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Raksanoh V, Shank L, Prangkio P, Yentongchai M, Sakdee S, Imtong C, Angsuthanasombat C. Zn 2+-dependent autocatalytic activity of the Bordetella pertussis CyaA-hemolysin. Biochem Biophys Res Commun 2017; 485:720-724. [PMID: 28238785 DOI: 10.1016/j.bbrc.2017.02.113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 02/22/2017] [Indexed: 11/28/2022]
Abstract
Proteolytic degradation of the ∼100-kDa isolated RTX (Repeat-in-ToXin) subdomain (CyaA-RTX) of the Bordetella pertussis CyaA-hemolysin (CyaA-Hly) was evidently detected upon solely-prolonged incubation. Here, a truncated CyaA-Hly fragment (CyaA-HP/BI) containing hydrophobic and acylation regions connected with the first RTX block (BI1015-1088) was constructed as a putative precursor for investigating its potential autocatalysis. The 70-kDa His-tagged CyaA-HP/BI fragment which was over-expressed in Escherichia coli as insoluble aggregate was entirely solubilized with 4 M urea. After re-naturation in a Ni2+-NTA affinity column, the purified-refolded CyaA-HP/BI fragment in HEPES buffer (pH 7.4) supplemented with 2 mM CaCl2 was completely degraded upon incubation at 37 °C for 3 h. Addition of 1,10-phenanthroline‒an inhibitor of Zn2+-dependent metalloproteases markedly reduced the extent of degradation for CyaA-HP/BI and CyaA-RTX, but the degradative effect was clearly enhanced by addition of 100 mM ZnCl2. Structural analysis of a plausible CyaA-HP/BI model revealed a potential Zn2+-binding His-Asp cluster located between the acylation region and RTX-BI1015-1088. Moreover, Arg997‒one of the identified cleavage sites of the CyaA-RTX fragment was located in close proximity to the Zn2+-binding catalytic site. Overall results demonstrated for the first time that the observed proteolysis of CyaA-HP/BI and CyaA-RTX fragments is conceivably due to their Zn2+-dependent autocatalytic activity.
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Affiliation(s)
- Veerada Raksanoh
- Division of Biochemistry and Biochemical Technology, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Lalida Shank
- Division of Biochemistry and Biochemical Technology, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.
| | - Panchika Prangkio
- Division of Biochemistry and Biochemical Technology, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Mattayaus Yentongchai
- Bacterial Protein Toxin Research Cluster, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom 73170, Thailand
| | - Somsri Sakdee
- Bacterial Protein Toxin Research Cluster, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom 73170, Thailand
| | - Chompounoot Imtong
- Division of Biology, Department of Science, Faculty of Science and Technology, Prince of Songkla University, Pattani 94000, Thailand
| | - Chanan Angsuthanasombat
- Bacterial Protein Toxin Research Cluster, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom 73170, Thailand; Laboratory of Molecular Biophysics and Chemical Biology, Biophysics Institute for Research and Development (BIRD), Bangkok 10160, Thailand.
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2
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Akparov VK, Timofeev VI, Maghsoudi NN, Kuranova IP. Three-dimensional structure of porcine pancreatic carboxypeptidase B with an acetate ion and two zinc atoms in the active site. CRYSTALLOGR REP+ 2017. [DOI: 10.1134/s106377451702002x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Motahari A, Fattahi A. Theoretical aspects of the enhancement of metal binding affinity by intramolecular hydrogen bonding and modulating pKavalues. NEW J CHEM 2017. [DOI: 10.1039/c7nj02693e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The stability balance shows that the hydrogen bond network and modulation of pKavalues can enhance the metal binding affinity.
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Affiliation(s)
- Ahmad Motahari
- Faculty of Chemistry
- Sharif University of Technology
- P. O. Box 11365-9516
- Tehran
- Iran
| | - Alireza Fattahi
- Faculty of Chemistry
- Sharif University of Technology
- P. O. Box 11365-9516
- Tehran
- Iran
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4
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Li F, Xu D. Functional role of R462 in the degradation of hyaluronan catalyzed by hyaluronate lyase from Streptococcus pneumoniae. J Mol Model 2015; 21:196. [PMID: 26169310 DOI: 10.1007/s00894-015-2724-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/08/2015] [Indexed: 11/25/2022]
Abstract
Hyaluronan lyase from Streptococcus pneumoniae can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. Hyaluronan can regulate water balance, osmotic pressure, and act as an ion exchange resin. Followed by our recent work on the catalytic reaction mechanism and substrate binding mode, we in this work further investigate the functional role of active site arginine residue, R462, in the degradation of hyaluronan. The site directed mutagenesis simulation of R462A and R462Q were modeled using a combined quantum mechanical and molecular mechanical method. The overall substrate binding features upon mutations do not have significant changes. The energetic profiles for the reaction processes are essentially the same as that in wild type enzyme, but significant activation barrier height changes can be observed. Both mutants were shown to accelerate the overall enzymatic activity, e.g., R462A can reduce the barrier height by about 2.8 kcal mol(-1), while R462Q reduces the activation energy by about 2.9 kcal mol(-1). Consistent with the active site model calculated using density functional theory, our results can support that the positive charge on R462 guanidino side chain group plays a negative role in the catalysis. Finally, the functional role of R462 was proposed to facilitate the formation of initial enzyme-substrate complex, but not in the subsequent catalytic degradation reaction. Graphical Abstract Degradation of hyaluronan catalyzed by hyaluronate lyase from Streptococcus pneumoniae.
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Affiliation(s)
- Fengxue Li
- MOE Key Laboratory of Green Chemistry, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China
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5
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Bolia A, Gerek ZN, Ozkan SB. BP-Dock: a flexible docking scheme for exploring protein-ligand interactions based on unbound structures. J Chem Inf Model 2014; 54:913-25. [PMID: 24380381 DOI: 10.1021/ci4004927] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular docking serves as an important tool in modeling protein-ligand interactions. However, it is still challenging to incorporate overall receptor flexibility, especially backbone flexibility, in docking due to the large conformational space that needs to be sampled. To overcome this problem, we developed a novel flexible docking approach, BP-Dock (Backbone Perturbation-Dock) that can integrate both backbone and side chain conformational changes induced by ligand binding through a multi-scale approach. In the BP-Dock method, we mimic the nature of binding-induced events as a first-order approximation by perturbing the residues along the protein chain with a small Brownian kick one at a time. The response fluctuation profile of the chain upon these perturbations is computed using the perturbation response scanning method. These response fluctuation profiles are then used to generate binding-induced multiple receptor conformations for ensemble docking. To evaluate the performance of BP-Dock, we applied our approach on a large and diverse data set using unbound structures as receptors. We also compared the BP-Dock results with bound and unbound docking, where overall receptor flexibility was not taken into account. Our results highlight the importance of modeling backbone flexibility in docking for recapitulating the experimental binding affinities, especially when an unbound structure is used. With BP-Dock, we can generate a wide range of binding site conformations realized in nature even in the absence of a ligand that can help us to improve the accuracy of unbound docking. We expect that our fast and efficient flexible docking approach may further aid in our understanding of protein-ligand interactions as well as virtual screening of novel targets for rational drug design.
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Affiliation(s)
- Ashini Bolia
- Center for Biological Physics, Department of Physics, Arizona State University , Tempe, Arizona 85287, United States
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6
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Ribeiro JV, Tamames JAC, Cerqueira NMFSA, Fernandes PA, Ramos MJ. Volarea - A Bioinformatics Tool to Calculate the Surface Area and the Volume of Molecular Systems. Chem Biol Drug Des 2013; 82:743-55. [DOI: 10.1111/cbdd.12197] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/28/2013] [Accepted: 07/11/2013] [Indexed: 11/26/2022]
Affiliation(s)
- João V. Ribeiro
- REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
| | - Juan A. C. Tamames
- REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
| | - Nuno M. F. S. A. Cerqueira
- REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
| | - Pedro A. Fernandes
- REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
| | - Maria J. Ramos
- REQUIMTE; Departamento de Química e Bioquímica; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
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7
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Wu S, Zhang C, Cao R, Xu D, Guo H. pH-Dependent reactivity for glycyl-L-tyrosine in carboxypeptidase-A-catalyzed hydrolysis. J Phys Chem B 2011; 115:10360-7. [PMID: 21732684 DOI: 10.1021/jp2046504] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dipeptide glycyl-L-tyrosine (GY) can be either a substrate for carboxypeptidase A (CPA) or an inhibitor, depending on pH. In this work, we investigate the pH-dependent reactivity of this dipeptide in CPA-catalyzed hydrolysis using a combined quantum mechanical and molecular mechanical method. It is shown that the monoionic form of the dipeptide, prevalent at high pH, chelates the active site zinc ion, rendering the enzyme inactive. This inhibitory form is consistent with an earlier X-ray structure of the CPA-GY complex. On the other hand, the prevailing di-ionic form of the dipeptide at low pH was found to undergo hydrolysis via a nucleophilic mechanism, leading to an acyl-enzyme complex. The stability of this reaction intermediate is consistent with previous low-temperature solid-state NMR results. The calculated overall free-energy barrier of 20.1 kcal/mol is in excellent agreement with the experimental value of 19.9 kcal/mol.
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Affiliation(s)
- Shanshan Wu
- College of Chemistry, MOE Key Laboratory of Green Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China
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8
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Wu S, Zhang C, Xu D, Guo H. Catalysis of carboxypeptidase A: promoted-water versus nucleophilic pathways. J Phys Chem B 2010; 114:9259-67. [PMID: 20583802 DOI: 10.1021/jp101448j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The catalytic mechanism of carboxypeptidase A (CPA) for the hydrolysis of ester substrates is investigated using hybrid quantum mechanical/molecular mechanical (QM/MM) methods and high-level density functional theory. The prevailing mechanism was found to utilize an active-site water molecule assisted by Glu270, and this so-called promoted-water pathway is similar to that in the CPA catalyzed proteolytic reaction (D. Xu and H. Guo, J. Am. Chem. Soc. 2009, 131, 9780). On the other hand, our simulations indicated the existence of an alternative pathway due to direct nucleophilic attack of Glu270 on the scissile carbonyl carbon. This so-called nucleophilic pathway, which is not viable in proteolytic reactions, leads to a stable acyl-enzyme complex. However, the nucleophilic pathway is nonproductive as it is blocked by a high barrier in the deacylation step. On the basis of results reported here and in our earlier publication, a unified model is proposed to account for nearly all experimental observations concerning the catalysis of CPA.
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Affiliation(s)
- Shanshan Wu
- College of Chemistry, MOE Key Laboratory of Green Chemistry & Technology, Sichuan University, Chengdu, Sichuan 610064, PR China
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9
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Fernández D, Pallarès I, Vendrell J, Avilés FX. Progress in metallocarboxypeptidases and their small molecular weight inhibitors. Biochimie 2010; 92:1484-500. [PMID: 20466032 DOI: 10.1016/j.biochi.2010.05.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 05/04/2010] [Indexed: 01/11/2023]
Abstract
In what corresponds to a life span, metallocarboxypeptidases (MCPs) have jumped from being mere contaminants in animal pancreas powders (in depression year 1929) to be key players in cellular and molecular processes (in yet-another-depression years 2009-2010). MCPs are unique zinc-dependent enzymes that catalyze the breakdown of the amide bond at the C-terminus of peptide and protein substrates and participate in the recovery of dietary amino acids, tissue organogenesis, neurohormone and cytokine maturation and other important physiological processes. More than 26 genes code for MCPs in the human genome, many of them still waiting to be fully understood in terms of physiological function. A variety of MCPs have been linked to diseases in man: acute pancreatitis and pancreas cancer, type 2 diabetes, Alzheimer's Disease, various types of cancer, and fibrinolysis and inflammation. Many of these discoveries have been made possible thanks to recent advances, as exemplified by plasma carboxypeptidases N and B, known for fifty and twenty years, respectively, which have had their structures released only very recently. Plasma carboxypeptidase B is a biological target for therapy because of its involvement in the coagulation/fibrinolysis processes. Besides, the widespread use of carboxypeptidase A as a benchmark metalloprotease since the early days of Biochemistry has allowed the identification and design of an increasingly vast repertory of small molecular weight inhibitors. With these two examples we wish to emphasize that MCPs have become part of the drug discovery portfolio of pharmaceutical companies and academic research laboratories. This paper will review key developments in the discovery and design of MCP small molecular weight inhibitors, with an emphasis on the discovery of chemically diverse entities. Although encouraging advances have been achieved in the last few years, the specificity and oral bioavailability of the new chemotherapeutic agents seem to pose a challenge to medicinal chemists.
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Affiliation(s)
- Daniel Fernández
- Departament de Bioquímica i Biologia Molecular, Facultat de Biociències and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
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10
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Koike R, Kidera A, Ota M. Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold. Protein Sci 2009; 18:2060-6. [PMID: 19670211 DOI: 10.1002/pro.218] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transferases and hydrolases catalyze different chemical reactions and express different dynamic responses upon ligand binding. To insulate the ligand molecule from the surrounding water, transferases bury it inside the protein by closing the cleft, while hydrolases undergo a small conformational change and leave the ligand molecule exposed to the solvent. Despite these distinct ligand-binding modes, some transferases and hydrolases are homologous. To clarify how such different catalytic modes are possible with the same scaffold, we examined the solvent accessibility of ligand molecules for 15 SCOP superfamilies, each containing both transferase and hydrolase catalytic domains. In contrast to hydrolases, we found that nine superfamilies of transferases use two major strategies, oligomerization and domain fusion, to insulate the ligand molecules. The subunits and domains that were recruited by the transferases often act as a cover for the ligand molecule. The other strategies adopted by transferases to insulate the ligand molecule are the relocation of catalytic sites, the rearrangement of secondary structure elements, and the insertion of peripheral regions. These findings provide insights into how proteins have evolved and acquired distinct functions with a limited number of scaffolds.
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11
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Xu D, Guo H. Quantum mechanical/molecular mechanical and density functional theory studies of a prototypical zinc peptidase (carboxypeptidase A) suggest a general acid-general base mechanism. J Am Chem Soc 2009; 131:9780-8. [PMID: 19552427 DOI: 10.1021/ja9027988] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carboxypeptidase A is a zinc-containing enzyme that cleaves the C-terminal residue in a polypeptide substrate. Despite much experimental work, there is still a significant controversy concerning its catalytic mechanism. In this study, the carboxypeptidase A-catalyzed hydrolysis of the hippuryl-L-Phe molecule (k(cat) = 17.7 +/- 0.7 s(-1)) is investigated using both density functional theory and a hybrid quantum mechanical/molecular mechanical approach. The enzymatic reaction was found to proceed via a promoted-water pathway with Glu270 serving as the general base and general acid. Free-energy calculations indicate that the first nucleophilic addition step is rate-limiting, with a barrier of 17.9 kcal/mol. Besides activating the zinc-bound water nucleophile, the zinc cofactor also serves as an electrophilic catalyst that stabilizes the substrate carbonyl oxygen during the formation of the tetrahedral intermediate. In the Michaelis complex, Arg127, rather than Zn(II), is responsible for the polarization of the substrate carbonyl and it also serves as the oxyanion hole. As a result, its mutation leads to a higher free-energy barrier, in agreement with experimental observations.
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Affiliation(s)
- Dingguo Xu
- MOE Key Laboratory of Green Chemistry & Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China.
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12
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Pérez-Nueno VI, Rabal O, Borrell JI, Teixidó J. APIF: a new interaction fingerprint based on atom pairs and its application to virtual screening. J Chem Inf Model 2009; 49:1245-60. [PMID: 19364101 DOI: 10.1021/ci900043r] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new interaction fingerprint (IF) called APIF (atom-pairs-based interaction fingerprint) has been developed for postprocessing protein-ligand docking results. Unlike other existing fingerprints which employ absolute locations of individual interactions, APIF considers the relative positions of pairs of interacting atoms. Docking-based virtual screening was performed with GOLD using the crystal structures of trypsin, rhinovirus, HIV protease, carboxypeptidase, and estrogen receptor-alpha as targets. A score derived from the similarity of the bit strings for each docking solution to that of a known reference binding mode was obtained. Comparisons between APIF, GoldScore function, and standard interaction fingerprint (CHIF) scores were performed using enrichment plots. Superior recovery rates were observed in the IF score cases. Comparable results were achieved by using either of the two interaction fingerprints, substantially improving GoldScore function enrichment factors. Binding mode analyses were also carried out in order to study the best method for selecting conformations with a binding mode similar to that of the reference crystallized complex. These showed that the first conformations retrieved by interaction fingerprint scores had a more similar binding mode to the reference complex than those retrieved by the GoldScore function.
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Affiliation(s)
- Violeta I Pérez-Nueno
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, 08017 Barcelona, Spain
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13
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Chen S, Li X, Ma H. New Approach for Local Structure Analysis of the Tyrosine Domain in Proteins by Using a Site-Specific and Polarity-Sensitive Fluorescent Probe. Chembiochem 2009; 10:1200-7. [DOI: 10.1002/cbic.200900003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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14
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Szeto MW, Mujika JI, Zurek J, Mulholland AJ, Harvey JN. QM/MM study on the mechanism of peptide hydrolysis by carboxypeptidase A. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.06.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Abstract
Although the number of known protein structures is increasing, the number of protein sequences without determined structures is still much larger. Three-dimensional (3D) protein structure information helps in the understanding of functional mechanisms, but solving structures by X-ray crystallography or NMR is often a lengthy and difficult process. A relatively fast way of determining a protein's 3D structure is to construct a computer model using homologous sequence and structure information. Much work has gone into algorithms that comprise the ORCHESTRAR homology modeling program in the SYBYL software package. This novel homology modeling tool combines algorithms for modeling conserved cores, variable regions, and side chains. The paradigm of using existing knowledge from multiple templates and the underlying protein environment knowledgebase is used in all of these algorithms, and will become even more powerful as the number of experimentally derived protein structures increases. To determine how ORCHESTRAR compares to Composer (a broadly used, but an older tool), homology models of 18 proteins were constructed using each program so that a detailed comparison of each step in the modeling process could be carried out. Proteins modeled include kinases, dihydrofolate reductase, HIV protease, and factor Xa. In almost all cases ORCHESTRAR produces models with lower root-mean-squared deviation (RMSD) values when compared with structures determined by X-ray crystallography or NMR. Moreover, ORCHESTRAR produced a homology model for three target sequences where Composer failed to produce any. Data for RMSD comparisons between structurally conserved cores, structurally variable regions, side-chain conformations are presented, as well as analyses of active site and protein-protein interface configurations.
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Affiliation(s)
- Michael A Dolan
- Tripos Informatics Research Center, 1699 South Hanley Road, St. Louis, Missouri 63144, USA.
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16
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Firth-Clark S, Kirton SB, Willems HMG, Williams A. De novo ligand design to partially flexible active sites: application of the ReFlex algorithm to carboxypeptidase A, acetylcholinesterase, and the estrogen receptor. J Chem Inf Model 2008; 48:296-305. [PMID: 18232679 DOI: 10.1021/ci700282u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reflex is a recent algorithm in the de novo ligand design software, SkelGen, that allows the flexibility of amino acid side chains in a protein to be taken into account during the drug-design process. In this paper the impact of flexibility on the solutions generated by the de novo design algorithm, when applied to carboxypeptidase A, acetylcholinesterase, and the estrogen receptor (ER), is investigated. The results for each of the targets indicate that when allowing side-chain movement in the active site, solutions are generated that were not accessible from the multiple static protein conformations available for these targets. Furthermore, an analysis of structures generated in a flexible versus a static ER active site suggests that these additional solutions are not merely noise but contain many interesting chemotypes.
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Affiliation(s)
- Stuart Firth-Clark
- De Novo Pharmaceuticals Ltd., Compass House, Vision Park, Chivers Way, Histon, Cambridge, United Kingdom CB24 9ZR.
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17
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Stark J, Powers R. Rapid protein-ligand costructures using chemical shift perturbations. J Am Chem Soc 2007; 130:535-45. [PMID: 18088118 DOI: 10.1021/ja0737974] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-based drug discovery requires the iterative determination of protein-ligand costructures in order to improve the binding affinity and selectivity of potential drug candidates. In general, X-ray and NMR structure determination methods are time consuming and are typically the limiting factor in the drug discovery process. The application of molecular docking simulations to filter and evaluate drug candidates has become a common method to improve the throughput and efficiency of structure-based drug design. Unfortunately, molecular docking methods suffer from common problems that include ambiguous ligand conformers or failure to predict the correct docked structure. A rapid approach to determine accurate protein-ligand costructures is described based on NMR chemical shift perturbation (CSP) data routinely obtained using 2D 1H-15N HSQC spectra in high-throughput ligand affinity screens. The CSP data is used to both guide and filter AutoDock calculations using our AutoDockFilter program. This method is demonstrated for 19 distinct protein-ligand complexes where the docked conformers exhibited an average rmsd of 1.17 +/- 0.74 A relative to the original X-ray structures for the protein-ligand complexes.
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Affiliation(s)
- Jaime Stark
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
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18
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Akparov VK, Grishin AM, Yusupova MP, Ivanova NM, Chestukhina GG. Structural principles of the wide substrate specificity of Thermoactinomyces vulgaris carboxypeptidase T. reconstruction of the carboxypeptidase B primary specificity pocket. BIOCHEMISTRY (MOSCOW) 2007; 72:416-23. [PMID: 17511606 DOI: 10.1134/s0006297907040086] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Site-directed mutagenesis in the active site of Thermoactinomyces vulgaris carboxypeptidase T (CpT), which is capable of hydrolyzing both hydrophobic and positively charged substrates, resulted in five mutants: CpT1 (A243G), CpT2 (D253G/T255D), CpT3 (A243G/D253G/T255D), CpT4 (G207S/A243G/D253G/T255D), and CpT5 (G207S/A243G/T250A/D253G/T255D). These mutants step-by-step reconstruct the primary specificity pocket of carboxypeptidase B (CpB), which is capable of cleaving only positively charged C-terminal residues. All of the mutants retained the substrate specificity of the wild-type CpT. Based on comparison of three-dimensional structures of CpB and the CpT5 model, it was suggested that the lower affinity of CpT5 for positively charged substrates than the affinity of CpB could be caused by differences in nature and spatial location of Leu247 and Ile247 and of His68 and Asp65 residues in CpT and CpB, respectively, and also in location of the water molecule bound with Ala250. An additional hydrophobic region was detected in the CpT active site formed by Tyr248, Leu247, Leu203, Ala243, CH3-group of Thr250, and CO-groups of Tyr248 and Ala243, which could be responsible for binding hydrophobic substrates. Thus, notwithstanding the considerable structural similarity of CpT and pancreatic carboxypeptidases, the mechanisms underlying their substrate specificities are different.
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Affiliation(s)
- V Kh Akparov
- Stepanov Laboratory of Protein Chemistry, Institute of Genetics and Selection of Industrial Microorganisms, 1-yi Dorozhnyi Proezd 1, 117545 Moscow, Russia.
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19
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Kim KH. Outliers in SAR and QSAR: is unusual binding mode a possible source of outliers? J Comput Aided Mol Des 2007; 21:63-86. [PMID: 17334823 DOI: 10.1007/s10822-007-9106-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Accepted: 01/09/2007] [Indexed: 11/30/2022]
Abstract
A lead optimization is usually carried out by structure-activity relationship (SAR) and/or quantitative structure-activity relationship (QSAR) studies. One of the assumptions in SAR and QSAR studies is that similar analogs bind to the same binding site in a similar binding mode. One often observes that there are outliers, especially in QSAR. However, most QSAR studies are carried out focusing their attention to the development of QSAR and leave the outliers without much attention. We searched a number of ligand-bound X-ray crystal structures from the protein structure database to find evidences that could indicate a possible source of outliers in SAR or QSAR. Our results show that unusual binding mode could be a source of outliers.
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Affiliation(s)
- Ki Hwan Kim
- Hope Drug Discovery Research Laboratory, 260 Southgate Drive, Vernon Hills, IL 60061, USA.
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Cai W, Pei J, Grishin NV. Reconstruction of ancestral protein sequences and its applications. BMC Evol Biol 2004; 4:33. [PMID: 15377393 PMCID: PMC522809 DOI: 10.1186/1471-2148-4-33] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2004] [Accepted: 09/17/2004] [Indexed: 11/16/2022] Open
Abstract
Background Modern-day proteins were selected during long evolutionary history as descendants of ancient life forms. In silico reconstruction of such ancestral protein sequences facilitates our understanding of evolutionary processes, protein classification and biological function. Additionally, reconstructed ancestral protein sequences could serve to fill in sequence space thus aiding remote homology inference. Results We developed ANCESCON, a package for distance-based phylogenetic inference and reconstruction of ancestral protein sequences that takes into account the observed variation of evolutionary rates between positions that more precisely describes the evolution of protein families. To improve the accuracy of evolutionary distance estimation and ancestral sequence reconstruction, two approaches are proposed to estimate position-specific evolutionary rates. Comparisons show that at large evolutionary distances our method gives more accurate ancestral sequence reconstruction than PAML, PHYLIP and PAUP*. We apply the reconstructed ancestral sequences to homology inference and functional site prediction. We show that the usage of hypothetical ancestors together with the present day sequences improves profile-based sequence similarity searches; and that ancestral sequence reconstruction methods can be used to predict positions with functional specificity. Conclusions As a computational tool to reconstruct ancestral protein sequences from a given multiple sequence alignment, ANCESCON shows high accuracy in tests and helps detection of remote homologs and prediction of functional sites. ANCESCON is freely available for non-commercial use. Pre-compiled versions for several platforms can be downloaded from .
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Affiliation(s)
- Wei Cai
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX. 75390-9050, USA
| | - Jimin Pei
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX. 75390-9050, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX. 75390-9050, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX. 75390-9050, USA
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Lin YL, Lim C. Factors Governing the Protonation State of Zn-Bound Histidine in Proteins: A DFT/CDM Study. J Am Chem Soc 2004; 126:2602-12. [PMID: 14982470 DOI: 10.1021/ja038827r] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have performed systematic theoretical studies to elucidate the factors governing the His protonation/deprotonation state in Zn-binding sites, especially those containing the ubiquitous Zn-His-Asp/Glu triad. Specifically, we have addressed the following three questions: (1) How does the transfer of the Zn-bound His imidazole proton to the second-shell Asp/Glu carboxylate oxygen depend on the composition of the other first-shell ligands and the solvent accessibility of the metal-binding site? (2) Can any second-shell ligand with a proton acceptor group such as the backbone carbonyl oxygen also act as a proton acceptor? (3) What is the effect of the Asp/Glu in the Zn-His-Asp/Glu triad on the Zn-bound water protonation state? To address these questions, we used a combination of quantum mechanical and continuum dielectric methods to compute the free energies for deprotonating a Zn-bound imidazole/water in various Zn complexes. The calculations show that whether the Zn-bound His is protonated or deprotonated depends on (1) the solvent accessibility of the metal-binding site, and (2) the Lewis acid ability of Zn, which is indirectly determined by both the first- and the second-shell Zn ligands. The calculations also show that the effect of the Zn-His-Asp/Glu interaction on the nucleophilicity of the Zn-bound water depends on the solvent accessibility of the catalytic Zn site. Furthermore, they show that the Asp/Glu side chain in the Zn-His-Asp/Glu triad can increase the negative charge of its partner, His, and create an anionic hole that may stabilize a cation in buried cavities, provided that the Zn complex is cationic/neutral. The findings of this work are in accord with available experimental data.
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Affiliation(s)
- Yen-lin Lin
- Institute of Biomedical Science, Academic Sinica, Taipei 11529, Taiwan ROC
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22
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Clark RD, Strizhev A, Leonard JM, Blake JF, Matthew JB. Consensus scoring for ligand/protein interactions. J Mol Graph Model 2002; 20:281-95. [PMID: 11858637 DOI: 10.1016/s1093-3263(01)00125-5] [Citation(s) in RCA: 327] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Several different functions have been put forward for evaluating the energetics of ligand binding to proteins. Those employed in the DOCK, GOLD and FlexX docking programs have been especially widely used, particularly in connection with virtual high-throughput screening (vHTS) projects. Until recently, such evaluation functions were usually considered only in conjunction with the docking programs that relied on them. In such studies, the evaluation function in question actually fills two distinct roles: it serves as the objective function being optimized (fitness function), but is also the scoring function used to compare the candidate docking configurations generated by the program. We have used descriptions available in the open literature to create free-standing scoring functions based on those used in DOCK and GOLD, and have implemented the more recently formulated PMF [J. Med. Chem. 42 (1999) 791] scoring function as well. The performance of these functions was examined individually for each of several data sets for which both crystal structures and affinities are available, as was the performance of the FlexX scoring function. Various ways of combining individual scores into a consensus score (CScore) were also considered. The individual and consensus scores were also used to try to pick out configurations most similar to those found in crystal structures from among a set of candidate configurations produced by FlexX docking runs. We find that the reliability and interpretability of results can be improved by combining results from all four functions into a CScore.
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23
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Ewing TJ, Makino S, Skillman AG, Kuntz ID. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 2001; 15:411-28. [PMID: 11394736 DOI: 10.1023/a:1011115820450] [Citation(s) in RCA: 770] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In this paper we describe the search strategies developed for docking flexible molecules to macomolecular sites that are incorporated into the widely distributed DOCK software, version 4.0. The search strategies include incremental construction and random conformation search and utilize the existing Coulombic and Lennard-Jones grid-based scoring function. The incremental construction strategy is tested with a panel of 15 crystallographic testcases, created from 12 unique complexes whose ligands vary in size and flexibility. For all testcases, at least one docked position is generated within 2 A of the crystallographic position. For 7 of 15 testcases, the top scoring position is also within 2 A of the crystallographic position. The algorithm is fast enough to successfully dock a few testcases within seconds and most within 100 s. The incremental construction and the random search strategy are evaluated as database docking techniques with a database of 51 molecules docked to two of the crystallographic testcases. Incremental construction outperforms random search and is fast enough to reliably rank the database of compounds within 15 s per molecule on an SGI R10000 cpu.
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Affiliation(s)
- T J Ewing
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco 94143-0446, USA
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24
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Singleton M, Isupov M, Littlechild J. X-ray structure of pyrrolidone carboxyl peptidase from the hyperthermophilic archaeon Thermococcus litoralis. Structure 1999; 7:237-44. [PMID: 10368293 DOI: 10.1016/s0969-2126(99)80034-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
BACKGROUND Pyrrolidone carboxyl peptidases (pcps) are a group of exopeptidases responsible for the hydrolysis of N-terminal pyroglutamate residues from peptides and proteins. The bacterial and archaeal pcps are members of a conserved family of cysteine proteases. The pcp from the hyperthermophilic archaeon Thermococcus litoralis is more thermostable than the bacterial enzymes with which it has up to 40% sequence identity. The pcp activity in archaea and eubacteria is proposed to be involved in detoxification processes and in nutrient metabolism; eukaryotic counterparts of the enzyme are involved in the processing of biologically active peptides. RESULTS The crystal structure of pcp has been determined by multiple isomorphous replacement techniques at 1.73 A resolution and refined to an R factor of 18.7% (Rfree = 21.4%). The enzyme is a homotetramer of single open alpha/beta domain subunits, with a prominent hydrophobic core formed from loops coming together from each monomer. The active-site residues have been identified as a Cys143-His167-Glu80 catalytic triad. Structural homology to enzymes of different specificity and mechanism has been identified. CONCLUSIONS The Thermococcus pcp has no sequence or structural homology with other members of the cysteine protease family. It does, however, show considerable similarities to other hydrolytic enzymes of widely varying substrate specificity and mechanism, suggesting that they are the products of divergent evolution from a common ancestor. The enhanced thermostability of the T. litoralis pcp may arise from hydrophobic interactions between the subunits and the presence of intersubunit disulphide bridges.
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Affiliation(s)
- M Singleton
- Schools of Chemistry and Biological Sciences University of Exeter Stocker Road Exeter EX4 4QD, UK
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Böhm HJ. Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs. J Comput Aided Mol Des 1998; 12:309-23. [PMID: 9777490 DOI: 10.1023/a:1007999920146] [Citation(s) in RCA: 352] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A dataset of 82 protein-ligand complexes of known 3D structure and binding constant Ki was analysed to elucidate the important factors that determine the strength of protein-ligand interactions. The following parameters were investigated: the number and geometry of hydrogen bonds and ionic interactions between the protein and the ligand, the size of the lipophilic contact surface, the flexibility of the ligand, the electrostatic potential in the binding site, water molecules in the binding site, cavities along the protein-ligand interface and specific interactions between aromatic rings. Based on these parameters, a new empirical scoring function is presented that estimates the free energy of binding for a protein-ligand complex of known 3D structure. The function distinguishes between buried and solvent accessible hydrogen bonds. It tolerates deviations in the hydrogen bond geometry of up to 0.25 A in the length and up to 30 degrees in the hydrogen bond angle without penalizing the score. The new energy function reproduces the binding constants (ranging from 3.7 x 10(-2) M to 1 x 10(-14) M, corresponding to binding energies between -8 and -80 kJ/mol) of the dataset with a standard deviation of 7.3 kJ/mol corresponding to 1.3 orders of magnitude in binding affinity. The function can be evaluated very fast and is therefore also suitable for the application in a 3D database search or de novo ligand design program such as LUDI. The physical significance of the individual contributions is discussed.
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Affiliation(s)
- H J Böhm
- BASF AG, Central Research, Ludwigshafen, Germany
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26
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Abstract
We have determined the packing efficiency at the protein-water interface by calculating the volumes of atoms on the protein surface and nearby water molecules in 22 crystal structures. We find that an atom on the protein surface occupies, on average, a volume approximately 7% larger than an atom of equivalent chemical type in the protein core. In these calculations, larger volumes result from voids between atoms and thus imply a looser or less efficient packing. We further find that the volumes of individual atoms are not related to their chemical type but rather to their structural location. More exposed atoms have larger volumes. Moreover, the packing around atoms in locally concave, grooved regions of protein surfaces is looser than that around atoms in locally convex, ridge regions. This as a direct manifestation of surface curvature-dependent hydration. The net volume increase for atoms on the protein surface is compensated by volume decreases in water molecules near the surface. These waters occupy volumes smaller than those in the bulk solvent by up to 20%; the precise amount of this decrease is directly related to the extent of contact with the protein.
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Affiliation(s)
- M Gerstein
- Department of Structural Biology, Stanford University, CA 94305, USA
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