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Delfino D, Prandi B, Calcinai L, Ridolo E, Dellafiora L, Pedroni L, Nicoletta F, Cavazzini D, Tedeschi T, Folli C. Molecular Characterization of the Allergenic Arginine Kinase from the Edible Insect Hermetia illucens (Black Soldier Fly). Mol Nutr Food Res 2024; 68:e2300911. [PMID: 38629315 DOI: 10.1002/mnfr.202300911] [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: 12/22/2023] [Revised: 03/11/2024] [Indexed: 05/12/2024]
Abstract
SCOPE Arginine kinase (AK) is an important enzyme for energy metabolism of invertebrate cells by participating in the maintenance of constant levels of ATP. However, AK is also recognized as a major allergen in insects and crustaceans capable of cross-reactivity with sera of patients sensitized to orthologous proteins. In the perspective of introducing insects or their derivatives in the human diet in Western world, it is of primary importance to evaluate possible risks for allergic consumers. METHODS AND RESULTS This work reports the identification and characterization of AK from Hermetia illucens commonly known as the black soldier fly, a promising insect for human consumption. To evaluate allergenicity of AK from H. illucens, putative linear and conformational epitopes are identified by bioinformatics analyses, and Dot-Blot assays are carried out by using sera of patients allergic to shrimp or mites to validate the cross-reactivity. Gastrointestinal digestion reduces significantly the linear epitopes resulting in lower allergenicity, while the secondary structure is altered at increasing temperatures supporting the possible loss or reduction of conformational epitopes. CONCLUSION The results indicate that the possible allergenicity of AK should be taken in consideration when dealing with novel foods containing H. illucens or its derivatives.
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Affiliation(s)
- Danila Delfino
- Department of Food and Drug, University of Parma, Parma, 43124, Italy
| | - Barbara Prandi
- Department of Food and Drug, University of Parma, Parma, 43124, Italy
| | - Luisa Calcinai
- Department of Food and Drug, University of Parma, Parma, 43124, Italy
| | - Erminia Ridolo
- Allergy and Clinical Immunology, Medicine and Surgery Department, University of Parma, Parma, 43126, Italy
| | - Luca Dellafiora
- Department of Food and Drug, University of Parma, Parma, 43124, Italy
| | - Lorenzo Pedroni
- Department of Food and Drug, University of Parma, Parma, 43124, Italy
| | - Francesca Nicoletta
- Allergy and Clinical Immunology, Medicine and Surgery Department, University of Parma, Parma, 43126, Italy
| | - Davide Cavazzini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy
| | - Tullia Tedeschi
- Department of Food and Drug, University of Parma, Parma, 43124, Italy
| | - Claudia Folli
- Department of Food and Drug, University of Parma, Parma, 43124, Italy
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2
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Arifuzzaman M, Kwon E, Kim DY. Structural insights into the regulation of protein-arginine kinase McsB by McsA. Proc Natl Acad Sci U S A 2024; 121:e2320312121. [PMID: 38625935 PMCID: PMC11046695 DOI: 10.1073/pnas.2320312121] [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: 11/19/2023] [Accepted: 03/17/2024] [Indexed: 04/18/2024] Open
Abstract
In gram-positive bacteria, phosphorylated arginine functions as a protein degradation signal in a similar manner as ubiquitin in eukaryotes. The protein-arginine phosphorylation is mediated by the McsAB complex, where McsB possesses kinase activity and McsA modulates McsB activity. Although mcsA and mcsB are regulated within the same operon, the role of McsA in kinase activity has not yet been clarified. In this study, we determined the molecular mechanism by which McsA regulates kinase activity. The crystal structure of the McsAB complex shows that McsA binds to the McsB kinase domain through a second zinc-coordination domain and the subsequent loop region. This binding activates McsB kinase activity by rearranging the catalytic site, preventing McsB self-assembly, and enhancing stoichiometric substrate binding. The first zinc-coordination and coiled-coil domains of McsA further activate McsB by reassembling the McsAB oligomer. These results demonstrate that McsA is the regulatory subunit for the reconstitution of the protein-arginine kinase holoenzyme. This study provides structural insight into how protein-arginine kinase directs the cellular protein degradation system.
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Affiliation(s)
- Md Arifuzzaman
- College of Pharmacy, Yeungnam University, Gyeongsan38541, Republic of Korea
| | - Eunju Kwon
- Division of Life Science, Gyeongsang National University, Jinju52828, Republic of Korea
- Research Institute of Molecular Alchemy, Gyeongsang National University, Jinju52828, Republic of Korea
| | - Dong Young Kim
- College of Pharmacy, Yeungnam University, Gyeongsan38541, Republic of Korea
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3
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Albani S, Costanzi E, Hoang GL, Kuzikov M, Frings M, Ansari N, Demitri N, Nguyen TT, Rizzi V, Schulz JB, Bolm C, Zaliani A, Carloni P, Storici P, Rossetti G. Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. J Chem Inf Model 2024; 64:892-904. [PMID: 38051605 PMCID: PMC10865365 DOI: 10.1021/acs.jcim.3c01497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023]
Abstract
Many homodimeric enzymes tune their functions by exploiting either negative or positive cooperativity between subunits. In the SARS-CoV-2 Main protease (Mpro) homodimer, the latter has been suggested by symmetry in most of the 500 reported protease/ligand complex structures solved by macromolecular crystallography (MX). Here we apply the latter to both covalent and noncovalent ligands in complex with Mpro. Strikingly, our experiments show that the occupation of both active sites of the dimer originates from an excess of ligands. Indeed, cocrystals obtained using a 1:1 ligand/protomer stoichiometry lead to single occupation only. The empty binding site exhibits a catalytically inactive geometry in solution, as suggested by molecular dynamics simulations. Thus, Mpro operates through negative cooperativity with the asymmetric activity of the catalytic sites. This allows it to function with a wide range of substrate concentrations, making it resistant to saturation and potentially difficult to shut down, all properties advantageous for the virus' adaptability and resistance.
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Affiliation(s)
- Simone Albani
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- Faculty
of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen 52062, Germany
| | - Elisa Costanzi
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Gia Linh Hoang
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
| | - Maria Kuzikov
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
- Constructor University, School of Science, Campus Ring 1, Bremen 28759, Germany
| | - Marcus Frings
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Narjes Ansari
- Atomistic
Simulations, Italian Institute of Technology, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Nicola Demitri
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Toan T. Nguyen
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Valerio Rizzi
- School
of Pharmaceutical Sciences, University of
Geneva, Rue Michel Servet 1, 1206 Genève, Switzerland
| | - Jörg B. Schulz
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
| | - Carsten Bolm
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Andrea Zaliani
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg 22525, Germany
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
| | - Paolo Carloni
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Paola Storici
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Giulia Rossetti
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
- Jülich
Supercomputing Center (JSC), Forschungszentrum
Jülich, Jülich 52425, Germany
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4
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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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5
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The Arginine Kinase from the Tick Rhipicephalus sanguineus Is an Efficient Biocatalyst. Catalysts 2022. [DOI: 10.3390/catal12101178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Arginine kinase (AK) is a reversible enzyme that regulates invertebrates’ phosphagen arginine phosphate levels. AK also elicits an immune response in humans, and it is a major food allergen in crustacea and may be a target for novel antiparasitic drugs. Although AK has been primarily described in the shrimp, it is also present in other invertebrates, such as the brown tick Rhipicephalus sanguineus (Rs), the vector for Rocky Mountain Spotted Fever. Here we report the enzymatic activity and the crystal structure of AK from Rhipicephalus sanguineus (RsAK) in an open conformation without substrate or ligands and a theoretical structure of RsAK modeled bound with the substrate/product (Arg-ADP) in a closed conformation. The Michaelis-Menten kinetics confirmed that RsAK is an efficient biocatalyst due to its high kcat/Km parameter. The recombinant enzyme was expressed in bacteria and purified to a 20 mg/L culture yield. AK is an essential enzyme in invertebrates. Future work will be focused on the RsAK enzymatic inhibition that may lead to novel strategies to control this pest, a burden to animal and human health.
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6
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The characterization of novel monomeric creatine kinases in the early branching Alveolata species, Perkinsus marinus: Implications for phosphagen kinase evolution. Comp Biochem Physiol B Biochem Mol Biol 2022; 262:110758. [PMID: 35598705 DOI: 10.1016/j.cbpb.2022.110758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022]
Abstract
The genome of the unicellular molluscan parasite Perkinsus marinus contains at least five genes coding for putative creatine kinases (CK), a phosphoryl transfer enzyme which plays a key role in cellular energy transactions. Expression and kinetic analyses of three of the P. marinus CKs revealed them to be true CKs with catalytic properties in the range of typical metazoan CKs. A sequence comparison of the P. marinus CKs with a range of CK dimers and other dimeric phosphoryl transfer enzymes in this family (phosphagen kinases) showed that the P. marinus CKs lacked some of the critical residues involved in dimer stabilization, a trait all previously characterized CKs share. Size exclusion chromatography of all three expressed P. marinus CK constructs indicated they are monomeric, consistent with the observed lack of some critical dimer stabilizing residues. Phylogenetic analyses of the P. marinus CKs and putative dinoflagellate CKs with a broad range of monomeric and dimeric phosphagen kinases revealed that the Perkinsus CKs form a distinct, well-supported clade with dinoflagellate CKs which also lack the dimer stabilizing residues. Analysis of the genomic data for P. marinus showed the presence of putative genes for the two enzymes associated with creatine biosynthesis. CK in higher organisms plays a critical role in energy buffering in cell types displaying high and variable rates of ATP turnover. The presence of multiple CKs and the creatine biosynthetic pathway in P. marinus indicates that this unicellular parasite has the full complement of molecular machinery for CK-mediated energy buffering.
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7
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Kim DS, Jang K, Kim WS, Ryu M, Park JH, Kim YJ. Crystal Structure of H227A Mutant of Arginine Kinase in Daphnia magna Suggests the Importance of Its Stability. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030884. [PMID: 35164149 PMCID: PMC8839106 DOI: 10.3390/molecules27030884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022]
Abstract
Arginine kinase (AK) plays a crucial role in the survival of Daphnia magna, a water flea and a common planktonic invertebrate sensitive to water pollution, owing to the production of bioenergy. AK from D. magna (DmAK) has four highly conserved histidine residues, namely, H90, H227, H284, and H315 in the amino acid sequence. In contrast to DmAK WT (wild type), the enzyme activity of the H227A mutant decreases by 18%. To identify the structure-function relationship of this H227A mutant enzyme, the crystal 3D X-ray structure has been determined and an unfolding assay using anilino-1-naphthalenesulfonic acid (ANS) fluorescence has been undertaken. The results revealed that when compared to the DmAK WT, the hydrogen bonding between H227 and A135 was broken in the H227A crystal structure. This suggests that H227 residue, closed to the arginine binding site, plays an important role in maintaining the structural stability and maximizing the enzyme activity through hydrogen bonding with the backbone oxygen of A135.
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Affiliation(s)
- Da Som Kim
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea; (D.S.K.); (W.S.K.); (M.R.)
| | - Kiyoung Jang
- Department of Lifestyle Medicine, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan 54596, Korea;
| | - Wan Seo Kim
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea; (D.S.K.); (W.S.K.); (M.R.)
| | - Moonhee Ryu
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea; (D.S.K.); (W.S.K.); (M.R.)
| | - Jung Hee Park
- Division of Biotechnology, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea; (D.S.K.); (W.S.K.); (M.R.)
- Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
- Correspondence: (J.H.P.); (Y.J.K.)
| | - Yong Ju Kim
- Department of Lifestyle Medicine, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan 54596, Korea;
- Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea
- Department of Oriental Medicine Resources, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan 54596, Korea
- Correspondence: (J.H.P.); (Y.J.K.)
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8
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Petkowski JJ, Bains W, Seager S. Natural Products Containing 'Rare' Organophosphorus Functional Groups. Molecules 2019; 24:E866. [PMID: 30823503 PMCID: PMC6429109 DOI: 10.3390/molecules24050866] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/13/2019] [Accepted: 02/22/2019] [Indexed: 12/25/2022] Open
Abstract
Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.
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Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
| | - William Bains
- Rufus Scientific, 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK.
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
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9
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Reversing allosteric communication: From detecting allosteric sites to inducing and tuning targeted allosteric response. PLoS Comput Biol 2018; 14:e1006228. [PMID: 29912863 PMCID: PMC6023240 DOI: 10.1371/journal.pcbi.1006228] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 06/28/2018] [Accepted: 05/23/2018] [Indexed: 12/27/2022] Open
Abstract
The omnipresence of allosteric regulation together with the fundamental role of structural dynamics in this phenomenon have initiated a great interest to the detection of regulatory exosites and design of corresponding effectors. However, despite a general consensus on the key role of dynamics most of the earlier efforts on the prediction of allosteric sites are heavily crippled by the static nature of the underlying methods, which are either structure-based approaches seeking for deep surface pockets typical for “traditional” orthosteric drugs or sequence-based techniques exploiting the conservation of protein sequences. Because of the critical role of global protein dynamics in allosteric signaling, we investigate the hypothesis of reversibility in allosteric communication, according to which allosteric sites can be detected via the perturbation of the functional sites. The reversibility is tested here using our structure-based perturbation model of allostery, which allows one to analyze the causality and energetics of allosteric communication. We validate the “reverse perturbation” hypothesis and its predictive power on a set of classical allosteric proteins, then, on the independent extended benchmark set. We also show that, in addition to known allosteric sites, the perturbation of the functional sites unravels rather extended protein regions, which can host latent regulatory exosites. These protein parts that are dynamically coupled with functional sites can also be used for inducing and tuning allosteric communication, and an exhaustive exploration of the per-residue contributions to allosteric effects can eventually lead to the optimal modulation of protein activity. The site-effector interactions necessary for a specific mode and level of allosteric communication can be fine-tuned by adjusting the site’s structure to an available effector molecule and by the design or selection of an appropriate ligand. Recent advances in the development of allosteric drugs allow one to fully appreciate the sheer power of allosteric effectors in the avoiding toxicity, receptor desensitization and modulatory rather than on/off mode of action, compared to the traditional orthosteric compounds. The detection of allosteric sites is one of the major challenges in the quest for allosteric drugs. This work proposes a “reverse perturbation” approach for identifying allosteric sites as a result of a perturbation applied to the functional ones. We show that according to the traditional Monod-Changeux-Jacob’s definition of allostery, considering non-overlapping regulatory and functional sites is a critical prerequisite for the successful detection of allosteric sites. Using the reverse perturbation method, it is possible to determine wide protein regions with a potential to induce an allosteric response and to adjust its strength. Further studies on inducing and fine-tuning of allosteric signalling seem to be of a great importance for efficient design of non-orthosteric ligands in the development of novel drugs.
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10
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Peng Y, Hansen AL, Bruschweiler-Li L, Davulcu O, Skalicky JJ, Chapman MS, Brüschweiler R. The Michaelis Complex of Arginine Kinase Samples the Transition State at a Frequency That Matches the Catalytic Rate. J Am Chem Soc 2017; 139:4846-4853. [PMID: 28287709 DOI: 10.1021/jacs.7b00236] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Arginine kinase (AK), which is a member of the phosphagen kinase family, serves as a model system for studying the structural and dynamic determinants of biomolecular enzyme catalysis of all major states involved of the enzymatic cycle. These states are the apo state (substrate free), the Michaelis complex analogue AK:Arg:Mg·AMPPNP (MCA), a product complex analogue AK:pAIE:Mg·ADP (PCA), and the transition state analogue AK:Arg:Mg·ADP:NO3- (TSA). The conformational dynamics of these states have been studied by NMR relaxation dispersion measurements of the methyl groups of the Ile, Leu, and Val residues at two static magnetic fields. Although all states undergo significant amounts of μs-ms time scale dynamics, only the MCA samples a dominant excited state that resembles the TSA, as evidenced by the strong correlation between the relaxation dispersion derived chemical shift differences Δω and the equilibrium chemical shift differences Δδ of these states. The average lifetime of the MCA is 36 ms and the free energy difference to the TSA-like form is 8.5 kJ/mol. It is shown that the conformational energy landscape of the Michaelis complex analogue is shaped in a way that at room temperature it channels passage to the transition state, thereby determining the rate-limiting step of the phosphorylation reaction of arginine. Conversely, relaxation dispersion experiments of the TSA reveal that it samples the structures of the Michaelis complex analogue or the apo state as its dominant excited state. This reciprocal behavior shows that the free energy of the TSA, with all ligands bound, is lower by only about 8.9 kJ/mol than that of the Michaelis or apo complex conformations with the TSA ligands present.
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Affiliation(s)
| | | | | | - Omar Davulcu
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University , Portland, Oregon 97239, United States
| | - Jack J Skalicky
- Department of Biochemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - Michael S Chapman
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University , Portland, Oregon 97239, United States
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11
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Jiang S, Jia Z, Chen H, Wang L, Song L. The modulation of haemolymph arginine kinase on the extracellular ATP induced bactericidal immune responses in the Pacific oyster Crassostrea gigas. FISH & SHELLFISH IMMUNOLOGY 2016; 54:282-293. [PMID: 27033465 DOI: 10.1016/j.fsi.2016.03.153] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/23/2016] [Accepted: 03/22/2016] [Indexed: 06/05/2023]
Abstract
Arginine kinase is an important phosphagen kinase (PK) which plays an essential role in ATP buffering systems in invertebrates. In the present study, an arginine kinase (designated CgAK) was isolated by the lipopolysaccharide (LPS) affinity chromatography from the haemolymph of Crassostrea gigas. CgAK could directly bind to LPS in a concentration-dependent manner with the dissociation constant (Kd) of 2.46 × 10(-6) M. The interaction with LPS significantly decreased the ATP hydrolytic activity of CgAK, which in turn lead to the accumulation of ATP in vitro. The extracellular ATP stimulation could induce Ca(2+) influx, reactive oxygen species (ROS) production, and the release of lysosomal enzyme in the cellular immune response. In addition, ATP stimulation provoked the bactericidal activity towards Escherichia coli, and the scavenging ROS with N-acetyl-l-cysteine (NAC) abrogated the bactericidal activity, indicating that ATP stimulation could induce ROS-dependent antimicrobial activity in haemocytes. Collectively, the results demonstrated that the haemolymph CgAK could serve as an important purinergic regulator to modulate extracellular ATP, which might further have an important effect on the purinergic signaling-activated innate immune response of oyster.
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Affiliation(s)
- Shuai Jiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhihao Jia
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Hao Chen
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Lingling Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Linsheng Song
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China.
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12
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Lopez-Zavala AA, Sotelo-Mundo RR, Hernandez-Flores JM, Lugo-Sanchez ME, Sugich-Miranda R, Garcia-Orozco KD. Arginine kinase shows nucleoside diphosphate kinase-like activity toward deoxythymidine diphosphate. J Bioenerg Biomembr 2016; 48:301-8. [PMID: 27072556 DOI: 10.1007/s10863-016-9660-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/01/2016] [Indexed: 12/13/2022]
Abstract
Arginine kinase (AK) (ATP: L-arginine phosphotransferase, E.C. 2.7.3.3) catalyzes the reversible transfer of ATP γ-phosphate group to L-arginine to synthetize phospho-arginine as a high-energy storage. Previous studies suggest additional roles for AK in cellular processes. Since AK is found only in invertebrates and it is homologous to creatine kinase from vertebrates, the objective of this work was to demonstrate nucleoside diphosphate kinase-like activity for shrimp AK. For this, AK from marine shrimp Litopenaeus vannamei (LvAK) was purified and its activity was assayed for phosphorylation of TDP using ATP as phosphate donor. Moreover, by using high-pressure liquid chromatography (HPLC) the phosphate transfer reaction was followed. Also, LvAK tryptophan fluorescence emission changes were detected by dTDP titration, suggesting that the hydrophobic environment of Trp 221, which is located in the top of the active site, is perturbed upon dTDP binding. The kinetic constants for both substrates Arg and dTDP were calculated by isothermal titration calorimetry (ITC). Besides, docking calculations suggested that dTDP could bind LvAK in the same cavity where ATP bind, and LvAK basic residues (Arg124, 126 and 309) stabilize the dTDP phosphate groups and the pyrimidine base interact with His284 and Ser122. These results suggest that LvAK bind and phosphorylate dTDP being ATP the phosphate donor, thus describing a novel alternate nucleoside diphosphate kinase-like activity for this enzyme.
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Affiliation(s)
- Alonso A Lopez-Zavala
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Calle Rosales y Blvd. Luis Encinas s/n, Col. Centro, Hermosillo, Sonora, 83000, México
| | - Rogerio R Sotelo-Mundo
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora, 83304, México
| | - Jose M Hernandez-Flores
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora, 83304, México
| | - Maria E Lugo-Sanchez
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora, 83304, México
| | - Rocio Sugich-Miranda
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Calle Rosales y Blvd. Luis Encinas s/n, Col. Centro, Hermosillo, Sonora, 83000, México
| | - Karina D Garcia-Orozco
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora, 83304, México.
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13
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Guarnera E, Berezovsky IN. Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication. PLoS Comput Biol 2016; 12:e1004678. [PMID: 26939022 PMCID: PMC4777440 DOI: 10.1371/journal.pcbi.1004678] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/25/2015] [Indexed: 11/18/2022] Open
Abstract
Allostery is one of the pervasive mechanisms through which proteins in living systems carry out enzymatic activity, cell signaling, and metabolism control. Effective modeling of the protein function regulation requires a synthesis of the thermodynamic and structural views of allostery. We present here a structure-based statistical mechanical model of allostery, allowing one to observe causality of communication between regulatory and functional sites, and to estimate per residue free energy changes. Based on the consideration of ligand free and ligand bound systems in the context of a harmonic model, corresponding sets of characteristic normal modes are obtained and used as inputs for an allosteric potential. This potential quantifies the mean work exerted on a residue due to the local motion of its neighbors. Subsequently, in a statistical mechanical framework the entropic contribution to allosteric free energy of a residue is directly calculated from the comparison of conformational ensembles in the ligand free and ligand bound systems. As a result, this method provides a systematic approach for analyzing the energetics of allosteric communication based on a single structure. The feasibility of the approach was tested on a variety of allosteric proteins, heterogeneous in terms of size, topology and degree of oligomerization. The allosteric free energy calculations show the diversity of ways and complexity of scenarios existing in the phenomenology of allosteric causality and communication. The presented model is a step forward in developing the computational techniques aimed at detecting allosteric sites and obtaining the discriminative power between agonistic and antagonistic effectors, which are among the major goals in allosteric drug design. The 50th anniversary of Monod-Changeux-Jacob seminal paper “Allosteric proteins and cellular control systems” became the hallmark of a new wave in the allostery studies and the turning point in our vision of allostery and its implications in protein engineering and drug design. Recent experimental and theoretical works clearly show relevance of allosteric phenomenon to drug design, unraveling advantages of allosteric drugs in comparison to traditional orthosteric compounds. Remarkable simplicity of allosteric effectors and, at the same time, their potentially high specificity is one of the most important traits. The non conserved nature of allosteric ligands is a basis for avoiding drug resistance, and existence of latent regulatory sites make them attractive drug targets. The model presented in this work provides a theoretical framework for the quantification of the causality and energetics of allosteric regulation, which is a prerequisite for design of effector molecules with required characteristics. The synthesis between the thermodynamics of allostery and the intrinsic atomic nature of proteins and their interactions with the allosteric effectors accomplished in this work is a small initial step in the long endeavor towards future allosteric drugs.
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Affiliation(s)
- Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (ASTAR), Singapore
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (ASTAR), Singapore.,Department of Biological Sciences (DBS), National University of Singapore (NUS), Singapore
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14
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Okazaki N, Motomura S, Okazoe N, Yano D, Suzuki T. Cooperativity and evolution of Tetrahymena two-domain arginine kinase. Int J Biol Macromol 2015; 79:696-703. [PMID: 26049117 DOI: 10.1016/j.ijbiomac.2015.05.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/15/2015] [Accepted: 05/24/2015] [Indexed: 11/30/2022]
Abstract
Tetrahymena pyriformis contains two arginine kinases, a 40-kDa enzyme (AK1) with a myristoylation signal sequence at the N-terminus and a two-domain 80-kDa enzyme (AK2). The former is localized mainly in cilia and the latter is in the cytoplasm. AK1 was successfully synthesized using an insect cell-free protein synthesis system and subjected to peptide mass fingerprinting (PMF) analysis. The masses corresponding to unmodified N-terminal tryptic peptide or N-terminal myristoylated peptide were not observed, suggesting that N-terminal peptides were not ionized in this analysis. We performed PMF analyses for two other phosphagen kinases (PKs) with myristoylation signals, an AK from Nematostella vectensis and a PK from Ectocarpus siliculosus. In both cases, the myristoylated, N-terminal peptides were clearly identified. The differences between the experimental and theoretical masses were within 0.0165-0.0583 Da, supporting the accuracy of the identification. Domains 1 and 2 of Tetrahymena two-domain AK2 were expressed separately in Escherichia coli and the extent of cooperativity was estimated on the basis of their kinetic constants. The results suggested that each of the domains functions independently, namely no cooperativity is displayed between the two domains. This is in sharp contrast to the two-domain AK from Anthopleura.
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Affiliation(s)
- Noriko Okazaki
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520 Japan
| | - Shou Motomura
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520 Japan
| | - Nanaka Okazoe
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520 Japan
| | - Daichi Yano
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520 Japan
| | - Tomohiko Suzuki
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520 Japan.
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15
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Chouno K, Yano D, Uda K, Fujita T, Iwasaki N, Suzuki T. Arginine kinases from the marine feather star Tropiometra afra macrodiscus: The first finding of a prenylation signal sequence in metazoan phosphagen kinases. Comp Biochem Physiol B Biochem Mol Biol 2015; 187:55-61. [PMID: 25964010 DOI: 10.1016/j.cbpb.2015.04.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/28/2015] [Accepted: 04/29/2015] [Indexed: 01/10/2023]
Abstract
Two arginine kinase cDNAs (AK1 and AK2) were isolated from the marine feather star Tropiometra afra macrodiscus, and the gene structure (exon/intron organization) of AK1 was determined. The cDNA-derived amino acid sequences and the exon/intron organization of the Tropiometra AK1 gene were homologous to those of a human creatine kinase (CK) as well as the AK of the sea cucumber Stichopus. Phylogenetic analysis also supports the close relationship between human CKs and echinoderm AKs, indicating that the latter AKs evolved from an ancestral CK gene. We observed that the Tropiometra AK1 gene has a novel C-terminal extension (approximately 50 amino acid residues) encoded by a unique exon. Moreover, a typical prenylation signal sequence (CSLL) was found at the C-terminal end of this extension, suggesting that AK1 is anchored to a membrane. AK2 had no such C-terminal extension. This is the first finding of a prenylation signal in metazoan phosphagen kinases. Recombinant Tropiometra AK1 and AK2 enzymes were successfully expressed in Escherichia coli, and their kinetic constants were determined. Both enzymes showed activity comparable to that of typical invertebrate AKs.
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Affiliation(s)
- Kaai Chouno
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
| | - Daichi Yano
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
| | - Kouji Uda
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan
| | - Toshihiko Fujita
- Department of Zoology, National Museum of Nature and Science, Tsukuba 305-0005, Japan
| | - Nozomu Iwasaki
- Faculty of Geo-environment Science, Rissho University, Magechi 1700, Kumagaya 360-0194, Japan
| | - Tomohiko Suzuki
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan.
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16
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Merceron R, Awama AM, Montserret R, Marcillat O, Gouet P. The substrate-free and -bound crystal structures of the duplicated taurocyamine kinase from the human parasite Schistosoma mansoni. J Biol Chem 2015; 290:12951-63. [PMID: 25837252 DOI: 10.1074/jbc.m114.628909] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Indexed: 01/01/2023] Open
Abstract
The taurocyamine kinase from the blood fluke Schistosoma mansoni (SmTK) belongs to the phosphagen kinase (PK) family and catalyzes the reversible Mg(2+)-dependent transfer of a phosphoryl group between ATP and taurocyamine. SmTK is derived from gene duplication, as are all known trematode TKs. Our crystallographic study of SmTK reveals the first atomic structure of both a TK and a PK with a bilobal structure. The two unliganded lobes present a canonical open conformation and interact via their respective C- and N-terminal domains at a helix-mediated interface. This spatial arrangement differs from that observed in true dimeric PKs, in which both N-terminal domains make contact. Our structures of SmTK complexed with taurocyamine or l-arginine compounds explain the mechanism by which an arginine residue of the phosphagen specificity loop is crucial for substrate specificity. An SmTK crystal was soaked with the dead end transition state analog (TSA) components taurocyamine-NO3 (2-)-MgADP. One SmTK monomer was observed with two bound TSAs and an asymmetric conformation, with the first lobe semiclosed and the second closed. However, isothermal titration calorimetry and enzyme kinetics experiments showed that the two lobes function independently. A small angle x-ray scattering model of SmTK-TSA in solution with two closed active sites was generated.
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Affiliation(s)
- Romain Merceron
- From the Institut de Biologie et Chimie des Protéines, BMSSI-IBCP, UMR 5086 CNRS Université Lyon 1, 7, Passage du Vercors, 69367 Lyon Cedex 07, France and
| | - Ayman M Awama
- the Institut de Chimie et Biochimie Moléculaire et Supramoléculaire, UMR 5246 CNRS Université Lyon 1, 69622 Villeurbanne, France
| | - Roland Montserret
- From the Institut de Biologie et Chimie des Protéines, BMSSI-IBCP, UMR 5086 CNRS Université Lyon 1, 7, Passage du Vercors, 69367 Lyon Cedex 07, France and
| | - Olivier Marcillat
- the Institut de Chimie et Biochimie Moléculaire et Supramoléculaire, UMR 5246 CNRS Université Lyon 1, 69622 Villeurbanne, France
| | - Patrice Gouet
- From the Institut de Biologie et Chimie des Protéines, BMSSI-IBCP, UMR 5086 CNRS Université Lyon 1, 7, Passage du Vercors, 69367 Lyon Cedex 07, France and
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17
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Wang Z, Qiao Z, Ye S, Zhang R. Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains. ACTA ACUST UNITED AC 2015; 71:779-89. [PMID: 25849389 DOI: 10.1107/s1399004715001169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/20/2015] [Indexed: 12/27/2022]
Abstract
Tandem duplications and fusions of single genes have led to magnificent expansions in the divergence of protein structures and functions over evolutionary timescales. One of the possible results is polydomain enzymes with interdomain cooperativities, few examples of which have been structurally characterized at the full-length level to explore their innate synergistic mechanisms. This work reports the crystal structures of a double-domain phosphagen kinase in both apo and ligand-bound states, revealing a novel asymmetric L-shaped arrangement of the two domains. Unexpectedly, the interdomain connections are not based on a flexible hinge linker but on a rigid secondary-structure element: a long α-helix that tethers the tandem domains in relatively fixed positions. Besides the connective helix, the two domains also contact each other directly and form an interdomain interface in which hydrogen bonds and hydrophobic interactions further stabilize the L-shaped domain arrangement. Molecular-dynamics simulations show that the interface is generally stable, suggesting that the asymmetric domain arrangement crystallographically observed in the present study is not a conformational state simply restrained by crystal-packing forces. It is possible that the asymmetrically arranged tandem domains could provide a structural basis for further studies of the interdomain synergy.
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Affiliation(s)
- Zhiming Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Zhu Qiao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Sheng Ye
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Rongguang Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
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18
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The effect of Zn2+ on Exopalaemon carinicauda arginine kinase: Computational simulations including unfolding kinetics. Process Biochem 2015. [DOI: 10.1016/j.procbio.2014.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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19
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Geng HL, Bian MR, Liu Y, Cao J, Chen C, Wang ZY, Li ZY, Zeng LY, Wang XY, Wu QY, Xu KL. The D14 and R138 ion pair is involved in dimeric arginine kinase activity, structural stability and folding. Int J Biol Macromol 2014; 66:302-10. [DOI: 10.1016/j.ijbiomac.2014.02.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 02/18/2014] [Accepted: 02/19/2014] [Indexed: 11/25/2022]
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20
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Palmer A, Begres BN, Van Houten JM, Snider MJ, Fraga D. Characterization of a putative oomycete taurocyamine kinase: Implications for the evolution of the phosphagen kinase family. Comp Biochem Physiol B Biochem Mol Biol 2013; 166:173-81. [PMID: 23978736 DOI: 10.1016/j.cbpb.2013.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/12/2013] [Accepted: 08/14/2013] [Indexed: 11/16/2022]
Abstract
Phosphagen kinases (PKs) are known to be distributed throughout the animal kingdom, but have recently been discovered in some protozoan and bacterial species. Within animal species, these enzymes play a critical role in energy homeostasis by catalyzing the reversible transfer of a high-energy phosphoryl group from Mg⋅ATP to an acceptor molecule containing a guanidinium group. In this work, a putative PK gene was identified in the oomycete Phytophthora sojae that was predicted, based on sequence homology, to encode a multimeric hypotaurocyamine kinase. The recombinant P. sojae enzyme was purified and shown to catalyze taurocyamine phosphorylation efficiently (kcat/KM (taurocyamine) = 2 × 10(5) M(-1) s(-1)) and glycocyamine phosphorylation only weakly (kcat/KM (glycocyamine) = 2 × 10(2) M(-1) s(-1)), but lacked any observable kinase activity with the more ubiquitous guanidinium substrates, creatine or arginine. Additionally, the enzyme was observed to be dimeric but lacked cooperativity between the subunits in forming a transition state analog complex. These results suggest that protozoan PKs may exhibit more diversity in substrate specificity than was previously thought.
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Affiliation(s)
- Allyson Palmer
- Program in Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH 44691, USA
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21
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Crystal structure of shrimp arginine kinase in binary complex with arginine—a molecular view of the phosphagen precursor binding to the enzyme. J Bioenerg Biomembr 2013; 45:511-8. [DOI: 10.1007/s10863-013-9521-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/03/2013] [Indexed: 12/20/2022]
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22
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Mutation of residue arginine 330 of arginine kinase results in the generation of the oxidized form more susceptible. Int J Biol Macromol 2013; 54:238-43. [DOI: 10.1016/j.ijbiomac.2012.12.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Revised: 12/10/2012] [Accepted: 12/10/2012] [Indexed: 11/19/2022]
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23
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Clark SA, Davulcu O, Chapman MS. Crystal structures of arginine kinase in complex with ADP, nitrate, and various phosphagen analogs. Biochem Biophys Res Commun 2012; 427:212-7. [PMID: 22995310 DOI: 10.1016/j.bbrc.2012.09.053] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 09/09/2012] [Indexed: 11/29/2022]
Abstract
Arginine kinase catalyzes the reversible transfer of a phosphoryl group between ATP and l-arginine and is a monomeric homolog of the human enzyme creatine kinase. Arginine and creatine kinases belongs to the phosphagen kinase family of enzymes, which consists of eight known members, each of which is specific for its own phosphagen. Here, the source of phosphagen specificity in arginine kinase is investigated through the use of phosphagen analogs. Crystal structures have been determined for Limulus polyphemus arginine kinase with one of four arginine analogs bound in a transition state analog complex: l-ornithine, l-citrulline, imino-l-ornithine, and d-arginine. In all complexes, the enzyme achieves a closed conformation very similar to that of the cognate transition state analog complex, but differences are observed in the configurations of bound ligands. Arginine kinase exhibits no detectable activity towards ornithine, citrulline, or imino-l-ornithine, and only trace activity towards d-arginine. The crystal structures presented here demonstrate that phosphagen specificity is derived neither from a lock-and-key mechanism nor a modulation of induced-fit conformational changes, but potentially from subtle distortions in bound substrate configurations.
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Affiliation(s)
- Shawn A Clark
- Institute of Molecular Biophysics, Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306-4380, USA
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24
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Rivière G, Hologne M, Marcillat O, Lancelin JM. Dynamical properties of the loop 320s of substrate-free and substrate-bound muscle creatine kinase by NMR: evidence for independent subunits. FEBS J 2012; 279:2863-75. [PMID: 22715856 DOI: 10.1111/j.1742-4658.2012.08667.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Muscle creatine kinase (MCK; EC2.7.3.2) is a 86 kDa homodimer that belongs to the family of guanidino kinases. MCK has been intensively studied for several decades, but it is still not known why it is a dimer because this quaternary structure does not translate into obvious structural or functional advantages over the homologous monomeric arginine kinase. In particular, it remains to be demonstrated whether MCK subunits are independent. Here, we describe NMR chemical-shift perturbation and relaxation experiments designed to study the active site 320s flexible loop of this enzyme. The analysis was performed with the enzyme in its ligand-free and MgADP-complexed forms, as well as with the transition-state analogue abortive complex (MCK-Mg-ADP-creatine-nitrate ion). Our data indicate that each subunit can bind substrates independently.
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Affiliation(s)
- Gwladys Rivière
- Institut des Sciences Analytiques, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
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25
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Lopez-Zavala AA, Sotelo-Mundo RR, Garcia-Orozco KD, Isac-Martinez F, Brieba LG, Rudiño-Piñera E. Crystallization and X-ray diffraction studies of arginine kinase from the white Pacific shrimp Litopenaeus vannamei. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:783-5. [PMID: 22750864 PMCID: PMC3388921 DOI: 10.1107/s1744309112020180] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/04/2012] [Indexed: 11/10/2022]
Abstract
Crystals of an unligated monomeric arginine kinase from the Pacific whiteleg shrimp Litopenaeus vannamei (LvAK) were successfully obtained using the microbatch method. Crystallization conditions and preliminary X-ray diffraction analysis to 1.25 Å resolution are reported. Data were collected at 100 K on NSLS beamline X6A. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 56.5, b = 70.2, c = 81.7 Å. One monomer per asymmetric unit was found, with a Matthews coefficient (V(M)) of 2.05 Å(3) Da(-1) and 40% solvent content. Initial phases were determined by molecular replacement using a homology model of LvAK as the search model. Refinement was performed with PHENIX, with final R(work) and R(free) values of 0.15 and 0.19, respectively. Biological analysis of the structure is currently in progress.
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Affiliation(s)
- Alonso A. Lopez-Zavala
- Laboratorio de Biología Molecular de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Carretera a La Victoria km 0.6, Apartado Postal 1735, 83304 Hermosillo, SON, Mexico
| | - Rogerio R. Sotelo-Mundo
- Laboratorio de Biología Molecular de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Carretera a La Victoria km 0.6, Apartado Postal 1735, 83304 Hermosillo, SON, Mexico
| | - Karina D. Garcia-Orozco
- Laboratorio de Biología Molecular de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Carretera a La Victoria km 0.6, Apartado Postal 1735, 83304 Hermosillo, SON, Mexico
| | - Felipe Isac-Martinez
- Laboratorio de Biología Molecular de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Carretera a La Victoria km 0.6, Apartado Postal 1735, 83304 Hermosillo, SON, Mexico
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados (CINVESTAV Unidad Irapuato), Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, 36500 Irapuato, GTO, Mexico
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Avernida Universidad #2001, Col. Chamilpa, 62210 Cuernavaca, MOR, Mexico
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26
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Suzuki T, Yamamoto K, Tada H, Uda K. Cold-adapted features of arginine kinase from the deep-sea clam Calyptogena kaikoi. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2012; 14:294-303. [PMID: 22016076 DOI: 10.1007/s10126-011-9411-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 09/29/2011] [Indexed: 05/31/2023]
Abstract
The heterodont clam Calyptogena kaikoi, which inhabits depths exceeding 3,500 m where low ambient temperatures prevail, has an unusual two-domain arginine kinase (AK) with molecular mass of 80 kDa, twice that of typical AKs. The purpose of this work is to investigate the nature of the adaptations of this AK for functioning at low temperatures. Recombinant C. kaikoi AK constructs were expressed, and their two-substrate kinetic constants (k(cat), K(a), and K(ia)) were determined at 10°C and 25°C, respectively. When measured at 25°C, the K(ia) values were tenfold larger than those for corresponding K(a) values, while at 10°C, the K(ia) values decreased remarkably, but the K (a) values were almost unchanged. The Calyptogena two-domain enzyme has threefold higher catalytic efficiency, calculated by k (cat)/(K(a)(ARG)·K(ia)(ATP) ), at 10°C, than that at 25°C, reflecting adaptation for function at reduced ambient temperatures. The activation energy (E(a)) and thermodynamic parameters were determined for Calyptogena two-domain enzyme and compared with those of two-domain enzymes from mesophilic Corbicula and Anthopleura. The value for E(a) of Calyptogena enzyme were about half of those for mesophilic enzymes, and a larger decrease in entropy was observed in Calyptogena AK reaction. Although large decrease in entropy increases the ΔG(o‡) value and consequently lowers the k(cat) value, this is compensated with its lower E(a) value thereby minimizing the reduction in its k(cat) value. These thermodynamic properties, together with the kinetic ones, are also present in the separated domain 2 of the Calyptogena two-domain enzyme.
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Affiliation(s)
- Tomohiko Suzuki
- Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan.
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27
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Impact of intra-subunit interactions on the dimeric arginine kinase activity and structural stability. Int J Biol Macromol 2011; 49:822-31. [DOI: 10.1016/j.ijbiomac.2011.07.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 07/23/2011] [Accepted: 07/26/2011] [Indexed: 11/22/2022]
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28
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Wu QY, Li F, Wang XY, Chen ZJ. Impact of inter-subunit interactions on the dimeric arginine kinase activity and structural stability. Arch Biochem Biophys 2011; 512:61-8. [PMID: 21549684 DOI: 10.1016/j.abb.2011.04.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 04/20/2011] [Accepted: 04/22/2011] [Indexed: 11/19/2022]
Abstract
Arginine kinase (AK) is a key enzyme for cellular energy metabolism, catalyzing the reversible phosphoryl transfer from phosphoarginine to ADP in invertebrates. In this study, the inter-subunit hydrogen bonds between the Q53 and D200 and between D57 and D200 were disrupted to explore their roles in the activity and structural stability of Stichopus japonicus (S. japonicus) AK. Mutating Q53 and/or D57 to alanine (A) can cause pronounced loss of activity and substrate synergism, and cause distinct conformational changes. Spectroscopic experiments indicated that mutations destroying the inter-subunit hydrogen bonds impaired the structure of dimer AK, and resulted in a partially unfolded state. The inability to fold to the functional compact state made the mutants prone to be inactivated and aggregate under environmental stresses. Restoring hydrogen bonds in Q53E and D57E mutants could rescue the loss of activity and substrate synergism, and conformational changes. All those results suggested that the inter-subunit interactions played a key role in keeping the activity, substrate synergism and structural stability of dimer AK. The result herein may provide a clue in understanding the folding and self-assembly processes of oligomeric proteins.
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Affiliation(s)
- Qing-Yun Wu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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29
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Bush DJ, Kirillova O, Clark SA, Davulcu O, Fabiola F, Xie Q, Somasundaram T, Ellington WR, Chapman MS. The structure of lombricine kinase: implications for phosphagen kinase conformational changes. J Biol Chem 2011; 286:9338-50. [PMID: 21212263 DOI: 10.1074/jbc.m110.202796] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lombricine kinase is a member of the phosphagen kinase family and a homolog of creatine and arginine kinases, enzymes responsible for buffering cellular ATP levels. Structures of lombricine kinase from the marine worm Urechis caupo were determined by x-ray crystallography. One form was crystallized as a nucleotide complex, and the other was substrate-free. The two structures are similar to each other and more similar to the substrate-free forms of homologs than to the substrate-bound forms of the other phosphagen kinases. Active site specificity loop 309-317, which is disordered in substrate-free structures of homologs and is known from the NMR of arginine kinase to be inherently dynamic, is resolved in both lombricine kinase structures, providing an improved basis for understanding the loop dynamics. Phosphagen kinases undergo a segmented closing on substrate binding, but the lombricine kinase ADP complex is in the open form more typical of substrate-free homologs. Through a comparison with prior complexes of intermediate structure, a correlation was revealed between the overall enzyme conformation and the substrate interactions of His(178). Comparative modeling provides a rationale for the more relaxed specificity of these kinases, of which the natural substrates are among the largest of the phosphagen substrates.
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Affiliation(s)
- D Jeffrey Bush
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
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30
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Niu X, Bruschweiler-Li L, Davulcu O, Skalicky JJ, Brüschweiler R, Chapman MS. Arginine kinase: joint crystallographic and NMR RDC analyses link substrate-associated motions to intrinsic flexibility. J Mol Biol 2010; 405:479-96. [PMID: 21075117 DOI: 10.1016/j.jmb.2010.11.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 09/21/2010] [Accepted: 11/01/2010] [Indexed: 11/15/2022]
Abstract
The phosphagen kinase family, including creatine and arginine kinases (AKs), catalyzes the reversible transfer of a "high-energy" phosphate between ATP and a phosphoguanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differences among a recent set of AK structures were interpreted as a plastic deformation. Here, the structure of Limulus substrate-free AK is refined against high-resolution crystallographic data and compared quantitatively with NMR chemical shifts and residual dipolar couplings (RDCs). This demonstrates the feasibility of this type of RDC analysis of proteins that are large by NMR standards (42 kDa) and illuminates the solution structure, free from crystal-packing constraints. Detailed comparison of the 1.7 Å resolution substrate-free crystal structure against the 1.7 Å transition-state analog complex shows large substrate-induced domain motions that can be broken down into movements of smaller quasi-rigid bodies. The solution-state structure of substrate-free AK is most consistent with an equilibrium of substrate-free and substrate-bound structures, with the substrate-free form dominating, but with varying displacements of the quasi-rigid groups. Rigid-group rotations evident from the crystal structures are about axes previously associated with intrinsic millisecond dynamics using NMR relaxation dispersion. Thus, "substrate-induced" motions are along modes that are intrinsically flexible in the substrate-free enzyme and likely involve some degree of conformational selection.
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Affiliation(s)
- Xiaogang Niu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
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31
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Cooperativity in the two-domain arginine kinase from the sea anemone Anthopleura japonicus. II. Evidence from site-directed mutagenesis studies. Int J Biol Macromol 2010; 47:250-4. [DOI: 10.1016/j.ijbiomac.2010.04.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 04/17/2010] [Accepted: 04/22/2010] [Indexed: 11/20/2022]
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