Herein, we elucidate the reaction mechanism at the molecular level through quantum chemistry calculations and ab initio molecular dynamics (AIMD) simulations. Computations suggest a multistep reaction mechanism that initiates from the adsorption of CO2 by Tz to form a CO2-Tz complex (named reactant complex (RC)). Then, the RC either is reduced by electrons that were generated at the air-liquid interface of the water microdroplet and then undergoes intramolecular proton transfer (PT) or switches the reduction and PT steps to form a [HCO2-(Tz-H)]- complex (named PC-). Subsequently, PC- undergoes reduction and the C-N bond dissociates to generate COOH- and [Tz-H]- (m/z = 69). COOH- easily converts to HCOOH and is captured at m/z = 45 in mass spectroscopy. Notably, the intramolecular PT step can be significantly lowered by the oriented electric field at the interface and a water-bridge mechanism. The mechanism is further confirmed by testing multiple azoles. The AIMD simulations reveal a novel proton transfer mechanism where water serves as a transporter and is shown to play an important role dynamically. Moreover, the transient •COOH captured by the experiment is proposed to be partly formed by the reaction with H•, pointing again to the importance of the air-water interface. This work provides valuable insight into the important mechanistic, kinetic, and dynamic features of converting gas-phase CO2 to valuable products by azoles or amines dissolved in water microdroplets.
Collapse
Affiliation(s)
- Ke Gong
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Yifan Meng
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Richard N Zare
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jing Xie
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| |
Collapse
|
4
|
Hellmold N, Eberwein M, Phan MHT, Kümmel S, Einsle O, Deobald D, Adrian L. Dehalococcoides mccartyi strain CBDB1 takes up protons from the cytoplasm to reductively dehalogenate organohalides indicating a new modus of proton motive force generation. Front Microbiol 2023; 14:1305108. [PMID: 38192294 PMCID: PMC10772276 DOI: 10.3389/fmicb.2023.1305108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
Proton translocation across the cytoplasmic membrane is a vital process for all organisms. Dehalococcoides strains are strictly anaerobic organohalide respiring bacteria that lack quinones and cytochromes but express a large membrane-bound protein complex (OHR complex) proposed to generate a proton gradient. However, its functioning is unclear. By using a dehalogenase-based enzyme activity assay with deuterium-labelled water in various experimental designs, we obtained evidence that the halogen atom of the halogenated electron acceptor is substituted with a proton from the cytoplasm. This suggests that the protein complex couples exergonic electron flux through the periplasmic subunits of the OHR complex to the endergonic transport of protons from the cytoplasm across the cytoplasmic membrane against the proton gradient to the halogenated electron acceptor. Using computational tools, we located two proton-conducting half-channels in the AlphaFold2-predicted structure of the OmeB subunit of the OHR complex, converging in a highly conserved arginine residue that could play a proton gatekeeper role. The cytoplasmic proton half-channel in OmeB is connected to a putative proton-conducting path within the reductive dehalogenase subunit. Our results indicate that the reductive dehalogenase and its halogenated substrate serve as both electron and proton acceptors, providing insights into the proton translocation mechanism within the OHR complex and contributing to a better understanding of energy conservation in D. mccartyi strains. Our results reveal a very simple mode of energy conservation in anaerobic bacteria, showing that proton translocation coupled to periplasmic electron flow might have importance also in other microbial processes and biotechnological applications.
Collapse
Affiliation(s)
- Nadine Hellmold
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Marie Eberwein
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - My Hanh Thi Phan
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Steffen Kümmel
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Oliver Einsle
- Institute of Biochemistry, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany
| | - Darja Deobald
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Lorenz Adrian
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| |
Collapse
|
5
|
Zaman N, Azam SS. Discrete Dynamics of Warhead Modulation on Covalent Inhibition of Oxyr: A QM/MM Study. J Phys Chem B 2023. [PMID: 37377002 DOI: 10.1021/acs.jpcb.2c07376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
The bacterial transcriptional factor OxyR, a peroxide sensor conserved in bacterial virulence pathways, has the capability to exhibit exceptional reactivity toward hydrogen peroxide (H2O2). H2O2 is essential for oxidizing cysteine thiolates to maintain cellular redox homeostasis and is dispensable for bacterial growth that can potentially mitigate drug resistance, thus underlining OxyR as a valuable target. We employ quantum mechanics/molecular mechanics (QM/MM) umbrella sampling (US) simulations at the DFTB3/MM level of theory and propose a reaction mechanism with four potential covalent inhibitors. The potential of mean force reveals the direct role of intrinsic reactivity of inhibitors, for instance, benzothiophenes and modified experimental inhibitors with methyl oxo-enoate warhead-activated carbonyl samples in the first step of reaction, which shed light on the significance of proton transfer indispensable for full inhibition, whereas the nitrile inhibitor undergoes a stepwise mechanism with a small proton-transfer energy barrier and lower imaginary frequencies that materialize instantly after nucleophilic attack. To unveil the molecular determinants of respective binding affinities, transition states along the reaction path are optimized and characterized with B3LYP 6-31+G(d,p). Furthermore, the post-simulation analysis indicates the catalytic triad (His130/Cys199/Thr129), thermodynamically favored for inhibition, which restricts water molecules from acting as the potential source of protonation/deprotonation. This study thus serves as a preamble to add variation in the proposed structures and unveils the impact of functional groups lying in warheads that modulate the kinetics of proton transfer, which will certainly aid to design more selective and efficient irreversible inhibitors of OxyR.
Collapse
Affiliation(s)
- Naila Zaman
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| |
Collapse
|
6
|
Butcher RJ, Purdy AP. 2-Ethyl-4-methyl-1 H-imidazol-3-ium bromide. IUCRDATA 2022; 7:x221172. [PMID: 36628188 PMCID: PMC9815129 DOI: 10.1107/s2414314622011725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
In the title mol-ecular salt, C6H11N2 +·Br-, the components are linked by N-H⋯Br⋯H-N hydrogen bonds into C(8)chains of alternating cations and anions propagating in the b-axis direction; these chains are cross-linked in the c-axis direction by weak C-H⋯Br hydrogen bonds.
Collapse
Affiliation(s)
- Ray J. Butcher
- Department of Chemistry, Howard University, 525 College Street NW, Washington DC 20059, USA,Correspondence e-mail:
| | - Andrew P. Purdy
- Chemistry Division, Code 6123, Naval Research Laboratory, 4555 Overlook Av, SW, Washington DC 20375-5342, USA
| |
Collapse
|
7
|
Queen A, Bhutto HN, Yousuf M, Syed MA, Hassan MI. Carbonic anhydrase IX: A tumor acidification switch in heterogeneity and chemokine regulation. Semin Cancer Biol 2022; 86:899-913. [PMID: 34998944 DOI: 10.1016/j.semcancer.2022.01.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/30/2021] [Accepted: 01/03/2022] [Indexed: 02/07/2023]
Abstract
The primary physiological process of respiration produces carbon dioxide (CO2) that reacts with water molecules which subsequently liberates bicarbonate (HCO-3) and protons. Carbonic anhydrases (CAs) are the primary catalyst involved in this conversion. More than 16 isoforms of human CAs show organ or subcellular specific activity. Dysregulation of each CA is associated with multiple pathologies. Out of these members, the overexpression of membrane-bound carbonic anhydrase IX (CAIX) is associated explicitly with hypoxic tumors or various solid cancers. CAIX helps tumors deal with higher CO2 by sequestering it with bicarbonate ions and helping cancer cells to grow in a comparatively hypoxic or acidic environment, thus acting as a pH adaptation switch. CAIX-mediated adaptations in cancer cells include angiogenesis, metabolic alterations, tumor heterogeneity, drug resistance, and regulation of cancer-specific chemokines. This review comprehensively collects and describe the cancer-specific expression mechanism and role of CAIX in cancer growth, progression, heterogeneity, and its structural insight to develop future combinatorial targeted cancer therapies.
Collapse
Affiliation(s)
- Aarfa Queen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Humaira Naaz Bhutto
- Department of Biotechnology, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohd Yousuf
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mansoor Ali Syed
- Department of Biotechnology, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
| |
Collapse
|
8
|
Kumar S, Deshpande PA. Efficient proton shuttle makes SazCA an excellent CO 2 hydration enzyme. J Biomol Struct Dyn 2022:1-10. [PMID: 35862658 DOI: 10.1080/07391102.2022.2100828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The fastest member of the carbonic anhydrase family catalysing the reversible hydration of carbon dioxide to bicarbonate ions has been recently reported to be SazCA. While thermostable, this enzyme shows exceptional activity at 353 K for the reaction. This study explores the molecular basis for the exceptional activity of SazCA, in contrast to SspCA, probed using molecular dynamics simulations. Our simulations, carried out at different temperatures, indicate the presence of efficient proton shuttle between the active zinc centre and His64 residue in the two enzymes. The proton accepting His64 residue was identified to have in and out conformations with the in conformations being supportive to proton acceptance. Our simulations show a large population of in conformations in SazCA making the enzyme exhibit an exceptional activity. The RMSF and H-bonds analysis confirmed the role of His2 and His207 in supporting the attainment of in conformations in SazCA resulting in exceptional activity.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shashi Kumar
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Parag A Deshpande
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India
| |
Collapse
|
9
|
Post-translational modifications in tumor-associated carbonic anhydrases. Amino Acids 2021; 54:543-558. [PMID: 34436666 DOI: 10.1007/s00726-021-03063-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/05/2021] [Indexed: 12/31/2022]
Abstract
Human carbonic anhydrases IX (hCA IX) and XII (hCA XII) are two proteins associated with tumor formation and development. These enzymes have been largely investigated both from a biochemical and a functional point of view. However, limited data are currently available on the characterization of their post-translational modifications (PTMs) and the functional implication of these structural changes in the tumor environment. In this review, we summarize existing literature data on PTMs of hCA IX and hCA XII, such as disulphide bond formation, phosphorylation, O-/N-linked glycosylation, acetylation and ubiquitination, highlighting, when possible, their specific role in cancer pathological processes.
Collapse
|
10
|
Di Fiore A, Supuran CT, Scaloni A, De Simone G. Human carbonic anhydrases and post-translational modifications: a hidden world possibly affecting protein properties and functions. J Enzyme Inhib Med Chem 2021; 35:1450-1461. [PMID: 32648529 PMCID: PMC7470082 DOI: 10.1080/14756366.2020.1781846] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Human carbonic anhydrases (CAs) have become a well-recognized target for the design of inhibitors and activators with biomedical applications. Accordingly, an enormous amount of literature is available on their biochemical, functional and structural aspects. Nevertheless post-translational modifications (PTMs) occurring on these enzymes and their functional implications have been poorly investigated so far. To fill this gap, in this review we have analysed all PTMs occurring on human CAs, as deriving from the search in dedicated databases, showing a widespread occurrence of modification events in this enzyme family. By combining these data with sequence alignments, inspection of 3 D structures and available literature, we have summarised the possible functional implications of these PTMs. Although in some cases a clear correlation between a specific PTM and the CA function has been highlighted, many modification events still deserve further dedicated studies.
Collapse
Affiliation(s)
- Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini-National Research Council, Napoli, Italy
| | - Claudiu T Supuran
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, University of Firenze, Sesto Fiorentino, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Napoli, Italy
| | | |
Collapse
|
11
|
Zanetti-Polzi L, Aschi M, Daidone I. Cooperative protein-solvent tuning of proton transfer energetics: carbonic anhydrase as a case study. Phys Chem Chem Phys 2021; 22:19975-19981. [PMID: 32857091 DOI: 10.1039/d0cp03652h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We investigate the coupling between the proton transfer (PT) energetics and the protein-solvent dynamics using the intra-molecular PT in wild type (wt) human carbonic anhydrase II and its ten-fold faster mutant Y7F/N67Q as a test case. We calculate the energy variation upon PT, and from that we also calculate the PT reaction free energy, making use of a hybrid quantum mechanics/molecular dynamics approach. In agreement with the experimental data, we obtain that the reaction free energy is basically the same in the two systems. Yet, we show that the instantaneous PT energy is on average lower in the mutant possibly contributing to the faster PT rate. Analysis of the contribution to the PT energetics of the solvent and of each protein residue, also not in the vicinity of the active site, provides evidence for electrostatic tuning of the PT energy arising from the combined effect of the solvent and the protein environment. These findings open up a way to the more general task of the rational design of mutants with either enhanced or reduced PT rate.
Collapse
Affiliation(s)
| | - Massimiliano Aschi
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67010 L'Aquila, Italy.
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67010 L'Aquila, Italy.
| |
Collapse
|
12
|
Kaczor PT, Wolska AD, Mozrzymas JW. α 1 Subunit Histidine 55 at the Interface between Extracellular and Transmembrane Domains Affects Preactivation and Desensitization of the GABA A Receptor. ACS Chem Neurosci 2021; 12:562-572. [PMID: 33471498 PMCID: PMC7875458 DOI: 10.1021/acschemneuro.0c00781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
![]()
The
GABAA receptor is a member of the Cys-loop family
and plays a crucial role in the adult mammalian brain inhibition.
Although the static structure of this receptor is emerging, the molecular
mechanisms underlying its conformational transitions remain elusive.
It is known that in the Cys-loop receptors, the interface between
extracellular and transmembrane domains plays a key role in transmitting
the “activation wave” down to the channel gate in the
pore. It has been previously reported that histidine 55 (H55), located
centrally at the interfacial β1−β2 loop of the
α1 subunit, is important in the receptor activation,
but it is unknown which specific gating steps it is affecting. In
the present study, we addressed this issue by taking advantage of
the state-of-the-art macroscopic and single-channel recordings together
with extensive modeling. Considering that H55 is known to affect the
local electrostatic landscape and because it is neighbored by two
negatively charged aspartates, a well conserved feature in the α
subunits, we considered substitution with negative (E) and positive
(K) residues. We found that these mutations markedly affected the
receptor gating, altering primarily preactivation and desensitization
transitions. Importantly, opposite effects were observed for these
two mutations strongly suggesting involvement of electrostatic interactions.
Single-channel recordings suggested also a minor effect on opening/closing
transitions which did not depend on the electric charge of the substituting
amino acid. Altogether, we demonstrate that H55 mutations affect primarily
preactivation and desensitization most likely by influencing local
electrostatic interactions at the receptor interface.
Collapse
Affiliation(s)
- Przemyslaw T. Kaczor
- Department of Biophysics and Neuroscience, Wroclaw Medical University, Chalubinskiego 3a, Wroclaw, Dolnoślaskie 50-368, Poland
| | - Aleksandra D. Wolska
- Department of Biophysics and Neuroscience, Wroclaw Medical University, Chalubinskiego 3a, Wroclaw, Dolnoślaskie 50-368, Poland
| | - Jerzy W. Mozrzymas
- Department of Biophysics and Neuroscience, Wroclaw Medical University, Chalubinskiego 3a, Wroclaw, Dolnoślaskie 50-368, Poland
| |
Collapse
|
13
|
Wang F, Tan X, Wu T, Zheng LS, Chen GQ, Zhang X. Ni-Catalyzed asymmetric reduction of α-keto-β-lactams via DKR enabled by proton shuttling. Chem Commun (Camb) 2020; 56:15557-15560. [PMID: 33244528 DOI: 10.1039/d0cc05599a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chiral α-hydroxy-β-lactams are key fragments of many bioactive compounds and antibiotics, and the development of efficient synthetic methods for these compounds is of great value. The highly enantioselective dynamic kinetic resolution (DKR) of α-keto-β-lactams was realized via a novel proton shuttling strategy. A wide range of α-keto-β-lactams were reduced efficiently and enantioselectively by Ni-catalyzed asymmetric hydrogenation, providing the corresponding α-hydroxy-β-lactam derivatives with high yields and enantioselectivities (up to 92% yield, up to 94% ee). Deuterium-labelling experiments indicate that phenylphosphinic acid plays a pivotal role in the DKR of α-keto-β-lactams by promoting the enolization process. The synthetic potential of this protocol was demonstrated by its application in the synthesis of a key intermediate of Taxol and (+)-epi-Cytoxazone.
Collapse
Affiliation(s)
- Fangyuan Wang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, People's Republic of China
| | | | | | | | | | | |
Collapse
|
14
|
Huang BR, Liu YS, Lai SW, Lin HJ, Shen CK, Yang LY, Lu DY. CAIX Regulates GBM Motility and TAM Adhesion and Polarization through EGFR/STAT3 under Hypoxic Conditions. Int J Mol Sci 2020; 21:ijms21165838. [PMID: 32823915 PMCID: PMC7461579 DOI: 10.3390/ijms21165838] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/02/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023] Open
Abstract
Carbonic anhydrases (CAs) are acid-base regulatory proteins that modulate a variety of physiological functions. Recent findings have shown that CAIX is particularly upregulated in glioblastoma multiforme (GBM) and is associated with a poor patient outcome and survival rate. An analysis of the GSE4290 dataset of patients with gliomas showed that CAIX was highly expressed in GBM and was negatively associated with prognosis. The expression of CAIX under hypoxic conditions in GBM significantly increased in protein, mRNA, and transcriptional activity. Importantly, CAIX upregulation also regulated GBM motility, monocyte adhesion to GBM, and the polarization of tumor-associated monocytes/macrophages (TAM). Furthermore, the overexpression of CAIX was observed in intracranial GBM cells. Additionally, epidermal growth factor receptor/signal transducer and activator of transcription 3 regulated CAIX expression under hypoxic conditions by affecting the stability of hypoxia-inducible factor 1α. In contrast, the knockdown of CAIX dramatically abrogated the change in GBM motility and monocyte adhesion to GBM under hypoxic conditions. Our results provide a comprehensive understanding of the mechanisms of CAIX in the GBM microenvironment. Hence, novel therapeutic targets of GBM progression are possibly developed.
Collapse
Affiliation(s)
- Bor-Ren Huang
- Department of Neurosurgery, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung 42743, Taiwan;
- School of Medicine, Tzu Chi University, Hualien 97004, Taiwan
| | - Yu-Shu Liu
- Department of Pharmacology, School of Medicine, China Medical University, Taichung 40402, Taiwan; (Y.-S.L.); (H.-J.L.)
- Department of Physiology, School of Medicine, China Medical University, Taichung 40402, Taiwan
| | - Sheng-Wei Lai
- Graduate Institute of Basic Medical Science, China Medical University, Taichung 40402, Taiwan;
| | - Hui-Jung Lin
- Department of Pharmacology, School of Medicine, China Medical University, Taichung 40402, Taiwan; (Y.-S.L.); (H.-J.L.)
| | - Ching-Kai Shen
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan;
| | - Liang-Yo Yang
- Department of Physiology, School of Medicine, China Medical University, Taichung 40402, Taiwan
- Laboratory for Neural Repair, China Medical University Hospital, Taichung 40402, Taiwan
- Biomedical Technology R&D Center, China Medical University Hospital, Taichung 40402, Taiwan
- Correspondence: (L.-Y.Y.); (D.-Y.L.); Tel.: +886-4-2205-3366 (ext. 1615) (L.-Y.Y.); +886-4-2205-3366 (ext. 2253) (D.-Y.L.)
| | - Dah-Yuu Lu
- Department of Pharmacology, School of Medicine, China Medical University, Taichung 40402, Taiwan; (Y.-S.L.); (H.-J.L.)
- Department of Photonics and Communication Engineering, Asia University, Taichung 41354, Taiwan
- Correspondence: (L.-Y.Y.); (D.-Y.L.); Tel.: +886-4-2205-3366 (ext. 1615) (L.-Y.Y.); +886-4-2205-3366 (ext. 2253) (D.-Y.L.)
| |
Collapse
|
15
|
Yin CY, Zhang SS, Zhong JT, Zhou SH. Pepsin and Laryngeal and Hypopharyngeal Carcinomas. Clin Exp Otorhinolaryngol 2020; 14:159-168. [PMID: 32734742 PMCID: PMC8111387 DOI: 10.21053/ceo.2020.00465] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 07/17/2020] [Indexed: 02/08/2023] Open
Abstract
Laryngeal and hypopharyngeal carcinomas are common malignant tumors of the head and neck, and the incidence of both is increasing. Laryngopharyngeal reflux refers to the retrograde flow of gastric contents into the larynx, oropharynx, and/or nasopharynx. It remains controversial whether laryngopharyngeal reflux is a risk factor for laryngeal and hypopharyngeal cancers. The refluxing substances mainly include hydrochloric acid, pepsin, and occasionally bile acids and bile salts, as well as bacteria that colonize the gastrointestinal tract. Loss of epithelium in the mucous membrane of the larynx and hypopharynx is thought to be caused by pepsin. Here, we review the relationships between laryngopharyngeal reflux and both laryngeal and hypopharyngeal carcinomas, as well as the significance of pepsin, methods of clinical detection, and the mechanism of carcinogenesis.
Collapse
Affiliation(s)
- Cheng-Yi Yin
- Department of Otolaryngology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Otolaryngology, The First People's Hospital of Huzhou City, Zhejiang, China
| | - Sha-Sha Zhang
- Department of Otolaryngology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jiang-Tao Zhong
- Department of Otolaryngology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shui-Hong Zhou
- Department of Otolaryngology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
16
|
Jin S, Vullo D, Bua S, Nocentini A, Supuran CT, Gao YG. Structural and biochemical characterization of novel carbonic anhydrases from Phaeodactylum tricornutum. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:676-686. [PMID: 32627740 DOI: 10.1107/s2059798320007202] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/28/2020] [Indexed: 01/08/2023]
Abstract
Carbonic anhydrases (CAs) are a well characterized family of metalloenzymes that are highly efficient in facilitating the interconversion between carbon dioxide and bicarbonate. Recently, CA activity has been associated with the LCIB (limiting CO2-inducible protein B) protein family, which has been an interesting target in aquatic photosynthetic microorganisms. To gain further insight into the catalytic mechanism of this new group of CAs, the X-ray structure of a highly active LCIB homolog (PtLCIB3) from the diatom Phaeodactylum tricornutum was determined. The CA activities of PtLCIB3, its paralog PtLCIB4 and a variety of their mutants were also measured. It was discovered that PtLCIB3 has a classic β-CA fold and its overall structure is highly similar to that of its homolog PtLCIB4. Subtle structural alterations between PtLCIB3 and PtLCIB4 indicate that an alternative proton-shuttle cavity could perhaps be one reason for their remarkable difference in CA activity. A potential alternative proton-shuttle route in the LCIB protein family is suggested based on these results.
Collapse
Affiliation(s)
- Shengyang Jin
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Daniela Vullo
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Silvia Bua
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Alessio Nocentini
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Claudiu T Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Yong Gui Gao
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| |
Collapse
|
17
|
Sanyanga TA, Nizami B, Bishop ÖT. Mechanism of Action of Non-Synonymous Single Nucleotide Variations Associated with α-Carbonic Anhydrase II Deficiency. Molecules 2019; 24:E3987. [PMID: 31690045 PMCID: PMC6864701 DOI: 10.3390/molecules24213987] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/18/2019] [Accepted: 10/24/2019] [Indexed: 12/12/2022] Open
Abstract
Human carbonic anhydrase II (CA-II) is a Zinc (Zn 2 + ) metalloenzyme responsible for maintenance of acid-base balance within the body through the reversible hydration of CO 2 to produce protons (H + ) and bicarbonate (BCT). Due to its importance, alterations to the amino acid sequence of the protein as a result of single nucleotide variations (nsSNVs) have detrimental effects on homeostasis. Six pathogenic CA-II nsSNVs, K18E, K18Q, H107Y, P236H, P236R and N252D were identified, and variant protein models calculated using homology modeling. The effect of each nsSNV was analyzed using motif analysis, molecular dynamics (MD) simulations, principal component (PCA) and dynamic residue network (DRN) analysis. Motif analysis identified 11 functionally important motifs in CA-II. RMSD data indicated subtle SNV effects, while PCA analysis revealed that the presence of BCT results in greater conformational sampling and free energy in proteins. DRN analysis showed variant allosteric effects, and the average betweenness centrality (BC) calculations identified Glu117 as the most important residue for communication in CA-II. The presence of BCT was associated with a reduction to Glu117 usage in all variants, suggesting implications for Zn 2 + dissociation from the CA-II active site. In addition, reductions to Glu117 usage are associated with increases in the usage of the primary and secondary Zn 2 + ligands; His94, His96, His119 and Asn243 highlighting potential compensatory mechanisms to maintain Zn 2 + within the active site. Compared to traditional MD simulation investigation, DRN analysis provided greater insights into SNV mechanism of action, indicating its importance for the study of missense mutation effects in proteins and, in broader terms, precision medicine related research.
Collapse
Affiliation(s)
- Taremekedzwa Allan Sanyanga
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa.
| | - Bilal Nizami
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa.
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117 Budapest, Hungary.
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa.
| |
Collapse
|
18
|
Abstract
We herein describe the design and synthesis of a catalytically active peptide–gold nanoparticle conjugate (Pep-Au-NP) that binds Zn(II) within its peptide monolayer and develops carbonic anhydrase activity. Specifically, a modified variant of the β-sheet forming IHIHIQI-peptide (IHQ), which forms an interstrand 3-His Zn(II)-binding site, was used as a ligand for spherical gold nanoparticles (Au-NPs). The resulting immobilized peptide maintains its ability to form β-sheets, as determined by circular dichroism (CD)-spectroscopy and, thus, maintains its ability to form Zn(II)-binding sites. The addition of Zn(II)-ions to the peptide–gold nanoparticle conjugates (Au@IHQ-NP) resulted in significant improvements in rates of ester hydrolysis of 4-nitrophenyl acetate (4-NPA) and the hydration of CO2 compared to the unconjugated peptide variants. Recycling of the catalyst revealed that Au@IHQ-NP remains intact with at least 94% of its initial activity after five rounds of CO2 hydration. The herein reported results reveal that Pep-Au-NPs are able to perform reactions catalyzed by natural metalloenzymes and open up new possibilities for the implementation of these conjugates.
Collapse
|
19
|
De Simone G, Di Fiore A, Truppo E, Langella E, Vullo D, Supuran CT, Monti SM. Exploration of the residues modulating the catalytic features of human carbonic anhydrase XIII by a site-specific mutagenesis approach. J Enzyme Inhib Med Chem 2019; 34:1506-1510. [PMID: 31431090 PMCID: PMC6713127 DOI: 10.1080/14756366.2019.1653290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Carbonic anhydrases (CAs) are ubiquitous metallo-enzymes that catalyse the reversible hydration of carbon dioxide to bicarbonate and proton. In humans there are 15 isoforms among which only 12 are catalytically active. Since active human (h) CAs show different efficiency, the understanding of the molecular determinants affecting it is a matter of debate. Here we investigated, by a site-specific mutagenesis approach, residues modulating the catalytic features of one of the least investigated cytosolic isoform, i.e. hCA XIII. Results showed that residues assisting the formation of an ordered solvent network within the catalytic site as well as those forming a histidine cluster on the protein surface are important to guarantee an efficient proton transfer.
Collapse
Affiliation(s)
| | - Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini-CNR , Naples , Italy
| | | | - Emma Langella
- Istituto di Biostrutture e Bioimmagini-CNR , Naples , Italy
| | - Daniela Vullo
- Neurofarba Department, Università degli Studi di Firenze, Sezione di Scienze Farmaceutiche e Nutraceutiche , Sesto Fiorentino , Florence , Italy
| | - Claudiu T Supuran
- Neurofarba Department, Università degli Studi di Firenze, Sezione di Scienze Farmaceutiche e Nutraceutiche , Sesto Fiorentino , Florence , Italy
| | | |
Collapse
|
20
|
Cook BJ, Polezhaev AV, Chen CH, Pink M, Caulton KG. A multimetal-ligand cooperative approach to CO2 activation. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.08.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
21
|
Messina KJ, Bevilacqua PC. Cellular Small Molecules Contribute to Twister Ribozyme Catalysis. J Am Chem Soc 2018; 140:10578-10582. [PMID: 30102530 PMCID: PMC6472948 DOI: 10.1021/jacs.8b06065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The number of self-cleaving small ribozymes has increased sharply in recent years. Advances have been made in describing these ribozymes in terms of four catalytic strategies: α describes in-line attack, β describes neutralization of the nonbridging oxygens, γ describes activation of the nucleophile, and δ describes stabilization of the leaving group. Current literature presents the rapid self-cleavage of the twister ribozyme in terms of all four of these classic catalytic strategies. Herein, we describe the nonspecific contribution of small molecules to ribozyme catalysis. At biological pH, the rate of the wild-type twister ribozyme is enhanced up to 5-fold in the presence of moderate buffer concentrations, similar to the 3-5-fold effects reported previously for buffer catalysis for protein enzymes. We observe this catalytic enhancement not only with standard laboratory buffers, but also with diverse biological small molecules, including imidazole, amino acids, and amino sugars. Brønsted plots suggest that small molecules assist in proton transfer, most likely with δ catalysis. Cellular small molecules provide a simple way to overcome the limited functional diversity of RNA and have the potential to participate in the catalytic mechanisms of many ribozymes in vivo.
Collapse
Affiliation(s)
- Kyle J. Messina
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Philip C. Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802 United States
| |
Collapse
|
22
|
Protective Role of Carbonic Anhydrases III and VII in Cellular Defense Mechanisms upon Redox Unbalance. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:2018306. [PMID: 30154947 PMCID: PMC6098850 DOI: 10.1155/2018/2018306] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 07/24/2018] [Indexed: 01/07/2023]
Abstract
Under oxidative stress conditions, several constitutive cellular defense systems are activated, which involve both enzymatic systems and molecules with antioxidant properties such as glutathione and vitamins. In addition, proteins containing reactive sulfhydryl groups may eventually undergo reversible redox modifications whose products act as protective shields able to avoid further permanent molecular oxidative damage either in stressful conditions or under pathological circumstances. After the recovery of normal redox conditions, the reduced state of protein sulfhydryl groups is restored. In this context, carbonic anhydrases (CAs) III and VII, which are human metalloenzymes catalyzing the reversible hydration of carbon dioxide to bicarbonate and proton, have been identified to play an antioxidant role in cells where oxidative damage occurs. Both proteins are mainly localized in tissues characterized by a high rate of oxygen consumption, and contain on their molecular surface two reactive cysteine residues eventually undergoing S-glutathionylation. Here, we will provide an overview on the molecular and functional features of these proteins highlighting their implications into molecular processes occurring during oxidative stress conditions.
Collapse
|
23
|
Buonanno M, Di Fiore A, Langella E, D'Ambrosio K, Supuran CT, Monti SM, De Simone G. The Crystal Structure of a hCA VII Variant Provides Insights into the Molecular Determinants Responsible for Its Catalytic Behavior. Int J Mol Sci 2018; 19:ijms19061571. [PMID: 29795045 PMCID: PMC6032174 DOI: 10.3390/ijms19061571] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 05/07/2018] [Accepted: 05/19/2018] [Indexed: 01/07/2023] Open
Abstract
Although important progress has been achieved in understanding the catalytic mechanism of Carbonic Anhydrases, a detailed picture of all factors influencing the catalytic efficiency of the various human isoforms is still missing. In this paper we report a detailed structural study and theoretical pKa calculations on a hCA VII variant. The obtained data were compared with those already known for another thoroughly investigated cytosolic isoform, hCA II. Our structural studies show that in hCA VII the network of ordered water molecules, which connects the zinc bound solvent molecule to the proton shuttle His64, is altered compared to hCA II, causing a reduction of the catalytic efficiency. Theoretical calculations suggest that changes in solvent network are related to the difference in pKa of the proton shuttle in the two enzymes. The residue that plays a major role in determining the diverse pKa values of the proton shuttle is the one in position four, namely His for hCA II and Gly for hCA VII. This residue is located on the protein surface, outside of the active site cavity. These findings are in agreement with our previous studies that highlighted the importance of histidines on the protein surface of hCA II (among which His4) as crucial residues for the high catalytic efficiency of this isoform.
Collapse
Affiliation(s)
- Martina Buonanno
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy.
| | - Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy.
| | - Emma Langella
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy.
| | - Katia D'Ambrosio
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy.
| | - Claudiu T Supuran
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Via U. Schiff 6, 50019 Florence, Italy.
| | - Simona Maria Monti
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy.
| | - Giuseppina De Simone
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy.
| |
Collapse
|
24
|
Kim JY, Kulik HJ. When Is Ligand pKa a Good Descriptor for Catalyst Energetics? In Search of Optimal CO2 Hydration Catalysts. J Phys Chem A 2018; 122:4579-4590. [DOI: 10.1021/acs.jpca.8b03301] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jeong Yun Kim
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
25
|
Čapkauskaitė E, Zubrienė A, Paketurytė V, Timm DD, Tumkevičius S, Matulis D. Thiazole-substituted benzenesulfonamides as inhibitors of 12 human carbonic anhydrases. Bioorg Chem 2018; 77:534-541. [PMID: 29459130 DOI: 10.1016/j.bioorg.2018.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/05/2018] [Accepted: 02/09/2018] [Indexed: 12/26/2022]
Abstract
Four series of para or meta - substituted thiazolylbenzenesulfonamides bearing Cl substituents were designed, synthesized, and evaluated as inhibitors of all 12 catalytically active recombinant human carbonic anhydrase (CA) isoforms. Observed affinities were determined by the fluorescent thermal shift assay and the intrinsic affinities were calculated based on the fractions of binding-ready deprotonated sulfonamide and CA bearing protonated hydroxide bound to the catalytic Zn(II) in the active site. Several compounds exhibited selectivity towards CA IX, an anticancer target. Intrinsic affinities reached 30 pM, while the observed affinities - 70 nM. The structure-intrinsic affinity relationship map of the compounds showed the energetic contributions of the thiazole ring and its substituents.
Collapse
Affiliation(s)
- Edita Čapkauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Vaida Paketurytė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - David D Timm
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania
| | - Sigitas Tumkevičius
- Department of Organic Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko 24, Vilnius LT-03225, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania.
| |
Collapse
|
26
|
Ip YK, Koh CZY, Hiong KC, Choo CYL, Boo MV, Wong WP, Neo ML, Chew SF. Carbonic anhydrase 2-like in the giant clam, Tridacna squamosa: characterization, localization, response to light, and possible role in the transport of inorganic carbon from the host to its symbionts. Physiol Rep 2017; 5:e13494. [PMID: 29199178 PMCID: PMC5727267 DOI: 10.14814/phy2.13494] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 10/13/2017] [Indexed: 11/24/2022] Open
Abstract
The fluted giant clam, Tridacna squamosa, lives in symbiosis with zooxanthellae which reside extracellularly inside a tubular system. Zooxanthellae fix inorganic carbon (Ci) during insolation and donate photosynthate to the host. Carbonic anhydrases catalyze the interconversion of CO2 and HCO3-, of which carbonic anhydrase 2 (CA2) is the most ubiquitous and involved in many biological processes. This study aimed to clone a CA2 homolog (CA2-like) from the fleshy and colorful outer mantle as well as the thin and whitish inner mantle of T. squamosa, to determine its cellular and subcellular localization, and to examine the effects of light exposure on its gene and protein expression levels. The cDNA coding sequence of CA2-like from T. squamosa comprised 789 bp, encoding 263 amino acids with an estimated molecular mass of 29.6 kDa. A phenogramic analysis of the deduced CA2-like sequence denoted an animal origin. CA2-like was not detectable in the shell-facing epithelium of the inner mantle adjacent to the extrapallial fluid. Hence, CA2-like is unlikely to participate directly in light-enhanced calcification. By contrast, the outer mantle, which contains the highest density of tertiary tubules and zooxanthellae, displayed high level of CA2-like expression, and CA2-like was localized to the tubule epithelial cells. More importantly, exposure to light induced significant increases in the protein abundance of CA2-like in the outer mantle. Hence, CA2-like could probably take part in the increased supply of inorganic carbon (Ci) from the host clam to the symbiotic zooxanthellae when the latter conduct photosynthesis to fix Ci during light exposure.
Collapse
Affiliation(s)
- Yuen K. Ip
- Department of Biological SciencesNational University of SingaporeSingapore
- The Tropical Marine Science InstituteNational University of SingaporeSingapore
| | - Clarissa Z. Y. Koh
- Department of Biological SciencesNational University of SingaporeSingapore
| | - Kum C. Hiong
- Department of Biological SciencesNational University of SingaporeSingapore
| | - Celine Y. L. Choo
- Department of Biological SciencesNational University of SingaporeSingapore
| | - Mel V. Boo
- Department of Biological SciencesNational University of SingaporeSingapore
| | - Wai P. Wong
- Department of Biological SciencesNational University of SingaporeSingapore
| | - Mei L. Neo
- St. John's Island National Marine LaboratoryNational University of SingaporeSingapore
| | - Shit F. Chew
- Natural Sciences and Science EducationNational Institute of EducationNanyang Technological UniversitySingapore
| |
Collapse
|
27
|
Čapkauskaitė E, Linkuvienė V, Smirnov A, Milinavičiūtė G, Timm DD, Kasiliauskaitė A, Manakova E, Gražulis S, Matulis D. Combinatorial Design of Isoform-Selective N-Alkylated Benzimidazole-Based Inhibitors of Carbonic Anhydrases. ChemistrySelect 2017. [DOI: 10.1002/slct.201700531] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Edita Čapkauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology; Vilnius University; Saulėtekio al. 7 Vilnius LT- 10257 Lithuania
| | - Vaida Linkuvienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology; Vilnius University; Saulėtekio al. 7 Vilnius LT- 10257 Lithuania
| | - Alexey Smirnov
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology; Vilnius University; Saulėtekio al. 7 Vilnius LT- 10257 Lithuania
| | - Goda Milinavičiūtė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology; Vilnius University; Saulėtekio al. 7 Vilnius LT- 10257 Lithuania
| | - David D. Timm
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology; Vilnius University; Saulėtekio al. 7 Vilnius LT- 10257 Lithuania
| | - Aistė Kasiliauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology; Vilnius University; Saulėtekio al. 7 Vilnius LT- 10257 Lithuania
| | - Elena Manakova
- Department of Protein - DNA Interactions, Institute of Biotechnology; Vilnius University
| | - Saulius Gražulis
- Department of Protein - DNA Interactions, Institute of Biotechnology; Vilnius University
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology; Vilnius University; Saulėtekio al. 7 Vilnius LT- 10257 Lithuania
| |
Collapse
|
28
|
Schörghuber J, Geist L, Platzer G, Konrat R, Lichtenecker RJ. Highly Selective Stable Isotope Labeling of Histidine Residues by Using a Novel Precursor in E. coli-Based Overexpression Systems. Chembiochem 2017; 18:1487-1491. [PMID: 28489326 DOI: 10.1002/cbic.201700192] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Indexed: 12/14/2022]
Abstract
The importance of NMR spectroscopy in unraveling the structural and dynamic properties of proteins is ever-expanding owing to progress in experimental techniques, hardware development, and novel labeling approaches. Multiple sophisticated methods of aliphatic residue labeling can be found in the literature, whereas the selective incorporation of NMR active isotopes into other amino acids still holds the potential for improvement. In order to close this methodological gap, we present a novel metabolic precursor for cell-based protein overexpression to assemble 13 C/2 H isotope patterns in the peptide backbone, as well as in side chain positions of a mechanistically distinguished histidine residue.
Collapse
Affiliation(s)
- Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, Währingerstrasse 38, 1090, Vienna, Austria
| | - Leonhard Geist
- Christian Doppler Laboratory for High-Content Structural Biology, and Biotechnology/Department of Structural and Computational Biology, University of Vienna, 1090, Vienna, Austria
| | - Gerald Platzer
- Christian Doppler Laboratory for High-Content Structural Biology, and Biotechnology/Department of Structural and Computational Biology, University of Vienna, 1090, Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology, and Biotechnology/Department of Structural and Computational Biology, University of Vienna, 1090, Vienna, Austria
| | - Roman J Lichtenecker
- Institute of Organic Chemistry, University of Vienna, Währingerstrasse 38, 1090, Vienna, Austria
| |
Collapse
|
29
|
Iqbal S, Saleem M, Azim MK, Taha M, Salar U, Khan KM, Perveen S, Choudhary MI. Carbohydrazones as new class of carbonic anhydrase inhibitors: Synthesis, kinetics, and ligand docking studies. Bioorg Chem 2017; 72:89-101. [DOI: 10.1016/j.bioorg.2017.03.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/28/2017] [Accepted: 03/28/2017] [Indexed: 11/30/2022]
|
30
|
Nemzer LR. A binary representation of the genetic code. Biosystems 2017; 155:10-19. [PMID: 28300609 DOI: 10.1016/j.biosystems.2017.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 12/23/2022]
Abstract
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA bases is assigned a unique 2-bit identifier, so that the 64 triplet codons are each indexed by a 6-bit label. The ordering of the bits reflects the hierarchical organization manifested by the DNA replication/repair and tRNA translation systems. In this system, transition and transversion mutations are naturally expressed as binary operations, and the severities of the different point mutations can be analyzed. Using a principal component analysis, it is shown that the physicochemical properties of amino acids related to protein folding also correlate with certain bit positions of their respective labels. Thus, the likelihood for a point mutation to be conservative, and less likely to cause a change in protein functionality, can be estimated.
Collapse
Affiliation(s)
- Louis R Nemzer
- Department of Chemistry and Physics, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Davie, FL, USA.
| |
Collapse
|
31
|
Monti DM, De Simone G, Langella E, Supuran CT, Di Fiore A, Monti SM. Insights into the role of reactive sulfhydryl groups of Carbonic Anhydrase III and VII during oxidative damage. J Enzyme Inhib Med Chem 2016; 32:5-12. [PMID: 27766895 PMCID: PMC6010095 DOI: 10.1080/14756366.2016.1225046] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Carbonic anhydrases (CAs) III and VII are two cytosolic isoforms of the α-CA family which catalyze the physiological reaction of carbon dioxide hydration to bicarbonate and proton. Despite these two enzymes share a 49% sequence identity and present a very similar three-dimensional structure, they show profound differences when comparing the specific activity for CO2 hydration reaction, with CA VII being much more active than CA III. Recently, CA III and CA VII have been proposed to play a new role as scavenger enzymes in cells where oxidative damage occurs. Here, we will examine functional and structural features of these two isoforms giving insights into their newly proposed protective role against oxidative stress.
Collapse
Affiliation(s)
- Daria M Monti
- a Department of Chemical Sciences , University of Naples Federico II , Naples , Italy
| | | | - Emma Langella
- b Institute of Biostructures and Bioimaging, CNR , Naples , Italy
| | - Claudiu T Supuran
- c Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche , Università degli Studi di Firenze , Florence , Italy
| | - Anna Di Fiore
- b Institute of Biostructures and Bioimaging, CNR , Naples , Italy
| | - Simona M Monti
- b Institute of Biostructures and Bioimaging, CNR , Naples , Italy
| |
Collapse
|
32
|
Taraphder S, Maupin CM, Swanson JJ, Voth GA. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II. J Phys Chem B 2016; 120:8389-404. [PMID: 27063577 PMCID: PMC5003118 DOI: 10.1021/acs.jpcb.6b02166] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/06/2016] [Indexed: 11/28/2022]
Abstract
The role of protein dynamics in enzyme catalysis is one of the most highly debated topics in enzymology. The main controversy centers around what may be defined as functionally significant conformational fluctuations and how, if at all, these fluctuations couple to enzyme catalyzed events. To shed light on this debate, the conformational dynamics along the transition path surmounting the highest free energy barrier have been herein investigated for the rate limiting proton transport event in human carbonic anhydrase (HCA) II. Special attention has been placed on whether the motion of an excess proton is correlated with fluctuations in the surrounding protein and solvent matrix, which may be rare on the picosecond and subpicosecond time scales of molecular motions. It is found that several active site residues, which do not directly participate in the proton transport event, have a significant impact on the dynamics of the excess proton. These secondary participants are shown to strongly influence the active site environment, resulting in the creation of water clusters that are conducive to fast, moderately slow, or slow proton transport events. The identification and characterization of these secondary participants illuminates the role of protein dynamics in the catalytic efficiency of HCA II.
Collapse
Affiliation(s)
- Srabani Taraphder
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - C. Mark Maupin
- Department
of Chemical and Biological Engineering, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United
States
| | - Jessica
M. J. Swanson
- Department
of Chemistry, Institute for Biophysical Dynamics, James Frank Institute,
and Computation Institute, University of
Chicago, 5735 South Ellis
Avenue, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department
of Chemistry, Institute for Biophysical Dynamics, James Frank Institute,
and Computation Institute, University of
Chicago, 5735 South Ellis
Avenue, Chicago, Illinois 60637, United States
| |
Collapse
|
33
|
Faridi S, Satyanarayana T. Characteristics of recombinant α-carbonic anhydrase of polyextremophilic bacterium Bacillus halodurans TSLV1. Int J Biol Macromol 2016; 89:659-68. [DOI: 10.1016/j.ijbiomac.2016.05.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 05/06/2016] [Accepted: 05/07/2016] [Indexed: 11/25/2022]
|
34
|
Faridi S, Satyanarayana T. Novel alkalistable α-carbonic anhydrase from the polyextremophilic bacterium Bacillus halodurans: characteristics and applicability in flue gas CO2 sequestration. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:15236-15249. [PMID: 27102616 DOI: 10.1007/s11356-016-6642-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/04/2016] [Indexed: 06/05/2023]
Abstract
The emissions of CO2 into the atmosphere have been constantly rising due to anthropogenic activities, which have led to global warming and climate change. Among various methods proposed for mitigating CO2 levels in the atmosphere, carbonic anhydrase (CA)-mediated carbon sequestration represents a greener and safer approach to capture and convert it into stable mineral carbonates. Despite the fact that CA is an extremely efficient metalloenzyme that catalyzes the hydration of CO2 (CO2 + H2O ↔ HCO3 (-) + H(+)) with a kcat of ∼10(6) s(-1), a thermostable, and alkalistable CA is desirable for the process to take place efficiently. The purified CA from alkaliphilic, moderately thermophilic, and halotolerant Bacillus halodurans TSLV1 (BhCA) is a homodimeric enzyme with a subunit molecular mass of ~37 kDa with stability in a broad pH range between 6.0 and 11.0. It has a moderate thermostability with a T1/2 of 24.0 ± 1.0 min at 60 °C. Based on the sensitivity of CA to specific inhibitors, BhCA is an α-CA; this has been confirmed by nucleotide/amino acid sequence analysis. This has a unique property of stimulation by SO4 (2-), and it remains unaffected by SO3 (2-), NOx, and most other components present in the flue gas. BhCA is highly efficient in accelerating the mineralization of CO2 as compared to commercial bovine carbonic anhydrase (BCA) and is also efficient in the sequestration of CO2 from the exhaust of petrol driven car, thus, a useful biocatalyst for sequestering CO2 from flue gas.
Collapse
Affiliation(s)
- Shazia Faridi
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - T Satyanarayana
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
| |
Collapse
|
35
|
Fletcher TL, Popelier PLA. Multipolar Electrostatic Energy Prediction for all 20 Natural Amino Acids Using Kriging Machine Learning. J Chem Theory Comput 2016; 12:2742-51. [DOI: 10.1021/acs.jctc.6b00457] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Timothy L. Fletcher
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain
| |
Collapse
|
36
|
Chen Y, Zhang L, Xu C, Vaidyanathan S. Dissolved inorganic carbon speciation in aquatic environments and its application to monitor algal carbon uptake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 541:1282-1295. [PMID: 26476067 DOI: 10.1016/j.scitotenv.2015.10.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/06/2015] [Accepted: 10/06/2015] [Indexed: 06/05/2023]
Abstract
Dissolved inorganic carbon (DIC) speciation is an important parameter that enables chemical and ecological changes in aquatic environments, such as the aquatic environmental impact of increasing atmospheric CO2 levels, to be monitored. We have examined and developed a sensitive and cost-effective 'back-titration' method to determine the DIC species and abundance in aqueous environments that is more accurate and reproducible than existing methods and is applicable in a range of fresh, brackish and sea waters. We propose the use of pHHCO3 (bicarbonate-dominant pH) and pH3.5 as the titration end points in the back-titration technique to accurately determine carbonate alkalinity. The proposed method has a higher accuracy and precision than other modified Gran's methods that are currently in use. The detection limit was found to be ~5 μmol kg(-1) with an accuracy within 1% and a precision (CV) within 0.2% and 0.5% at high and low level of carbonates, respectively. This method was successfully applied to monitor DIC in the aqueous medium of Nannochlopsis salina cultivation separately carried out with NaHCO3 and CO2 as the respective inorganic carbon source. The cells were able to grow in the NaHCO3 medium with a similar growth curve to cells with 0.039% CO2 (air). Increases in CO2 level stimulated lipid accumulation by diverting the fixed carbon from protein to lipids. The increased concentration of gaseous CO2 and the accompanying lower pH appears to significantly inhibit the growth of algae despite the presence of HCO3(-) when 20% CO2 was employed.
Collapse
Affiliation(s)
- Yimin Chen
- Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, People's Republic of China; ChELSI Institute, Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK; School of Environmental Science and Engineering, Liaoning Technical University, No. 47, Zhong Hua Rd, Fuxin City, Liaoning Province 123000, People's Republic of China.
| | - Liang Zhang
- School of Environmental Science and Engineering, Liaoning Technical University, No. 47, Zhong Hua Rd, Fuxin City, Liaoning Province 123000, People's Republic of China
| | - Changan Xu
- Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, People's Republic of China.
| | - Seetharaman Vaidyanathan
- ChELSI Institute, Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK.
| |
Collapse
|
37
|
X-Ray Structure and Mutagenesis Studies of the N-Isopropylammelide Isopropylaminohydrolase, AtzC. PLoS One 2015; 10:e0137700. [PMID: 26390431 PMCID: PMC4577212 DOI: 10.1371/journal.pone.0137700] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 08/19/2015] [Indexed: 12/01/2022] Open
Abstract
The N-isopropylammelide isopropylaminohydrolase from Pseudomonas sp. strain ADP, AtzC, provides the third hydrolytic step in the mineralization of s-triazine herbicides, such as atrazine. We obtained the X-ray crystal structure of AtzC at 1.84 Å with a weak inhibitor bound in the active site and then used a combination of in silico docking and site-directed mutagenesis to understand the interactions between AtzC and its substrate, isopropylammelide. The substitution of an active site histidine residue (His249) for an alanine abolished the enzyme’s catalytic activity. We propose a plausible catalytic mechanism, consistent with the biochemical and crystallographic data obtained that is similar to that found in carbonic anhydrase and other members of subtype III of the amidohydrolase family
Collapse
|
38
|
Thermostable Carbonic Anhydrases in Biotechnological Applications. Int J Mol Sci 2015; 16:15456-80. [PMID: 26184158 PMCID: PMC4519908 DOI: 10.3390/ijms160715456] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 01/10/2023] Open
Abstract
Carbonic anhydrases are ubiquitous metallo-enzymes which catalyze the reversible hydration of carbon dioxide in bicarbonate ions and protons. Recent years have seen an increasing interest in the utilization of these enzymes in CO2 capture and storage processes. However, since this use is greatly limited by the harsh conditions required in these processes, the employment of thermostable enzymes, both those isolated by thermophilic organisms and those obtained by protein engineering techniques, represents an interesting possibility. In this review we will provide an extensive description of the thermostable carbonic anhydrases so far reported and the main processes in which these enzymes have found an application.
Collapse
|
39
|
De Simone G, Monti SM, Alterio V, Buonanno M, De Luca V, Rossi M, Carginale V, Supuran CT, Capasso C, Di Fiore A. Crystal structure of the most catalytically effective carbonic anhydrase enzyme known, SazCA from the thermophilic bacterium Sulfurihydrogenibium azorense. Bioorg Med Chem Lett 2015; 25:2002-6. [PMID: 25817590 DOI: 10.1016/j.bmcl.2015.02.068] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/25/2015] [Accepted: 02/26/2015] [Indexed: 10/23/2022]
Abstract
Two thermostable α-carbonic anhydrases (α-CAs) isolated from thermophilic Sulfurihydrogenibium spp., namely SspCA (from S. yellowstonensis) and SazCA (from S. azorense), were shown in a previous work to possess interesting complementary properties. SspCA was shown to have an exceptional thermal stability, whereas SazCA demonstrated to be the most active α-CA known to date for the CO2 hydration reaction. Here we report the crystallographic structure of SazCA and the identification of the structural features responsible for its high catalytic activity, by comparing it with SspCA structure. These data are of relevance for the design of engineered proteins showing higher stability and catalytic activity than other α-CAs known to date.
Collapse
Affiliation(s)
- Giuseppina De Simone
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy.
| | - Simona Maria Monti
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Vincenzo Alterio
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Martina Buonanno
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy; Seconda Università di Napoli (SUN), 81100 Caserta, Italy
| | - Viviana De Luca
- Istituto di Bioscienze e Biorisorse-CNR, Via P. Castellino 111, 80131 Napoli, Italy
| | - Mosè Rossi
- Istituto di Bioscienze e Biorisorse-CNR, Via P. Castellino 111, 80131 Napoli, Italy
| | - Vincenzo Carginale
- Istituto di Bioscienze e Biorisorse-CNR, Via P. Castellino 111, 80131 Napoli, Italy
| | - Claudiu T Supuran
- Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy; NEUROFARBA Department, Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Clemente Capasso
- Istituto di Bioscienze e Biorisorse-CNR, Via P. Castellino 111, 80131 Napoli, Italy
| | - Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy.
| |
Collapse
|
40
|
Hughes TJ, Popelier PL. Where does charge reside in amino acids? The effect of side-chain protonation state on the atomic charges of Asp, Glu, Lys, His and Arg. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.07.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
41
|
D'Ambrosio K, Carradori S, Monti SM, Buonanno M, Secci D, Vullo D, Supuran CT, De Simone G. Out of the active site binding pocket for carbonic anhydrase inhibitors. Chem Commun (Camb) 2015; 51:302-5. [DOI: 10.1039/c4cc07320g] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
2-Benzylsulfinylbenzoic acid binds to human carbonic anhydrase II in a mode completely different from any other class of carbonic anhydrase inhibitors investigated so far.
Collapse
Affiliation(s)
| | - Simone Carradori
- Dipartimento di Chimica e Tecnologie del Farmaco
- Sapienza University of Rome
- 00185 Rome
- Italy
| | | | | | - Daniela Secci
- Dipartimento di Chimica e Tecnologie del Farmaco
- Sapienza University of Rome
- 00185 Rome
- Italy
| | - Daniela Vullo
- Universitá degli Studi di Firenze
- Polo Scientifico
- Laboratorio di Chimica Bioinorganica
- 50019 Sesto Fiorentino
- Italy
| | - Claudiu T. Supuran
- Universitá degli Studi di Firenze
- Polo Scientifico
- Laboratorio di Chimica Bioinorganica
- 50019 Sesto Fiorentino
- Italy
| | | |
Collapse
|
42
|
Shenderovich IG, Lesnichin SB, Tu C, Silverman DN, Tolstoy PM, Denisov GS, Limbach HH. NMR studies of active-site properties of human carbonic anhydrase II by using (15) N-labeled 4-methylimidazole as a local probe and histidine hydrogen-bond correlations. Chemistry 2014; 21:2915-29. [PMID: 25521423 DOI: 10.1002/chem.201404083] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 11/12/2014] [Indexed: 12/24/2022]
Abstract
By using a combination of liquid and solid-state NMR spectroscopy, (15) N-labeled 4-methylimidazole (4-MI) as a local probe of the environment has been studied: 1) in the polar, wet Freon CDF3 /CDF2 Cl down to 130 K, 2) in water at pH 12, and 3) in solid samples of the mutant H64A of human carbonic anhydrase II (HCA II). In the latter, the active-site His64 residue is replaced by alanine; the catalytic activity is, however, rescued by the presence of 4-MI. For the Freon solution, it is demonstrated that addition of water molecules not only catalyzes proton tautomerism but also lifts its quasidegeneracy. The possible hydrogen-bond clusters formed and the mechanism of the tautomerism are discussed. Information about the imidazole hydrogen-bond geometries is obtained by establishing a correlation between published (1) H and (15) N chemical shifts of the imidazole rings of histidines in proteins. This correlation is useful to distinguish histidines embedded in the interior of proteins and those at the surface, embedded in water. Moreover, evidence is obtained that the hydrogen-bond geometries of His64 in the active site of HCA II and of 4-MI in H64A HCA II are similar. Finally, the degeneracy of the rapid tautomerism of the neutral imidazole ring His64 reported by Shimahara et al. (J. Biol. Chem.- 2007, 282, 9646) can be explained with a wet, polar, nonaqueous active-site conformation in the inward conformation, similar to the properties of 4-MI in the Freon solution. The biological implications for the enzyme mechanism are discussed.
Collapse
Affiliation(s)
- Ilya G Shenderovich
- University of Regensburg, Universitätsstrasse 31, 93053 Regensburg (Germany).
| | | | | | | | | | | | | |
Collapse
|
43
|
Debus RJ. FTIR studies of metal ligands, networks of hydrogen bonds, and water molecules near the active site Mn₄CaO₅ cluster in Photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:19-34. [PMID: 25038513 DOI: 10.1016/j.bbabio.2014.07.007] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 11/26/2022]
Abstract
The photosynthetic conversion of water to molecular oxygen is catalyzed by the Mn₄CaO₅ cluster in Photosystem II and provides nearly our entire supply of atmospheric oxygen. The Mn₄CaO₅ cluster accumulates oxidizing equivalents in response to light-driven photochemical events within Photosystem II and then oxidizes two molecules of water to oxygen. The Mn₄CaO₅ cluster converts water to oxygen much more efficiently than any synthetic catalyst because its protein environment carefully controls the cluster's reactivity at each step in its catalytic cycle. This control is achieved by precise choreography of the proton and electron transfer reactions associated with water oxidation and by careful management of substrate (water) access and proton egress. This review describes the FTIR studies undertaken over the past two decades to identify the amino acid residues that are responsible for this control and to determine the role of each. In particular, this review describes the FTIR studies undertaken to characterize the influence of the cluster's metal ligands on its activity, to delineate the proton egress pathways that link the Mn₄CaO₅ cluster with the thylakoid lumen, and to characterize the influence of specific residues on the water molecules that serve as substrate or as participants in the networks of hydrogen bonds that make up the water access and proton egress pathways. This information will improve our understanding of water oxidation by the Mn₄CaO₅ catalyst in Photosystem II and will provide insight into the design of new generations of synthetic catalysts that convert sunlight into useful forms of storable energy. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
Collapse
Affiliation(s)
- Richard J Debus
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521-0129, USA.
| |
Collapse
|
44
|
Debus RJ. Evidence from FTIR Difference Spectroscopy That D1-Asp61 Influences the Water Reactions of the Oxygen-Evolving Mn4CaO5 Cluster of Photosystem II. Biochemistry 2014; 53:2941-55. [DOI: 10.1021/bi500309f] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| |
Collapse
|
45
|
The structural comparison between membrane-associated human carbonic anhydrases provides insights into drug design of selective inhibitors. Biopolymers 2014; 101:769-78. [DOI: 10.1002/bip.22456] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/10/2013] [Accepted: 12/13/2013] [Indexed: 01/08/2023]
|
46
|
Service RJ, Hillier W, Debus RJ. Network of Hydrogen Bonds near the Oxygen-Evolving Mn4CaO5 Cluster of Photosystem II Probed with FTIR Difference Spectroscopy. Biochemistry 2014; 53:1001-17. [DOI: 10.1021/bi401450y] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Rachel J. Service
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
| | - Warwick Hillier
- Research
School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Richard J. Debus
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
| |
Collapse
|
47
|
Long H, King PW, Chang CH. Proton Transport in Clostridium pasteurianum [FeFe] Hydrogenase I: A Computational Study. J Phys Chem B 2014; 118:890-900. [PMID: 24405487 DOI: 10.1021/jp408621r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Hai Long
- National Renewable Energy Laboratory, MS ESIF301, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Paul W. King
- National Renewable Energy Laboratory, MS ESIF301, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Christopher H. Chang
- National Renewable Energy Laboratory, MS ESIF301, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| |
Collapse
|
48
|
Boone CD, Pinard M, McKenna R, Silverman D. Catalytic mechanism of α-class carbonic anhydrases: CO2 hydration and proton transfer. Subcell Biochem 2014; 75:31-52. [PMID: 24146373 DOI: 10.1007/978-94-007-7359-2_3] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The carbonic anhydrases (CAs; EC 4.2.1.1) are a family of metalloenzymes that catalyze the reversible hydration of carbon dioxide (CO2) and dehydration of bicarbonate (HCO3 (-)) in a two-step ping-pong mechanism: [Formula: see text] CAs are ubiquitous enzymes and are categorized into five distinct classes (α, β, γ, δ and ζ). The α-class is found primarily in vertebrates (and the only class of CA in mammals), β is observed in higher plants and some prokaryotes, γ is present only in archaebacteria whereas the δ and ζ classes have only been observed in diatoms.The focus of this chapter is on α-CAs as the structure-function relationship is best understood for this class, in particular for humans. The reader is referred to other reviews for an overview of the structure and catalytic mechanism of the other CA classes. The overall catalytic site structure and geometry of α-CAs are described in the first section of this chapter followed by the kinetic studies, binding of CO2, and the proton shuttle network.
Collapse
Affiliation(s)
- Christopher D Boone
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA,
| | | | | | | |
Collapse
|
49
|
Abstract
Recent research has taught us that most protonated species are decidedly not well represented by a simple proton addition. What is the actual nature of the hydrogen ion (the "proton") when H(+), HA, H2A(+), and so forth are written in formulas, chemical equations, and acid catalyzed reactions? In condensed media, H(+) must be solvated and is nearly always dicoordinate, as illustrated by isolable bisdiethyletherate salts having H(OEt2)2(+) cations and weakly coordinating anions. Even carbocations such as protonated alkenes have significant C-H···anion hydrogen bonding that gives the active protons two-coordinate character. Hydrogen bonding is everywhere, particularly when acids are involved. In contrast to the normal, asymmetric O-H···O hydrogen bonding found in water, ice, and proteins, short, strong, low-barrier (SSLB) H-bonding commonly appears when strong acids are present. Unusually low frequency IR νOHO bands are a good indicator of SSLB H-bonds, and curiously, bands associated with group vibrations near H(+) in low-barrier H-bonding often disappear from the IR spectrum. Writing H3O(+) (the Eigen ion), as often appears in textbooks, might seem more realistic than H(+) for an ionized acid in water. However, this, too, is an unrealistic description of H(aq)(+). The dihydrated H(+) in the H5O2(+) cation (the Zundel ion) gets somewhat closer but still fails to rationalize all the experimental and computational data on H(aq)(+). Researchers do not understand the broad swath of IR absorption from H(aq)(+), known as the "continuous broad absorption" (cba). Theory has not reproduced the cba, but it appears to be the signature of delocalized protons whose motion is faster than the IR time scale. What does this mean for reaction mechanisms involving H(aq)(+)? For the past decade, the carborane acid H(CHB11Cl11) has been the strongest known Brønsted acid. (It is now surpassed by the fluorinated analogue H(CHB11F11).) Carborane acids are strong enough to protonate alkanes at room temperature, giving H2 and carbocations. They protonate chloroalkanes to give dialkylchloronium ions, which decay to carbocations. By partially protonating an oxonium cation, they get as close to the fabled H4O(2+) ion as can be achieved outside of a computer.
Collapse
Affiliation(s)
- Christopher A. Reed
- Department of Chemistry, University of California, Riverside, California 92521, USA
| |
Collapse
|
50
|
Boone CD, Gill S, Tu C, Silverman DN, McKenna R. Structural, catalytic and stabilizing consequences of aromatic cluster variants in human carbonic anhydrase II. Arch Biochem Biophys 2013; 539:31-7. [PMID: 24036123 DOI: 10.1016/j.abb.2013.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/30/2013] [Accepted: 09/02/2013] [Indexed: 11/24/2022]
Abstract
The presence of aromatic clusters has been found to be an integral feature of many proteins isolated from thermophilic microorganisms. Residues found in aromatic cluster interact via π-π or C-H⋯π bonds between the phenyl rings, which are among the weakest interactions involved in protein stability. The lone aromatic cluster in human carbonic anhydrase II (HCA II) is centered on F226 with the surrounding aromatics F66, F95 and W97 located 12 Å posterior the active site; a location which could facilitate proper protein folding and active site construction. The role of F226 in the structure, catalytic activity and thermostability of HCA II was investigated via site-directed mutagenesis of three variants (F226I/L/W) into this position. The measured catalytic rates of the F226 variants via (18)O-mass spectrometry were identical to the native enzyme, but differential scanning calorimetry studies revealed a 3-4 K decrease in their denaturing temperature. X-ray crystallographic analysis suggests that the structural basis of this destabilization is via disruption and/or removal of weak C-H⋯π interactions between F226 to F66, F95 and W97. This study emphasizes the importance of the delicate arrangement of these weak interactions among aromatic clusters in overall protein stability.
Collapse
Affiliation(s)
- Christopher D Boone
- Biochemistry & Molecular Biology, University of Florida, P.O. Box 100245, Gainesville, FL 32610, United States
| | | | | | | | | |
Collapse
|