1
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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.
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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
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2
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Deng J, Cui Q. Efficient Sampling of Cavity Hydration in Proteins with Nonequilibrium Grand Canonical Monte Carlo and Polarizable Force Fields. J Chem Theory Comput 2024; 20:1897-1911. [PMID: 38417108 DOI: 10.1021/acs.jctc.4c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Prediction of the hydration levels of protein cavities and active sites is important to both mechanistic analysis and ligand design. Due to the unique microscopic environment of these buried water molecules, a polarizable model is expected to be crucial for an accurate treatment of protein internal hydration in simulations. Here we adapt a nonequilibrium candidate Monte Carlo approach for conducting grand canonical Monte Carlo simulations with the Drude polarizable force field. The GPU implementation enables the efficient sampling of internal cavity hydration levels in biomolecular systems. We also develop an enhanced sampling approach referred to as B-walking, which satisfies detailed balance and readily combines with grand canonical integration to efficiently calculate quantitative binding free energies of water to protein cavities. Applications of these developments are illustrated in a solvent box and the polar ligand binding site in trypsin. Our simulation results show that including electronic polarization leads to a modest but clear improvement in the description of water position and occupancy compared to the crystal structure. The B-walking approach enhances the range of water sampling in different chemical potential windows and thus improves the accuracy of water binding free energy calculations.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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3
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Cai S, Tang H, Li B, Shao Y, Zhang D, Zheng H, Qiao T, Chu X, He G, Xue XS, Chen G. Formaldehyde-Mediated Hydride Liberation of Alkylamines for Intermolecular Reactions in Hexafluoroisopropanol. J Am Chem Soc 2024; 146:5952-5963. [PMID: 38408428 DOI: 10.1021/jacs.3c12215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The ability of alkylamines to spontaneously liberate hydride ions is typically restrained, except under specific intramolecular reaction settings. Herein, we demonstrate that this reactivity can be unlocked through simple treatment with formaldehyde in hexafluoroisopropanol (HFIP) solvent, thereby enabling various intermolecular hydride transfer reactions of alkylamines under mild conditions. Besides transformations of small molecules, these reactions enable unique late-stage modification of complex peptides. Mechanistic investigations uncover that the key to these intermolecular hydride transfer processes lies in the accommodating conformation of solvent-mediated macrocyclic transition states, where the aggregates of HFIP molecules act as dexterous proton shuttles. Importantly, negative hyperconjugation between the lone electron pair of nitrogen and the antibonding orbital of amine's α C-H bond plays a critical role in the C-H activation, promoting its hydride liberation.
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Affiliation(s)
- Shaokun Cai
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hong Tang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yingbo Shao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Danqi Zhang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hanliang Zheng
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Tianjiao Qiao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xin Chu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xiao-Song Xue
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
- Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
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4
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Bahrami F, Zhao Y. Carbonic anhydrase mimics with rationally designed active sites for fine-tuned catalytic activity and selectivity in ester hydrolysis. Catal Sci Technol 2023; 13:5702-5709. [PMID: 38013842 PMCID: PMC10544069 DOI: 10.1039/d3cy00704a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/21/2023] [Indexed: 11/29/2023]
Abstract
Numerous hydrolytic enzymes utilize zinc as a cofactor for catalysis. We here report water-soluble polymeric nanoparticles with zinc ions in active sites and a nearby base as a mimic of carbonic anhydrase (CA). Their pKa of 6.3-6.4 for zinc-bound water is lower than the 6.8-7.3 value for natural enzymes, which allows the catalyst to hydrolyze nonactivated alkyl esters under neutral conditions-a long sought-after goal for artificial esterases. The size and shape of the active site can be rationally tuned through a template used in molecular imprinting. Subtle structural changes in the template, including shifting an ethyl group by one C-N bond and removal of a methylene group, correlate directly with catalytic activity. A catalyst can be made to be highly specific or have broad substrate specificity through modular synthesis of templates.
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Affiliation(s)
- Foroogh Bahrami
- Department of Chemistry, Iowa State University Ames Iowa 50011-3111 USA +1 515 294 0105 +1 515 294 5845
| | - Yan Zhao
- Department of Chemistry, Iowa State University Ames Iowa 50011-3111 USA +1 515 294 0105 +1 515 294 5845
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5
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Raum HN, Fisher SZ, Weininger U. Energetics and dynamics of the proton shuttle of carbonic anhydrase II. Cell Mol Life Sci 2023; 80:286. [PMID: 37688664 PMCID: PMC10492700 DOI: 10.1007/s00018-023-04936-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/26/2023] [Accepted: 08/23/2023] [Indexed: 09/11/2023]
Abstract
Human carbonic anhydrase II catalyzes the reversible reaction of carbon dioxide and water to form bicarbonate and a proton. His64-mediated proton shuttling between the active site and the bulk solvent is rate limiting. Here we investigate the protonation behavior of His64 as well as its structural and dynamic features in a pH dependent way. We derive two pKa values for His64, 6.25 and 7.60, that we were able to assign to its inward and outward conformation. Furthermore, we show that His64 exists in both conformations equally, independent of pH. Both conformations display an equal distribution of their two neutral tautomeric states. The life time of each conformation is short and both states display high flexibility within their orientation. Therefore, His64 is never static, but rather poised to change conformation. These findings support an energetic, dynamic and solution ensemble-based framework for the high enzymatic activity of human carbonic anhydrase II.
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Affiliation(s)
- Heiner N Raum
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Suzanne Zoë Fisher
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362, Lund, Sweden
- Scientific Activities Division, European Spallation Source ERIC, P.O. Box 176, 22100, Lund, Sweden
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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6
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Demchenko AP. Proton transfer reactions: from photochemistry to biochemistry and bioenergetics. BBA ADVANCES 2023. [DOI: 10.1016/j.bbadva.2023.100085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
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7
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Arifuzzaman MD, Bose I, Bahrami F, Zhao Y. Imprinted Polymeric Nanoparticles as Artificial Enzymes for Ester Hydrolysis at Room Temperature and pH 7. CHEM CATALYSIS 2022; 2:2049-2065. [PMID: 38098612 PMCID: PMC10720975 DOI: 10.1016/j.checat.2022.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Natural esterases hydrolyze esters under physiological pHs but chemists often have to use strongly acidic or basic conditions for the same hydrolysis. We report synthetic nanoparticle catalysts that hydrolyze nonactivated alkyl esters at room temperature and neutral pH, with enzyme-like catalytic mechanisms and exquisite substrate selectivity. Unlike natural enzymes that denature easily at elevated temperatures, the synthetic catalysts become more active at higher temperatures.
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Affiliation(s)
| | | | - Foroogh Bahrami
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, U.S.A
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, U.S.A
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8
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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.
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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
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9
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Başaran E, Çakmak R, Şentürk M, Taskin-Tok T. Biological activity and molecular docking studies of some N-phenylsulfonamides against cholinesterases and carbonic anhydrase isoenzymes. J Mol Recognit 2022; 35:e2982. [PMID: 35842829 DOI: 10.1002/jmr.2982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/18/2022] [Accepted: 06/28/2022] [Indexed: 11/07/2022]
Abstract
In this research, a series of N-phenylsulfonamide derivatives (1-12) were designed, synthesized and investigated for their inhibitory potencies against carbonic anhydrase isoenzymes I, II and IX (hCA I, hCA II, and hCA IX) and cholinesterases (ChE), namely, acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). These compounds, whose inhibition potentials were evaluated for the first time, were characterized by spectroscopic techniques (1 H- and 13 C NMR and FT-IR). CA isoenzyme inhibitors are significant therapeutic targets, especially owing to their preventive/activation potential in the therapy processes of some diseases such as cancer, osteoporosis, and glaucoma. On the other hand, Cholinesterase inhibitors are valuable molecules with biological importance that can be employed in the therapy process of Alzheimer's patients. The results showed that the tested molecules had enzyme inhibition activities ranging from 9.7 to 93.7 nM against these five metabolic enzymes. Among the tested molecules, the methoxy and the hydroxyl group-containing compounds 10, 11, and 12 exhibited more enzyme inhibition activities when compared to standard compounds acetazolamide (AAZ), sulfapyridine, and sulfadiazine for CA isoenzymes and neostigmine for ChE, respectively. Of these three molecules, compound 12, which had a hydroxyl group in the para position in the aromatic ring, was determined to be the most active molecule against all enzymes. In silico work, molecular docking has also shown similar results and consistent with the experimental data in the study. As a result, we can say that some of the tested molecules might be used as promising inhibitor candidates for further studies on this topic.
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Affiliation(s)
- Eyüp Başaran
- Department of Chemistry and Chemical Processing Technologies, Vocational School of Technical Sciences, Batman University, Batman, Turkey
| | - Reşit Çakmak
- Medical Laboratory Techniques Program, Vocational School of Health Services, Batman University, Batman, Turkey
| | - Murat Şentürk
- Department of Biochemistry, Pharmacy Faculty, Ağrı Ibrahim Çecen University, Ağrı, Turkey
| | - Tugba Taskin-Tok
- Gaziantep University, Faculty of Arts and Sciences, Department of Chemistry, Gaziantep, Turkey.,Gaziantep University, Institute of Health Sciences, Department of Bioinformatics and Computational Biology, Gaziantep, Turkey
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10
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McConnell KD, Fitzkee NC, Emerson JP. Metal Ion Binding Induces Local Protein Unfolding and Destabilizes Human Carbonic Anhydrase II. Inorg Chem 2022; 61:1249-1253. [PMID: 34989562 PMCID: PMC8919859 DOI: 10.1021/acs.inorgchem.1c03271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Human carbonic anhydrase II (HCA) is a robust metalloprotein and an excellent biological model system to study the thermodynamics of metal ion coordination. Apo-HCA binds one zinc ion or two copper ions. We studied these binding processes at five temperatures (15-35 °C) using isothermal titration calorimetry, yielding thermodynamic parameters corrected for pH and buffer effects. We then sought to identify binding-induced structural changes. Our data suggest that binding at the active site organizes 6-8 residues; however, copper binding near the N-terminus results in a net unfolding of 6-7 residues. This surprising destabilization was confirmed using circular dichroism and protein stability measurements. Metal binding induced unfolding may represent an important regulatory mechanism, but it may be easily missed by NMR and X-ray crystallography. Thus, in addition to highlighting a highly novel binding-induced unfolding event, we demonstrate the value of calorimetry for studying the structural implications of metal binding.
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Affiliation(s)
- Kayla D. McConnell
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Nicholas C. Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Joseph P. Emerson
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
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11
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12
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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.
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Fu Y, Fan F, Zhang Y, Wang B, Cao Z. Conformational Change of H64 and Substrate Transportation: Insight Into a Full Picture of Enzymatic Hydration of CO 2 by Carbonic Anhydrase. Front Chem 2021; 9:706959. [PMID: 34307302 PMCID: PMC8299336 DOI: 10.3389/fchem.2021.706959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
The enzymatic hydration of CO2 into HCO3 - by carbonic anhydrase (CA) is highly efficient and environment-friendly measure for CO2 sequestration. Here extensive MM MD and QM/MM MD simulations were used to explore the whole enzymatic process, and a full picture of the enzymatic hydration of CO2 by CA was achieved. Prior to CO2 hydration, the proton transfer from the water molecule (WT1) to H64 is the rate-limiting step with the free energy barrier of 10.4 kcal/mol, which leads to the ready state with the Zn-bound OH-. The nucleophilic attack of OH- on CO2 produces HCO3 - with the free energy barrier of 4.4 kcal/mol and the free energy release of about 8.0 kcal/mol. Q92 as the key residue manipulates both CO2 transportation to the active site and release of HCO3 -. The unprotonated H64 in CA prefers in an inward orientation, while the outward conformation is favorable energetically for its protonated counterpart. The conformational transition of H64 between inward and outward correlates with its protonation state, which is mediated by the proton transfer and the product release. The whole enzymatic cycle has the free energy span of 10.4 kcal/mol for the initial proton transfer step and the free energy change of -6.5 kcal/mol. The mechanistic details provide a comprehensive understanding of the entire reversible conversion of CO2 into bicarbonate and roles of key residues in chemical and nonchemical steps for the enzymatic hydration of CO2.
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Affiliation(s)
- Yuzhuang Fu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Fangfang Fan
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Yuwei Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
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Hirakawa Y, Senda M, Fukuda K, Yu HY, Ishida M, Taira M, Kinbara K, Senda T. Characterization of a novel type of carbonic anhydrase that acts without metal cofactors. BMC Biol 2021; 19:105. [PMID: 34006275 PMCID: PMC8132391 DOI: 10.1186/s12915-021-01039-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/28/2021] [Indexed: 12/14/2022] Open
Abstract
Background Carbonic anhydrases (CAs) are universal metalloenzymes that catalyze the reversible conversion of carbon dioxide (CO2) and bicarbonate (HCO3-). They are involved in various biological processes, including pH control, respiration, and photosynthesis. To date, eight evolutionarily unrelated classes of CA families (α, β, γ, δ, ζ, η, θ, and ι) have been identified. All are characterized by an active site accommodating the binding of a metal cofactor, which is assumed to play a central role in catalysis. This feature is thought to be the result of convergent evolution. Results Here, we report that a previously uncharacterized protein group, named “COG4337,” constitutes metal-independent CAs from the newly discovered ι-class. Genes coding for COG4337 proteins are found in various bacteria and photosynthetic eukaryotic algae. Biochemical assays demonstrated that recombinant COG4337 proteins from a cyanobacterium (Anabaena sp. PCC7120) and a chlorarachniophyte alga (Bigelowiella natans) accelerated CO2 hydration. Unexpectedly, these proteins exhibited their activity under metal-free conditions. Based on X-ray crystallography and point mutation analysis, we identified a metal-free active site within the cone-shaped α+β barrel structure. Furthermore, subcellular localization experiments revealed that COG4337 proteins are targeted into plastids and mitochondria of B. natans, implicating their involvement in CO2 metabolism in these organelles. Conclusions COG4337 proteins shared a short sequence motif and overall structure with ι-class CAs, whereas they were characterized by metal independence, unlike any known CAs. Therefore, COG4337 proteins could be treated as a variant type of ι-class CAs. Our findings suggested that this novel type of ι-CAs can function even in metal-poor environments (e.g., the open ocean) without competition with other metalloproteins for trace metals. Considering the widespread prevalence of ι-CAs across microalgae, this class of CAs may play a role in the global carbon cycle. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01039-8.
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Affiliation(s)
- Yoshihisa Hirakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Kodai Fukuda
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hong Yang Yu
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.,School of High Energy Accelerator Science, SOKENDAI, 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Masaki Ishida
- Applied Research Laboratory, Radiation Science Center, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Masafumi Taira
- Support Center for Accelerator Science and Technology, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Kazushi Kinbara
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan. .,School of High Energy Accelerator Science, SOKENDAI, 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan. .,Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.
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15
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Yang Y, Tang N, Zhu Y, Zhang L, Cao X, Liu L, Xia W, Li P, Yang Y. A novel homozygous nonsense mutation in the CA2 gene (c.368G>A, p.W123X) linked to carbonic anhydrase II deficiency syndrome in a Chinese family. Metab Brain Dis 2021; 36:589-599. [PMID: 33555497 DOI: 10.1007/s11011-021-00677-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/24/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Carbonic anhydrase II deficiency syndrome is an autosomal recessive osteopetrosis with renal tubular acidosis and cerebral calcifications. We tried to detect the causative mutation for carbonic anhydrase II deficiency syndrome in a five-generation Chinese family. MATERIALS AND METHODS Genomic DNA was extracted from whole blood of the proband, his grandmother, parents, aunt, uncle and sister. The exomes were sequenced by whole exon sequencing followed by genetic analysis and Sanger sequencing validation. Then, physical and chemical properties studies and structure analysis were performed on mutated protein. Finally, Minigene model of vector plasmids for wild type and mutant type was constructed and transfected into human embryonic kidney 293T cells to further explore the expression change of CA2 transcript and protein after mutation. RESULTS Sequencing and genetic analysis have revealed the homozygous nonsense mutation of CA2 gene (c.368G > A, p.W123X) in the exon 4 of chromosome 8 of the proband, while it was not found in his grandmother, parents, aunt, uncle and sister. Furthermore, Sanger sequencing in the proband and his parents validated the mutation. Properties and structure of mutated CA2 proteins changed after mutation, especially in change of protein modification and hindrance of zinc ions binding, which may lead to decreased protein expression level of CA2. CONCLUSIONS We found a new homozygous nonsense mutation in CA2 gene (c.368G > A, p.W123X), which may be valuable in the early diagnosis and therapy of carbonic anhydrase II deficiency syndrome.
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Affiliation(s)
- Yan Yang
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China
| | - Nie Tang
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China
| | - Ying Zhu
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China
| | - Lei Zhang
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China
| | - Xu Cao
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China
| | - Limei Liu
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China
| | - Wei Xia
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China
| | - Pengqiu Li
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China
| | - Yi Yang
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China.
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China.
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16
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In Silico Investigation of Potential Applications of Gamma Carbonic Anhydrases as Catalysts of CO 2 Biomineralization Processes: A Visit to the Thermophilic Bacteria Persephonella hydrogeniphila, Persephonella marina, Thermosulfidibacter takaii, and Thermus thermophilus. Int J Mol Sci 2021; 22:ijms22062861. [PMID: 33799806 PMCID: PMC8000050 DOI: 10.3390/ijms22062861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 11/29/2022] Open
Abstract
Carbonic anhydrases (CAs) have been identified as ideal catalysts for CO2 sequestration. Here, we report the sequence and structural analyses as well as the molecular dynamics (MD) simulations of four γ-CAs from thermophilic bacteria. Three of these, Persephonella marina, Persephonella hydrogeniphila, and Thermosulfidibacter takaii originate from hydrothermal vents and one, Thermus thermophilus HB8, from hot springs. Protein sequences were retrieved and aligned with previously characterized γ-CAs, revealing differences in the catalytic pocket residues. Further analysis of the structures following homology modeling revealed a hydrophobic patch in the catalytic pocket, presumed important for CO2 binding. Monitoring of proton shuttling residue His69 (P. marina γ-CA numbering) during MD simulations of P. hydrogeniphila and P. marina’s γ-CAs (γ-PhCA and γ-PmCA), showed a different behavior to that observed in the γ-CA of Escherichia coli, which periodically coordinates Zn2+. This work also involved the search for hotspot residues that contribute to interface stability. Some of these residues were further identified as key in protein communication via betweenness centrality metric of dynamic residue network analysis. T. takaii’s γ-CA showed marginally lower thermostability compared to the other three γ-CA proteins with an increase in conformations visited at high temperatures being observed. Hydrogen bond analysis revealed important interactions, some unique and others common in all γ-CAs, which contribute to interface formation and thermostability. The seemingly thermostable γ-CA from T. thermophilus strangely showed increased unsynchronized residue motions at 423 K. γ-PhCA and γ-PmCA were, however, preliminarily considered suitable as prospective thermostable CO2 sequestration agents.
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17
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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.
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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
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18
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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.
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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.
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19
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Xin K, Chen Y, Zhang L, Xu B, Wang X, Wang G. Infrared photodissociation spectroscopic investigation on VO+ and NbO+ hydrolysis catalyzed by water molecules. Phys Chem Chem Phys 2021; 23:528-535. [DOI: 10.1039/d0cp04448b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We investigate the hydrolysis of vanadium/niobium monoxide cation (VO+/NbO+) with water molecules in the gas phase.
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Affiliation(s)
- Ke Xin
- School of Chemical Science and Engineering, Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University
- Shanghai
- China
| | - Yinjuan Chen
- School of Chemical Science and Engineering, Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University
- Shanghai
- China
| | - Luning Zhang
- School of Chemical Science and Engineering, Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University
- Shanghai
- China
| | - Bing Xu
- School of Chemical Science and Engineering, Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University
- Shanghai
- China
| | - Xuefeng Wang
- School of Chemical Science and Engineering, Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University
- Shanghai
- China
| | - Guanjun Wang
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University
- Shanghai 200438
- China
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20
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D’Ambrosio K, Di Fiore A, Buonanno M, Kumari S, Tiwari M, Supuran CT, Mishra CB, Monti SM, De Simone G. The crystal structures of 2-(4-benzhydrylpiperazin-1-yl)- N-(4-sulfamoylphenyl)acetamide in complex with human carbonic anhydrase II and VII provide insights into selective CA inhibitor development. NEW J CHEM 2021. [DOI: 10.1039/d0nj03544k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Our studies suggest that the acetamide linker and long tails are suitable structural features to design selective CA inhibitors.
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Affiliation(s)
| | - Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini-CNR
- Napoli
- Italy
| | | | - Shikha Kumari
- Dr. B. R. Ambedkar Centre for Biomedical Research
- University of Delhi
- Delhi
- India
| | - Manisha Tiwari
- Dr. B. R. Ambedkar Centre for Biomedical Research
- University of Delhi
- Delhi
- India
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21
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Kim JK, Lee C, Lim SW, Andring JT, Adhikari A, McKenna R, Kim CU. Structural insights into the effect of active-site mutation on the catalytic mechanism of carbonic anhydrase. IUCRJ 2020; 7:985-994. [PMID: 33209313 PMCID: PMC7642793 DOI: 10.1107/s2052252520011008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 08/11/2020] [Indexed: 05/26/2023]
Abstract
Enzymes are catalysts of biological processes. Significant insight into their catalytic mechanisms has been obtained by relating site-directed mutagenesis studies to kinetic activity assays. However, revealing the detailed relationship between structural modifications and functional changes remains challenging owing to the lack of information on reaction intermediates and of a systematic way of connecting them to the measured kinetic parameters. Here, a systematic approach to investigate the effect of an active-site-residue mutation on a model enzyme, human carbonic anhydrase II (CA II), is described. Firstly, structural analysis is performed on the crystallographic intermediate states of native CA II and its V143I variant. The structural comparison shows that the binding affinities and configurations of the substrate (CO2) and product (HCO3 -) are altered in the V143I variant and the water network in the water-replenishment pathway is restructured, while the proton-transfer pathway remains mostly unaffected. This structural information is then used to estimate the modifications of the reaction rate constants and the corresponding free-energy profiles of CA II catalysis. Finally, the obtained results are used to reveal the effect of the V143I mutation on the measured kinetic parameters (k cat and k cat/K m) at the atomic level. It is believed that the systematic approach outlined in this study may be used as a template to unravel the structure-function relationships of many other biologically important enzymes.
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Affiliation(s)
- Jin Kyun Kim
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Cheol Lee
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Seon Woo Lim
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jacob T. Andring
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Aniruddha Adhikari
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Chae Un Kim
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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22
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Rigual AJ, Cantero J, Risso M, Rodríguez P, Rodríguez S, Paulino M, Gamenara D, Veiga N. New mechanistic insights into the reversible aldol reaction catalysed by Rhamnulose-1-phosphate aldolase from Escherichia coli. MOLECULAR CATALYSIS 2020. [DOI: 10.1016/j.mcat.2020.111131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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23
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Manyumwa CV, Emameh RZ, Tastan Bishop Ö. Alpha-Carbonic Anhydrases from Hydrothermal Vent Sources as Potential Carbon Dioxide Sequestration Agents: In Silico Sequence, Structure and Dynamics Analyses. Int J Mol Sci 2020; 21:E8066. [PMID: 33138066 PMCID: PMC7662607 DOI: 10.3390/ijms21218066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 12/27/2022] Open
Abstract
With the increase in CO2 emissions worldwide and its dire effects, there is a need to reduce CO2 concentrations in the atmosphere. Alpha-carbonic anhydrases (α-CAs) have been identified as suitable sequestration agents. This study reports the sequence and structural analysis of 15 α-CAs from bacteria, originating from hydrothermal vent systems. Structural analysis of the multimers enabled the identification of hotspot and interface residues. Molecular dynamics simulations of the homo-multimers were performed at 300 K, 363 K, 393 K and 423 K to unearth potentially thermostable α-CAs. Average betweenness centrality (BC) calculations confirmed the relevance of some hotspot and interface residues. The key residues responsible for dimer thermostability were identified by comparing fluctuating interfaces with stable ones, and were part of conserved motifs. Crucial long-lived hydrogen bond networks were observed around residues with high BC values. Dynamic cross correlation fortified the relevance of oligomerization of these proteins, thus the importance of simulating them in their multimeric forms. A consensus of the simulation analyses used in this study suggested high thermostability for the α-CA from Nitratiruptor tergarcus. Overall, our novel findings enhance the potential of biotechnology applications through the discovery of alternative thermostable CO2 sequestration agents and their potential protein design.
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Affiliation(s)
- Colleen Varaidzo Manyumwa
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown 6140, South Africa;
| | - Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran;
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown 6140, South Africa;
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24
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Kim JK, Lee C, Lim SW, Adhikari A, Andring JT, McKenna R, Ghim CM, Kim CU. Elucidating the role of metal ions in carbonic anhydrase catalysis. Nat Commun 2020; 11:4557. [PMID: 32917908 PMCID: PMC7486293 DOI: 10.1038/s41467-020-18425-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 08/20/2020] [Indexed: 01/07/2023] Open
Abstract
Why metalloenzymes often show dramatic changes in their catalytic activity when subjected to chemically similar but non-native metal substitutions is a long-standing puzzle. Here, we report on the catalytic roles of metal ions in a model metalloenzyme system, human carbonic anhydrase II (CA II). Through a comparative study on the intermediate states of the zinc-bound native CA II and non-native metal-substituted CA IIs, we demonstrate that the characteristic metal ion coordination geometries (tetrahedral for Zn2+, tetrahedral to octahedral conversion for Co2+, octahedral for Ni2+, and trigonal bipyramidal for Cu2+) directly modulate the catalytic efficacy. In addition, we reveal that the metal ions have a long-range (~10 Å) electrostatic effect on restructuring water network in the active site. Our study provides evidence that the metal ions in metalloenzymes have a crucial impact on the catalytic mechanism beyond their primary chemical properties.
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Affiliation(s)
- Jin Kyun Kim
- grid.42687.3f0000 0004 0381 814XDepartment of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Cheol Lee
- grid.42687.3f0000 0004 0381 814XDepartment of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Seon Woo Lim
- grid.42687.3f0000 0004 0381 814XDepartment of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Aniruddha Adhikari
- grid.42687.3f0000 0004 0381 814XDepartment of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Jacob T. Andring
- grid.15276.370000 0004 1936 8091Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610 USA
| | - Robert McKenna
- grid.15276.370000 0004 1936 8091Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610 USA
| | - Cheol-Min Ghim
- grid.42687.3f0000 0004 0381 814XDepartment of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Chae Un Kim
- grid.42687.3f0000 0004 0381 814XDepartment of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
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25
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Clabbers MTB, Fisher SZ, Coinçon M, Zou X, Xu H. Visualizing drug binding interactions using microcrystal electron diffraction. Commun Biol 2020; 3:417. [PMID: 32737395 PMCID: PMC7395157 DOI: 10.1038/s42003-020-01155-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/15/2020] [Indexed: 01/30/2023] Open
Abstract
Visualizing ligand binding interactions is important for structure-based drug design and fragment-based screening methods. Rapid and uniform soaking with potentially reduced lattice defects make small macromolecular crystals attractive targets for studying drug binding using microcrystal electron diffraction (MicroED). However, so far no drug binding interactions could unambiguously be resolved by electron diffraction alone. Here, we use MicroED to study the binding of a sulfonamide inhibitor to human carbonic anhydrase isoform II (HCA II). We show that MicroED data can efficiently be collected on a conventional transmission electron microscope from thin hydrated microcrystals soaked with the clinical drug acetazolamide (AZM). The data are of high enough quality to unequivocally fit and resolve the bound inhibitor. We anticipate MicroED can play an important role in facilitating in-house fragment screening for drug discovery, complementing existing methods in structural biology such as X-ray and neutron diffraction. Clabbers et al. utilize MicroED to present the structure of both apo and inhibitor-bound human carbonic anhydrase II at a high resolution to clearly identify the interaction of the inhibitor, acetazolamide. This method eases the difficulty of both crystallizing the protein and soaking the inhibitor in a smaller protein crystal.
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26
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Koruza K, Murray AB, Mahon BP, Hopkins JB, Knecht W, McKenna R, Fisher SZ. Biophysical Characterization of Cancer-Related Carbonic Anhydrase IX. Int J Mol Sci 2020; 21:E5277. [PMID: 32722392 PMCID: PMC7432807 DOI: 10.3390/ijms21155277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 12/19/2022] Open
Abstract
Upregulation of carbonic anhydrase IX (CA IX) is associated with several aggressive forms of cancer and promotes metastasis. CA IX is normally constitutively expressed at low levels in selective tissues associated with the gastrointestinal tract, but is significantly upregulated upon hypoxia in cancer. CA IX is a multi-domain protein, consisting of a cytoplasmic region, a single-spanning transmembrane helix, an extracellular CA catalytic domain, and a proteoglycan-like (PG) domain. Considering the important role of CA IX in cancer progression and the presence of the unique PG domain, little information about the PG domain is known. Here, we report biophysical characterization studies to further our knowledge of CA IX. We report the 1.5 Å resolution crystal structure of the wild-type catalytic domain of CA IX as well as small angle X-ray scattering and mass spectrometry of the entire extracellular region. We used matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry to characterize the spontaneous degradation of the CA IX PG domain and confirm that it is only the CA IX catalytic domain that forms crystals. Small angle X-ray scattering analysis of the intact protein indicates that the PG domain is not randomly distributed and adopts a compact distribution of shapes in solution. The observed dynamics of the extracellular domain of CA IX could have physiological relevance, including observed cleavage and shedding of the PG domain.
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Affiliation(s)
- Katarina Koruza
- Department of Biology & Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (K.K.); (W.K.)
| | - A. Briana Murray
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; (A.B.M.); (R.M.)
| | - Brian P. Mahon
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA;
| | - Jesse B. Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA;
| | - Wolfgang Knecht
- Department of Biology & Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (K.K.); (W.K.)
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; (A.B.M.); (R.M.)
| | - S. Zoë Fisher
- Department of Biology & Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362 Lund, Sweden; (K.K.); (W.K.)
- Scientific Activities Division, European Spallation Source ERIC, Tunavägen 24, 22100 Lund, Sweden
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27
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Abstract
Neutron and X-ray crystallography are complementary to each other. While X-ray scattering is directly proportional to the number of electrons of an atom, neutrons interact with the atomic nuclei themselves. Neutron crystallography therefore provides an excellent alternative in determining the positions of hydrogens in a biological molecule. In particular, since highly polarized hydrogen atoms (H+) do not have electrons, they cannot be observed by X-rays. Neutron crystallography has its own limitations, mainly due to inherent low flux of neutrons sources, and as a consequence, the need for much larger crystals and for different data collection and analysis strategies. These technical challenges can however be overcome to yield crucial structural insights about protonation states in enzyme catalysis, ligand recognition, as well as the presence of unusual hydrogen bonds in proteins.
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28
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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.
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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
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29
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Affiliation(s)
- Gengnan Li
- Center for Interfacial Reaction Engineering and School of Chemical, Biological, and Materials Engineering, The University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Bin Wang
- Center for Interfacial Reaction Engineering and School of Chemical, Biological, and Materials Engineering, The University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Daniel E. Resasco
- Center for Interfacial Reaction Engineering and School of Chemical, Biological, and Materials Engineering, The University of Oklahoma, Norman, Oklahoma 73019, United States
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30
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Alterio V, Kellner M, Esposito D, Liesche-Starnecker F, Bua S, Supuran CT, Monti SM, Zeidler R, De Simone G. Biochemical and Structural Insights into Carbonic Anhydrase XII/Fab6A10 Complex. J Mol Biol 2019; 431:4910-4921. [DOI: 10.1016/j.jmb.2019.10.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/26/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022]
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31
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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.
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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.
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32
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Intact carbonic acid is a viable protonating agent for biological bases. Proc Natl Acad Sci U S A 2019; 116:20837-20843. [PMID: 31570591 DOI: 10.1073/pnas.1909498116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Carbonic acid H2CO3 (CA) is a key constituent of the universal CA/bicarbonate/CO2 buffer maintaining the pH of both blood and the oceans. Here we demonstrate the ability of intact CA to quantitatively protonate bases with biologically-relevant pKas and argue that CA has a previously unappreciated function as a major source of protons in blood plasma. We determine with high precision the temperature dependence of pKa(CA), pKa(T) = -373.604 + 16,500/T + 56.478 ln T. At physiological-like conditions pKa(CA) = 3.45 (I = 0.15 M, 37 °C), making CA stronger than lactic acid. We further demonstrate experimentally that CA decomposition to H2O and CO2 does not impair its ability to act as an ordinary carboxylic acid and to efficiently protonate physiological-like bases. The consequences of this conclusion are far reaching for human physiology and marine biology. While CA is somewhat less reactive than (H+)aq, it is more than 1 order of magnitude more abundant than (H+)aq in the blood plasma and in the oceans. In particular, CA is about 70× more abundant than (H+)aq in the blood plasma, where we argue that its overall protonation efficiency is 10 to 20× greater than that of (H+)aq, often considered to be the major protonating agent there. CA should thus function as a major source for fast in vivo acid-base reactivity in the blood plasma, possibly penetrating intact into membranes and significantly helping to compensate for (H+)aq's kinetic deficiency in sustaining the large proton fluxes that are vital for metabolic processes and rapid enzymatic reactions.
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33
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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.
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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
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Koruza K, Lafumat B, Nyblom M, Mahon BP, Knecht W, McKenna R, Fisher SZ. Structural comparison of protiated, H/D-exchanged and deuterated human carbonic anhydrase IX. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:895-903. [PMID: 31588921 PMCID: PMC6778848 DOI: 10.1107/s2059798319010027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/12/2019] [Indexed: 11/13/2022]
Abstract
In this work, the X-ray crystal structures of four different deuterium-labelled versions of a surface variant of human carbonic anhydrase IX are compared and discussed. The results show that the overall structure and active-site organization of each version are essentially the same, paving the way for future neutron protein crystallography studies. Human carbonic anhydrase IX (CA IX) expression is upregulated in hypoxic solid tumours, promoting cell survival and metastasis. This observation has made CA IX a target for the development of CA isoform-selective inhibitors. To enable structural studies of CA IX–inhibitor complexes using X-ray and neutron crystallography, a CA IX surface variant (CA IXSV; the catalytic domain with six surface amino-acid substitutions) has been developed that can be routinely crystallized. Here, the preparation of protiated (H/H), H/D-exchanged (H/D) and deuterated (D/D) CA IXSV for crystallographic studies and their structural comparison are described. Four CA IXSV X-ray crystal structures are compared: two H/H crystal forms, an H/D crystal form and a D/D crystal form. The overall active-site organization in each version is essentially the same, with only minor positional changes in active-site solvent, which may be owing to deuteration and/or resolution differences. Analysis of the crystal contacts and packing reveals different arrangements of CA IXSV compared with previous reports. To our knowledge, this is the first report comparing three different deuterium-labelled crystal structures of the same protein, marking an important step in validating the active-site structure of CA IXSV for neutron protein crystallography.
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Affiliation(s)
- K Koruza
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
| | - B Lafumat
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
| | - M Nyblom
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
| | - B P Mahon
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - W Knecht
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
| | - R McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - S Z Fisher
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
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35
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Koruza K, Mahon BP, Blakeley MP, Ostermann A, Schrader TE, McKenna R, Knecht W, Fisher SZ. Using neutron crystallography to elucidate the basis of selective inhibition of carbonic anhydrase by saccharin and a derivative. J Struct Biol 2019; 205:147-154. [DOI: 10.1016/j.jsb.2018.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/30/2018] [Accepted: 12/21/2018] [Indexed: 11/25/2022]
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36
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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]
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37
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Roston D, Lu X, Fang D, Demapan D, Cui Q. Analysis of Phosphoryl-Transfer Enzymes with QM/MM Free Energy Simulations. Methods Enzymol 2018; 607:53-90. [PMID: 30149869 DOI: 10.1016/bs.mie.2018.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We discuss the application of quantum mechanics/molecular mechanics (QM/MM) free energy simulations to the analysis of phosphoryl transfers catalyzed by two enzymes: alkaline phosphatase and myosin. We focus on the nature of the transition state and the issue of mechanochemical coupling, respectively, in the two enzymes. The results illustrate unique insights that emerged from the QM/MM simulations, especially concerning the interpretation of experimental data regarding the nature of enzymatic transition states and coupling between global structural transition and catalysis in the active site. We also highlight a number of technical issues worthy of attention when applying QM/MM free energy simulations, and comment on a number of technical and mechanistic issues that require further studies.
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Affiliation(s)
- Daniel Roston
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Dong Fang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Darren Demapan
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States.
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38
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Parida R, Giri S. Negative influence of pK a on activation energy barrier: A case study for double proton transfer reaction in inorganic acid dimers. J Comput Chem 2018; 39:993-998. [PMID: 29424042 DOI: 10.1002/jcc.25177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 11/06/2022]
Abstract
Strength of acid can be determined by means of pKa value. Attempts have been made to find a relationship between pKa and activation energy barrier for a double proton transfer (DPT) reaction in inorganic acid dimers. Negative influence of pKa is observed on activation energy (Ea ) which is contrary to the general convention of pKa . Four different levels of theories with two different basis sets have been used to calculate the activation energy barrier of the DPT reaction in inorganic acid dimers. A model based on first and second order polynomial has been created to find the relationship between activation energy for DPT reaction. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Rakesh Parida
- Department of Chemistry, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Santanab Giri
- Department of Chemistry, National Institute of Technology, Rourkela, Odisha, 769008, India
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39
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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.
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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.
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40
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Koruza K, Lafumat B, Végvári Á, Knecht W, Fisher S. Deuteration of human carbonic anhydrase for neutron crystallography: Cell culture media, protein thermostability, and crystallization behavior. Arch Biochem Biophys 2018. [DOI: 10.1016/j.abb.2018.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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41
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Supuran CT, Alterio V, Di Fiore A, D' Ambrosio K, Carta F, Monti SM, De Simone G. Inhibition of carbonic anhydrase IX targets primary tumors, metastases, and cancer stem cells: Three for the price of one. Med Res Rev 2018; 38:1799-1836. [PMID: 29635752 DOI: 10.1002/med.21497] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/22/2018] [Accepted: 03/02/2018] [Indexed: 12/12/2022]
Abstract
Human carbonic anhydrase (CA) IX is a tumor-associated protein, since it is scarcely present in normal tissues, but highly overexpressed in a large number of solid tumors, where it actively contributes to survival and metastatic spread of tumor cells. Due to these features, the characterization of its biochemical, structural, and functional features for drug design purposes has been extensively carried out, with consequent development of several highly selective small molecule inhibitors and monoclonal antibodies to be used for different purposes. Aim of this review is to provide a comprehensive state-of-the-art of studies performed on this enzyme, regarding structural, functional, and biomedical aspects, as well as the development of molecules with diagnostic and therapeutic applications for cancer treatment. A brief description of additional pharmacologic applications for CA IX inhibition in other diseases, such as arthritis and ischemia, is also provided.
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Affiliation(s)
- Claudiu T Supuran
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Florence, Italy
| | | | - Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini-CNR, Naples, Italy
| | | | - Fabrizio Carta
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Florence, Italy
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42
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Kovalevsky A, Aggarwal M, Velazquez H, Cuneo MJ, Blakeley MP, Weiss KL, Smith JC, Fisher SZ, McKenna R. "To Be or Not to Be" Protonated: Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and Simulation. Structure 2018; 26:383-390.e3. [PMID: 29429876 DOI: 10.1016/j.str.2018.01.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/15/2017] [Accepted: 01/10/2018] [Indexed: 10/18/2022]
Abstract
Human carbonic anhydrases (hCAs) play various roles in cells, and have been drug targets for decades. Sequence similarities of hCA isoforms necessitate designing specific inhibitors, which requires detailed structural information for hCA-inhibitor complexes. We present room temperature neutron structures of hCA II in complex with three clinical drugs that provide in-depth analysis of drug binding, including protonation states of the inhibitors, hydration water structure, and direct visualization of hydrogen-bonding networks in the enzyme's active site. All sulfonamide inhibitors studied bind to the Zn metal center in the deprotonated, anionic, form. Other chemical groups of the drugs can remain neutral or be protonated when bound to hCA II. MD simulations have shown that flexible functional groups of the inhibitors may alter their conformations at room temperature and occupy different sub-sites. This study offers insights into the design of specific drugs to target cancer-related hCA isoform IX.
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Affiliation(s)
- Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Mayank Aggarwal
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hector Velazquez
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Biochemistry and Cellular Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Matthew J Cuneo
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Matthew P Blakeley
- Large Scale Structures Group, Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Kevin L Weiss
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jeremy C Smith
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Biochemistry and Cellular Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - S Zoë Fisher
- Scientific Activities Division, Science Directorate, European Spallation Source ERIC, 22100 Lund, Sweden; Department of Biology, Lund University, 35 Sölvegatan, 22362 Lund, Sweden
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
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43
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Morris RH. Mechanisms of the H2- and transfer hydrogenation of polar bonds catalyzed by iron group hydrides. Dalton Trans 2018; 47:10809-10826. [DOI: 10.1039/c8dt01804a] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This Perspective describes the mechanism-based development of iron-group catalysts for the asymmetric hydrogenation of ketones and imines.
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44
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Brahmachari U, Gonthier JF, Sherrill CD, Barry BA. Chloride Maintains a Protonated Internal Water Network in the Photosynthetic Oxygen Evolving Complex. J Phys Chem B 2017; 121:10327-10337. [DOI: 10.1021/acs.jpcb.7b08358] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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45
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Kumar V, Pilati T, Quici S, Chierotti MR, Nervi C, Gobetto R, Resnati G. Proton in a Confined Space: Structural Studies of H + ⊂Crypt-111 Iodide and Some Halogen-Bonded Derivatives. Chemistry 2017; 23:14462-14468. [PMID: 28657685 DOI: 10.1002/chem.201701699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 06/27/2017] [Indexed: 11/06/2022]
Abstract
Experimental observations and modeling data are reported on the solid-state structural features of crypt- 111⋅HI (1) and the three-component co-crystals that 1 forms with α,ω-diiodoperfluoroalkanes 2 a-d. X-ray analyses indicate that, in all five systems and at low temperature, the caged proton is covalently bonded to a single nitrogen atom and is involved in a network of intramolecular hydrogen bonds. In contrast, room-temperature, solid-state 15 N NMR spectroscopy suggests magnetic equivalency of the two N atoms of crypt-111 in both 1 and co-crystals of 1 with diiodoperfluoroalkanes. Computational modelling confirms that the acidic hydrogen inside the cavity preferentially sits along the internitrogen axis and is covalently bonded to one nitrogen. The computed energy barriers suggest that the hopping of the encapsulated proton between the two N atoms of the cage can occur in the halogen-bonded co-crystals of 1⋅2, but it is hardly possible in the pure H+ ⊂crypt-111 iodide 1. These different pictures of the proton position and dynamics obtained by using different techniques and conditions confirm the unique characteristics of the confined space within the cavity of crypr-111 and the distinctive features of processes occurring therein.
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Affiliation(s)
- Vijith Kumar
- Nanostructured Fluorinated Materials Laboratory (NFMLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milan, Italy
| | - Tullio Pilati
- Nanostructured Fluorinated Materials Laboratory (NFMLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milan, Italy
| | - Silvio Quici
- CNR, Istituto di Scienze e Tecnologie Molecolari, Via C. Golgi 19, 20133, Milan, Italy
| | - Michele R Chierotti
- Department of Chemistry and NIS, University of Turin, Via P. Giuria 7, 10125, Turin, Italy
| | - Carlo Nervi
- Department of Chemistry and NIS, University of Turin, Via P. Giuria 7, 10125, Turin, Italy
| | - Roberto Gobetto
- Department of Chemistry and NIS, University of Turin, Via P. Giuria 7, 10125, Turin, Italy
| | - Giuseppe Resnati
- Nanostructured Fluorinated Materials Laboratory (NFMLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milan, Italy
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46
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Improved molecular recognition of Carbonic Anhydrase IX by polypeptide conjugation to acetazolamide. Bioorg Med Chem 2017; 25:5838-5848. [DOI: 10.1016/j.bmc.2017.09.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/10/2017] [Accepted: 09/13/2017] [Indexed: 02/04/2023]
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47
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Hou GL, Wang XB, Valiev M. Formation of (HCOO–)(H2SO4) Anion Clusters: Violation of Gas-Phase Acidity Predictions. J Am Chem Soc 2017; 139:11321-11324. [DOI: 10.1021/jacs.7b05964] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Gao-Lei Hou
- Physical
Sciences Division, Pacific Northwest National Laboratory, 902 Battelle
Boulevard, P.O. Box 999, MS K8-88, Richland, Washington 99352, United States
| | - Xue-Bin Wang
- Physical
Sciences Division, Pacific Northwest National Laboratory, 902 Battelle
Boulevard, P.O. Box 999, MS K8-88, Richland, Washington 99352, United States
| | - Marat Valiev
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
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48
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Katada M, Hsu PJ, Fujii A, Kuo JL. Temperature and Size Dependence of Characteristic Hydrogen-Bonded Network Structures with Ion Core Switching in Protonated (Methanol)6–10–(Water)1 Mixed Clusters: A Revisit. J Phys Chem A 2017; 121:5399-5413. [DOI: 10.1021/acs.jpca.7b03762] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marusu Katada
- Department
of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Po-Jen Hsu
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
| | - Asuka Fujii
- Department
of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Jer-Lai Kuo
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan
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49
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Bhattacherjee A, Wategaonkar S. Role of the C(2)–H Hydrogen Bond Donor in Gas-Phase Microsolvation of Imidazole Derivatives with ROH (R = CH3, C2H5). J Phys Chem A 2017; 121:4283-4295. [DOI: 10.1021/acs.jpca.7b03329] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aditi Bhattacherjee
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
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Oksanen E, Chen JCH, Fisher SZ. Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules. Molecules 2017; 22:molecules22040596. [PMID: 28387738 PMCID: PMC6154725 DOI: 10.3390/molecules22040596] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 11/21/2022] Open
Abstract
The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, the protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. This article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.
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Affiliation(s)
- Esko Oksanen
- Science Directorate, European Spallation Source ERIC, Tunavägen 24, 22100 Lund, Sweden.
- Department of Biochemistry and Structural Biology, Lund University, Sölvegatan 39, 22362 Lund, Sweden.
| | - Julian C-H Chen
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Suzanne Zoë Fisher
- Science Directorate, European Spallation Source ERIC, Tunavägen 24, 22100 Lund, Sweden.
- Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.
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