1
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O'Malley A, Sankaran S, Carriuolo A, Khatri K, Kowal K, Chruszcz M. Structural homology of mite profilins to plant profilins is not indicative of allergic cross-reactivity. Biol Chem 2024; 405:367-381. [PMID: 38662449 DOI: 10.1515/hsz-2023-0366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/03/2024] [Indexed: 06/02/2024]
Abstract
Structural and allergenic characterization of mite profilins has not been previously pursued to a similar extent as plant profilins. Here, we describe structures of profilins originating from Tyrophagus putrescentiae (registered allergen Tyr p 36.0101) and Dermatophagoides pteronyssinus (here termed Der p profilin), which are the first structures of profilins from Arachnida. Additionally, the thermal stabilities of mite and plant profilins are compared, suggesting that the high number of cysteine residues in mite profilins may play a role in their increased stability. We also examine the cross-reactivity of plant and mite profilins as well as investigate the relevance of these profilins in mite inhalant allergy. Despite their high structural similarity to other profilins, mite profilins have low sequence identity with plant and human profilins. Subsequently, these mite profilins most likely do not display cross-reactivity with plant profilins. At the same time the profilins have highly conserved poly(l-proline) and actin binding sites.
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Affiliation(s)
- Andrea O'Malley
- Department of Biochemistry and Molecular Biology, 3078 Michigan State University , 603 Wilson Road, East Lansing, MI 48824, USA
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Sahana Sankaran
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Avery Carriuolo
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Kriti Khatri
- Department of Biochemistry and Molecular Biology, 3078 Michigan State University , 603 Wilson Road, East Lansing, MI 48824, USA
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Krzysztof Kowal
- Department of Experimental Allergology and Immunology, Medical University of Bialystok, Sklodowskiej-Curie 24, 15-276, Bialystok, Poland
| | - Maksymilian Chruszcz
- Department of Biochemistry and Molecular Biology, 3078 Michigan State University , 603 Wilson Road, East Lansing, MI 48824, USA
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
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2
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Dicks L, Wales DJ. Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins. J Phys Chem B 2022; 126:8381-8390. [PMID: 36257022 PMCID: PMC9623586 DOI: 10.1021/acs.jpcb.2c04647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Rotamers, namely amino acid side chain conformations common to many different peptides, can be compiled into libraries. These rotamer libraries are used in protein modeling, where the limited conformational space occupied by amino acid side chains is exploited. Here, we construct a sequence-dependent rotamer library from simulations of all possible tripeptides, which provides rotameric states dependent on adjacent amino acids. We observe significant sensitivity of rotamer populations to sequence and find that the library is successful in locating side chain conformations present in crystal structures. The library is designed for applications with basin-hopping global optimization, where we use it to propose moves in conformational space. The addition of rotamer moves significantly increases the efficiency of protein structure prediction within this framework, and we determine parameters to optimize efficiency.
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Affiliation(s)
- L. Dicks
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom,IBM
Research, The Hartree Centre STFC Laboratory,
Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - D. J. Wales
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom,
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3
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Minor W, Cymborowski M, Borek D, Cooper DR, Chruszcz M, Otwinowski Z. Optimal structure determination from sub-optimal diffraction data. Protein Sci 2022; 31:259-268. [PMID: 34783106 PMCID: PMC8740829 DOI: 10.1002/pro.4235] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/06/2021] [Accepted: 11/09/2021] [Indexed: 01/03/2023]
Abstract
Herein we present the newest version of the HKL-3000 system that integrates data collection, data reduction, phasing, model building, refinement, and validation. The system significantly accelerates the process of structure determination and has proven its high value for the determination of very high-quality structures. The heuristic for choosing the best approach for every step of structure determination for various quality samples and diffraction data has been optimized. The latest modifications increase the likelihood of a successful structure determination with challenging data. The HKL-3000 is a successor of HKL and HKL-2000 programs. The use of the HKL family of programs has been reported for over 73,000 PDB deposits, that is, almost 50% of macromolecular structures determined with X-ray diffraction.
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Affiliation(s)
- Wladek Minor
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginia
| | - Marcin Cymborowski
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginia
| | - Dominika Borek
- Department of BiophysicsThe University of Texas Southwestern Medical CenterDallasTexas,Department of BiochemistryThe University of Texas Southwestern Medical CenterDallasTexas
| | - David R. Cooper
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginia
| | - Maksymilian Chruszcz
- Department of Chemistry and BiochemistryUniversity of South CarolinaColumbiaSouth Carolina
| | - Zbyszek Otwinowski
- Department of BiophysicsThe University of Texas Southwestern Medical CenterDallasTexas,Department of BiochemistryThe University of Texas Southwestern Medical CenterDallasTexas
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4
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Chojnowski G, Simpkin AJ, Leonardo DA, Seifert-Davila W, Vivas-Ruiz DE, Keegan RM, Rigden DJ. findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM. IUCRJ 2022; 9:86-97. [PMID: 35059213 PMCID: PMC8733886 DOI: 10.1107/s2052252521011088] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 10/22/2021] [Indexed: 05/15/2023]
Abstract
Although experimental protein-structure determination usually targets known proteins, chains of unknown sequence are often encountered. They can be purified from natural sources, appear as an unexpected fragment of a well characterized protein or appear as a contaminant. Regardless of the source of the problem, the unknown protein always requires characterization. Here, an automated pipeline is presented for the identification of protein sequences from cryo-EM reconstructions and crystallographic data. The method's application to characterize the crystal structure of an unknown protein purified from a snake venom is presented. It is also shown that the approach can be successfully applied to the identification of protein sequences and validation of sequence assignments in cryo-EM protein structures.
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Affiliation(s)
- Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
- Correspondence e-mail:
| | - Adam J. Simpkin
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Diego A. Leonardo
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-120, Brazil
| | | | - Dan E. Vivas-Ruiz
- Laboratorio de Biología Molecular, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Avenida Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima, Peru
| | - Ronan M. Keegan
- Rutherford Appleton Laboratory, Research Complex at Harwell, UKRI-STFC, Didcot OX11 0FA, United Kingdom
| | - Daniel J. Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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5
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Czub MP, Boulton AM, Rastelli EJ, Tasker NR, Maskrey TS, Blanco IK, McQueeney KE, Bushweller JH, Minor W, Wipf P, Sharlow ER, Lazo JS. Structure of the Complex of an Iminopyridinedione Protein Tyrosine Phosphatase 4A3 Phosphatase Inhibitor with Human Serum Albumin. Mol Pharmacol 2020; 98:648-657. [PMID: 32978326 DOI: 10.1124/molpharm.120.000131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Protein tyrosine phosphatase (PTP) 4A3 is frequently overexpressed in human solid tumors and hematologic malignancies and is associated with tumor cell invasion, metastasis, and a poor patient prognosis. Several potent, selective, and allosteric small molecule inhibitors of PTP4A3 were recently identified. A lead compound in the series, JMS-053 (7-imino-2-phenylthieno[3,2-c]pyridine-4,6(5H,7H)-dione), has a long plasma half-life (∼ 24 hours) in mice, suggesting possible binding to serum components. We confirmed by isothermal titration calorimetry that JMS-053 binds to human serum albumin. A single JMS-053 binding site was identified by X-ray crystallography in human serum albumin at drug site 3, which is also known as subdomain IB. The binding of JMS-053 to human serum albumin, however, did not markedly alter the overall albumin structure. In the presence of serum albumin, the potency of JMS-053 as an in vitro inhibitor of PTP4A3 and human A2780 ovarian cancer cell growth was reduced. The reversible binding of JMS-053 to serum albumin may serve to increase JMS-053's plasma half-life and thus extend the delivery of the compound to tumors. SIGNIFICANCE STATEMENT: X-ray crystallography revealed that a potent, reversible, first-in-class small molecule inhibitor of the oncogenic phosphatase protein tyrosine phosphatase 4A3 binds to at least one site on human serum albumin, which is likely to extend the compound's plasma half-life and thus assist in drug delivery into tumors.
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Affiliation(s)
- Mateusz P Czub
- Departments of Molecular Physiology and Biological Physics (M.P.C., A.M.B., J.H.B., W.M.) and Pharmacology (K.E.M., E.R.S., J.S.L.) and Center for Structural Genomics of Infectious Diseases (CSGID) (M.P.C., W.M.), University of Virginia, Charlottesville, Virginia; Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania (E.J.R., N.R.T., T.S.M., P.W.); and KeViRx, Inc., Charlottesville, Virginia (I.K.B., E.R.S., J.S.L.)
| | - Adam M Boulton
- Departments of Molecular Physiology and Biological Physics (M.P.C., A.M.B., J.H.B., W.M.) and Pharmacology (K.E.M., E.R.S., J.S.L.) and Center for Structural Genomics of Infectious Diseases (CSGID) (M.P.C., W.M.), University of Virginia, Charlottesville, Virginia; Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania (E.J.R., N.R.T., T.S.M., P.W.); and KeViRx, Inc., Charlottesville, Virginia (I.K.B., E.R.S., J.S.L.)
| | - Ettore J Rastelli
- Departments of Molecular Physiology and Biological Physics (M.P.C., A.M.B., J.H.B., W.M.) and Pharmacology (K.E.M., E.R.S., J.S.L.) and Center for Structural Genomics of Infectious Diseases (CSGID) (M.P.C., W.M.), University of Virginia, Charlottesville, Virginia; Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania (E.J.R., N.R.T., T.S.M., P.W.); and KeViRx, Inc., Charlottesville, Virginia (I.K.B., E.R.S., J.S.L.)
| | - Nikhil R Tasker
- Departments of Molecular Physiology and Biological Physics (M.P.C., A.M.B., J.H.B., W.M.) and Pharmacology (K.E.M., E.R.S., J.S.L.) and Center for Structural Genomics of Infectious Diseases (CSGID) (M.P.C., W.M.), University of Virginia, Charlottesville, Virginia; Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania (E.J.R., N.R.T., T.S.M., P.W.); and KeViRx, Inc., Charlottesville, Virginia (I.K.B., E.R.S., J.S.L.)
| | - Taber S Maskrey
- Departments of Molecular Physiology and Biological Physics (M.P.C., A.M.B., J.H.B., W.M.) and Pharmacology (K.E.M., E.R.S., J.S.L.) and Center for Structural Genomics of Infectious Diseases (CSGID) (M.P.C., W.M.), University of Virginia, Charlottesville, Virginia; Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania (E.J.R., N.R.T., T.S.M., P.W.); and KeViRx, Inc., Charlottesville, Virginia (I.K.B., E.R.S., J.S.L.)
| | - Isabella K Blanco
- Departments of Molecular Physiology and Biological Physics (M.P.C., A.M.B., J.H.B., W.M.) and Pharmacology (K.E.M., E.R.S., J.S.L.) and Center for Structural Genomics of Infectious Diseases (CSGID) (M.P.C., W.M.), University of Virginia, Charlottesville, Virginia; Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania (E.J.R., N.R.T., T.S.M., P.W.); and KeViRx, Inc., Charlottesville, Virginia (I.K.B., E.R.S., J.S.L.)
| | - Kelley E McQueeney
- Departments of Molecular Physiology and Biological Physics (M.P.C., A.M.B., J.H.B., W.M.) and Pharmacology (K.E.M., E.R.S., J.S.L.) and Center for Structural Genomics of Infectious Diseases (CSGID) (M.P.C., W.M.), University of Virginia, Charlottesville, Virginia; Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania (E.J.R., N.R.T., T.S.M., P.W.); and KeViRx, Inc., Charlottesville, Virginia (I.K.B., E.R.S., J.S.L.)
| | - John H Bushweller
- Departments of Molecular Physiology and Biological Physics (M.P.C., A.M.B., J.H.B., W.M.) and Pharmacology (K.E.M., E.R.S., J.S.L.) and Center for Structural Genomics of Infectious Diseases (CSGID) (M.P.C., W.M.), University of Virginia, Charlottesville, Virginia; Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania (E.J.R., N.R.T., T.S.M., P.W.); and KeViRx, Inc., Charlottesville, Virginia (I.K.B., E.R.S., J.S.L.)
| | - Wladek Minor
- Departments of Molecular Physiology and Biological Physics (M.P.C., A.M.B., J.H.B., W.M.) and Pharmacology (K.E.M., E.R.S., J.S.L.) and Center for Structural Genomics of Infectious Diseases (CSGID) (M.P.C., W.M.), University of Virginia, Charlottesville, Virginia; Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania (E.J.R., N.R.T., T.S.M., P.W.); and KeViRx, Inc., Charlottesville, Virginia (I.K.B., E.R.S., J.S.L.)
| | - Peter Wipf
- Departments of Molecular Physiology and Biological Physics (M.P.C., A.M.B., J.H.B., W.M.) and Pharmacology (K.E.M., E.R.S., J.S.L.) and Center for Structural Genomics of Infectious Diseases (CSGID) (M.P.C., W.M.), University of Virginia, Charlottesville, Virginia; Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania (E.J.R., N.R.T., T.S.M., P.W.); and KeViRx, Inc., Charlottesville, Virginia (I.K.B., E.R.S., J.S.L.)
| | - Elizabeth R Sharlow
- Departments of Molecular Physiology and Biological Physics (M.P.C., A.M.B., J.H.B., W.M.) and Pharmacology (K.E.M., E.R.S., J.S.L.) and Center for Structural Genomics of Infectious Diseases (CSGID) (M.P.C., W.M.), University of Virginia, Charlottesville, Virginia; Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania (E.J.R., N.R.T., T.S.M., P.W.); and KeViRx, Inc., Charlottesville, Virginia (I.K.B., E.R.S., J.S.L.)
| | - John S Lazo
- Departments of Molecular Physiology and Biological Physics (M.P.C., A.M.B., J.H.B., W.M.) and Pharmacology (K.E.M., E.R.S., J.S.L.) and Center for Structural Genomics of Infectious Diseases (CSGID) (M.P.C., W.M.), University of Virginia, Charlottesville, Virginia; Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania (E.J.R., N.R.T., T.S.M., P.W.); and KeViRx, Inc., Charlottesville, Virginia (I.K.B., E.R.S., J.S.L.)
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6
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Mrugała B, Miłaczewska A, Porebski PJ, Niedzialkowska E, Guzik M, Minor W, Borowski T. A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates. FEBS J 2020; 288:1366-1386. [PMID: 32592631 DOI: 10.1111/febs.15462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/09/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Kanamycin A is an aminoglycoside antibiotic isolated from Streptomyces kanamyceticus and used against a wide spectrum of bacteria, including Mycobacterium tuberculosis. Biosynthesis of kanamycin involves an oxidative deamination step catalyzed by kanamycin B dioxygenase (KanJ), thereby the C2' position of kanamycin B is transformed into a keto group upon release of ammonia. Here, we present for the first time, structural models of KanJ with several ligands, which along with the results of ITC binding assays and HPLC activity tests explain substrate specificity of the enzyme. The large size of the binding pocket suggests that KanJ can accept a broad range of substrates, which was confirmed by activity tests. Specificity of the enzyme with respect to its substrate is determined by the hydrogen bond interactions between the methylamino group of the antibiotic and highly conserved Asp134 and Cys150 as well as between hydroxyl groups of the substrate and Asn120 and Gln80. Upon antibiotic binding, the C terminus loop is significantly rearranged and Gln80 and Asn120, which are directly involved in substrate recognition, change their conformations. Based on reaction energy profiles obtained by density functional theory (DFT) simulations, we propose a mechanism of ketone formation involving the reactive FeIV = O and proceeding either via OH rebound, which yields a hemiaminal intermediate or by abstraction of two hydrogen atoms, which leads to an imine species. At acidic pH, the latter involves a lower barrier than the OH rebound, whereas at basic pH, the barrier leading to an imine vanishes completely. DATABASES: Structural data are available in PDB database under the accession numbers: 6S0R, 6S0T, 6S0U, 6S0W, 6S0V, 6S0S. Diffraction images are available at the Integrated Resource for Reproducibility in Macromolecular Crystallography at http://proteindiffraction.org under DOIs: 10.18430/m36s0t, 10.18430/m36s0u, 10.18430/m36s0r, 10.18430/m36s0s, 10.18430/m36s0v, 10.18430/m36s0w. A data set collection of computational results is available in the Mendeley Data database under DOI: 10.17632/sbyzssjmp3.1 and in the ioChem-BD database under DOI: 10.19061/iochem-bd-4-18.
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Affiliation(s)
- Beata Mrugała
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Anna Miłaczewska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Przemyslaw Jerzy Porebski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Ewa Niedzialkowska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Maciej Guzik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
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7
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Czub MP, Handing KB, Venkataramany BS, Cooper DR, Shabalin IG, Minor W. Albumin-Based Transport of Nonsteroidal Anti-Inflammatory Drugs in Mammalian Blood Plasma. J Med Chem 2020; 63:6847-6862. [PMID: 32469516 DOI: 10.1021/acs.jmedchem.0c00225] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Every day, hundreds of millions of people worldwide take nonsteroidal anti-inflammatory drugs (NSAIDs), often in conjunction with multiple other medications. In the bloodstream, NSAIDs are mostly bound to serum albumin (SA). We report the crystal structures of equine serum albumin complexed with four NSAIDs (ibuprofen, ketoprofen, etodolac, and nabumetone) and the active metabolite of nabumetone (6-methoxy-2-naphthylacetic acid, 6-MNA). These compounds bind to seven drug-binding sites on SA. These sites are generally well-conserved between equine and human SAs, but ibuprofen binds to both SAs in two drug-binding sites, only one of which is common. We also compare the binding of ketoprofen by equine SA to binding of it by bovine and leporine SAs. Our comparative analysis of known SA complexes with FDA-approved drugs clearly shows that multiple medications compete for the same binding sites, indicating possibilities for undesirable physiological effects caused by drug-drug displacement or competition with common metabolites. We discuss the consequences of NSAID binding to SA in a broader scientific and medical context, particularly regarding achieving desired therapeutic effects based on an individual's drug regimen.
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Affiliation(s)
- Mateusz P Czub
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Katarzyna B Handing
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Barat S Venkataramany
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - David R Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
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8
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Minasov G, Lam MR, Rosas-Lemus M, Sławek J, Woinska M, Shabalin IG, Shuvalova L, Palsson BØ, Godzik A, Minor W, Satchell KJF. Comparison of metal-bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis. Protein Sci 2020; 29:1618-1628. [PMID: 32306515 DOI: 10.1002/pro.3876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 11/06/2022]
Abstract
Protein degradation by aminopeptidases is involved in bacterial responses to stress. Escherichia coli produces two metal-dependent M17 family leucine aminopeptidases (LAPs), aminopeptidase A (PepA) and aminopeptidase B (PepB). Several structures have been solved for PepA as well as other bacterial M17 peptidases. Herein, we report the first structures of a PepB M17 peptidase. The E. coli PepB protein structure was determined at a resolution of 2.05 and 2.6 Å. One structure has both Zn2+ and Mn2+ , while the second structure has two Zn2+ ions bound to the active site. A 2.75 Å apo structure is also reported for PepB from Yersinia pestis. Both proteins form homohexamers, similar to the overall arrangement of PepA and other M17 peptidases. However, the divergent N-terminal domain in PepB is much larger resulting in a tertiary structure that is more expanded. Modeling of a dipeptide substrate into the C-terminal LAP domain reveals contacts that account for PepB to uniquely cleave after aspartate.
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Affiliation(s)
- George Minasov
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA
| | - Matthew R Lam
- Department of Molecular Biosciences, Weinberg School of Arts and Sciences, Northwestern University, Evanston, Illinois, USA
| | - Monica Rosas-Lemus
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA
| | - Joanna Sławek
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Magdalena Woinska
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Ivan G Shabalin
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Ludmilla Shuvalova
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA
| | - Bernhard Ø Palsson
- Department of Bioengineering and Pediatrics, University of California, San Diego, California, USA
| | - Adam Godzik
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA.,Department of Biomedical Sciences, University of California, Riverside School of Medicine, Riverside, California, USA
| | - Wladek Minor
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Center for Structural Genomics of Infectious Diseases, Northwestern University, Chicago, Illinois, USA
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9
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Shabalin IG, Gritsunov A, Hou J, Sławek J, Miks CD, Cooper DR, Minor W, Christendat D. Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain. FEBS J 2019; 287:2235-2255. [PMID: 31750992 DOI: 10.1111/febs.15150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/05/2019] [Accepted: 11/19/2019] [Indexed: 01/19/2023]
Abstract
Tyrosine biosynthesis via the shikimate pathway is absent in humans and other animals, making it an attractive target for next-generation antibiotics, which is increasingly important due to the looming proliferation of multidrug-resistant pathogens. Tyrosine biosynthesis is also of commercial importance for the environmentally friendly production of numerous compounds, such as pharmaceuticals, opioids, aromatic polymers, and petrochemical aromatics. Prephenate dehydrogenase (PDH) catalyzes the penultimate step of tyrosine biosynthesis in bacteria: the oxidative decarboxylation of prephenate to 4-hydroxyphenylpyruvate. The majority of PDHs are competitively inhibited by tyrosine and consist of a nucleotide-binding domain and a dimerization domain. Certain PDHs, including several from pathogens on the World Health Organization priority list of antibiotic-resistant bacteria, possess an additional ACT domain. However, biochemical and structural knowledge was lacking for these enzymes. In this study, we successfully established a recombinant protein expression system for PDH from Bacillus anthracis (BaPDH), the causative agent of anthrax, and determined the structure of a BaPDH ternary complex with NAD+ and tyrosine, a binary complex with tyrosine, and a structure of an isolated ACT domain dimer. We also conducted detailed kinetic and biophysical analyses of the enzyme. We show that BaPDH is allosterically regulated by tyrosine binding to the ACT domains, resulting in an asymmetric conformation of the BaDPH dimer that sterically prevents prephenate binding to either active site. The presented mode of allosteric inhibition is unique compared to both the competitive inhibition established for other PDHs and to the allosteric mechanisms for other ACT-containing enzymes. This study provides new structural and mechanistic insights that advance our understanding of tyrosine biosynthesis in bacteria. ENZYMES: Prephenate dehydrogenase from Bacillus anthracis (PDH): EC database ID: 1.3.1.12. DATABASES: Coordinates and structure factors have been deposited in the Protein Data Bank (PDB) with accession numbers PDB ID: 6U60 (BaPDH complex with NAD+ and tyrosine), PDB ID: 5UYY (BaPDH complex with tyrosine), and PDB ID: 5V0S (BaPDH isolated ACT domain dimer). The diffraction images are available at http://proteindiffraction.org with DOIs: https://doi.org/10.18430/M35USC, https://doi.org/10.18430/M35UYY, and https://doi.org/10.18430/M35V0S.
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Affiliation(s)
- Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, USA
| | - Artyom Gritsunov
- Department of Cell and Systems Biology, University of Toronto, ON, Canada
| | - Jing Hou
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, USA
| | - Joanna Sławek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, USA.,Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Charles D Miks
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - David R Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, USA
| | - Dinesh Christendat
- Department of Cell and Systems Biology, University of Toronto, ON, Canada
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10
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Ho CM, Li X, Lai M, Terwilliger TC, Beck JR, Wohlschlegel J, Goldberg DE, Fitzpatrick AWP, Zhou ZH. Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu. Nat Methods 2019; 17:79-85. [PMID: 31768063 PMCID: PMC7494424 DOI: 10.1038/s41592-019-0637-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 08/20/2019] [Accepted: 10/07/2019] [Indexed: 12/11/2022]
Abstract
X-ray crystallography often requires non-native constructs involving mutations or truncations, and is challenged by membrane proteins and large multicomponent complexes. We present here a bottom-up endogenous structural proteomics approach whereby near-atomic-resolution cryo electron microscopy (cryoEM) maps are reconstructed ab initio from unidentified protein complexes enriched directly from the endogenous cellular milieu, followed by identification and atomic modeling of the proteins. The proteins in each complex are identified using cryoID, a program we developed to identify proteins in ab initio cryoEM maps. As a proof of principle, we applied this approach to the malaria-causing parasite Plasmodium falciparum, an organism that has resisted conventional structural-biology approaches, to obtain atomic models of multiple protein complexes implicated in intraerythrocytic survival of the parasite. Our approach is broadly applicable for determining structures of undiscovered protein complexes enriched directly from endogenous sources.
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Affiliation(s)
- Chi-Min Ho
- The Molecular Biology Institute, University of California, Los Angeles, CA, USA.,Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, CA, USA.,California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Xiaorun Li
- California NanoSystems Institute, University of California, Los Angeles, CA, USA.,Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Mason Lai
- Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, CA, USA.,California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Thomas C Terwilliger
- Los Alamos National Laboratory and the New Mexico Consortium, Los Alamos, NM, USA
| | - Josh R Beck
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.,Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Daniel E Goldberg
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | - Z Hong Zhou
- The Molecular Biology Institute, University of California, Los Angeles, CA, USA. .,Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, CA, USA. .,California NanoSystems Institute, University of California, Los Angeles, CA, USA.
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11
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Blus BJ, Koh J, Krolak A, Seo HS, Coutavas E, Blobel G. Allosteric modulation of nucleoporin assemblies by intrinsically disordered regions. SCIENCE ADVANCES 2019; 5:eaax1836. [PMID: 31807700 PMCID: PMC6881172 DOI: 10.1126/sciadv.aax1836] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 09/25/2019] [Indexed: 05/12/2023]
Abstract
Intrinsically disordered regions (IDRs) of proteins are implicated in key macromolecular interactions. However, the molecular forces underlying IDR function within multicomponent assemblies remain elusive. By combining thermodynamic and structural data, we have discovered an allostery-based mechanism regulating the soluble core region of the nuclear pore complex (NPC) composed of nucleoporins Nup53, Nic96, and Nup157. We have identified distinct IDRs in Nup53 that are functionally coupled when binding to partner nucleoporins and karyopherins (Kaps) involved in NPC assembly and nucleocytoplasmic transport. We show that the Nup53·Kap121 complex forms an ensemble of structures that destabilize Nup53 hub interactions. Our study provides a molecular framework for understanding how disordered and folded domains communicate within macromolecular complexes.
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Affiliation(s)
- Bartlomiej Jan Blus
- Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
- Corresponding author.
| | - Junseock Koh
- School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Aleksandra Krolak
- Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Elias Coutavas
- Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Günter Blobel
- Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
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12
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Lipowska J, Miks CD, Kwon K, Shuvalova L, Zheng H, Lewiński K, Cooper DR, Shabalin IG, Minor W. Pyrimidine biosynthesis in pathogens - Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae. Int J Biol Macromol 2019; 136:1176-1187. [PMID: 31207330 PMCID: PMC6686667 DOI: 10.1016/j.ijbiomac.2019.05.149] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/01/2019] [Accepted: 05/14/2019] [Indexed: 02/06/2023]
Abstract
The de novo pyrimidine biosynthesis pathway is essential for the proliferation of many pathogens. One of the pathway enzymes, dihydroorotase (DHO), catalyzes the reversible interconversion of N-carbamoyl-l-aspartate to 4,5-dihydroorotate. The substantial difference between bacterial and mammalian DHOs makes it a promising drug target for disrupting bacterial growth and thus an important candidate to evaluate as a response to antimicrobial resistance on a molecular level. Here, we present two novel three-dimensional structures of DHOs from Yersinia pestis (YpDHO), the plague-causing pathogen, and Vibrio cholerae (VcDHO), the causative agent of cholera. The evaluations of these two structures led to an analysis of all available DHO structures and their classification into known DHO types. Comparison of all the DHO active sites containing ligands that are listed in DrugBank was facilitated by a new interactive, structure-comparison and presentation platform. In addition, we examined the genetic context of characterized DHOs, which revealed characteristic patterns for different types of DHOs. We also generated a homology model for DHO from Plasmodium falciparum.
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Affiliation(s)
- Joanna Lipowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA 22908, USA; Faculty of Chemistry, Jagiellonian University, 30-387 Kraków, Poland
| | - Charles Dylan Miks
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Keehwan Kwon
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Ludmilla Shuvalova
- Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL 60611, USA
| | - Heping Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA 22908, USA
| | | | - David R Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA 22908, USA
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA 22908, USA.
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA 22908, USA.
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13
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Chojnowski G, Pereira J, Lamzin VS. Sequence assignment for low-resolution modelling of protein crystal structures. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:753-763. [PMID: 31373574 PMCID: PMC6677015 DOI: 10.1107/s2059798319009392] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/30/2019] [Indexed: 01/08/2023]
Abstract
Recent advances in automated protein model building using ARP/wARP are presented. The new methods include machine-learning-enhanced sequence assignment and loop building using a fragment database. The performance of automated model building in crystal structure determination usually decreases with the resolution of the experimental data, and may result in fragmented models and incorrect side-chain assignment. Presented here are new methods for machine-learning-based docking of main-chain fragments to the sequence and for their sequence-independent connection using a dedicated library of protein fragments. The combined use of these new methods noticeably increases sequence coverage and reduces fragmentation of the protein models automatically built with ARP/wARP.
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Affiliation(s)
- Grzegorz Chojnowski
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Joana Pereira
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Victor S Lamzin
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
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14
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Czub MP, Venkataramany BS, Majorek KA, Handing KB, Porebski PJ, Beeram SR, Suh K, Woolfork AG, Hage DS, Shabalin IG, Minor W. Testosterone meets albumin - the molecular mechanism of sex hormone transport by serum albumins. Chem Sci 2019; 10:1607-1618. [PMID: 30842823 PMCID: PMC6371759 DOI: 10.1039/c8sc04397c] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/07/2018] [Indexed: 12/23/2022] Open
Abstract
Serum albumin is the most abundant protein in mammalian blood plasma and is responsible for the transport of metals, drugs, and various metabolites, including hormones. We report the first albumin structure in complex with testosterone, the primary male sex hormone. Testosterone is bound in two sites, neither of which overlaps with the previously suggested Sudlow site I. We determined the binding constant of testosterone to equine and human albumins by two different methods: tryptophan fluorescence quenching and ultrafast affinity extraction. The binding studies and similarities between residues comprising the binding sites on serum albumins suggest that testosterone binds to the same sites on both proteins. Our comparative analysis of albumin complexes with hormones, drugs, and other biologically relevant compounds strongly suggests interference between a number of compounds present in blood and testosterone transport by serum albumin. We discuss a possible link between our findings and some phenomena observed in human patients, such as low testosterone levels in diabetic patients.
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Affiliation(s)
- Mateusz P Czub
- Department of Molecular Physiology and Biological Physics , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA . ;
- Center for Structural Genomics of Infectious Diseases (CSGID) , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA
| | - Barat S Venkataramany
- Department of Molecular Physiology and Biological Physics , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA . ;
| | - Karolina A Majorek
- Department of Molecular Physiology and Biological Physics , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA . ;
| | - Katarzyna B Handing
- Department of Molecular Physiology and Biological Physics , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA . ;
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA . ;
- Center for Structural Genomics of Infectious Diseases (CSGID) , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA
| | - Sandya R Beeram
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , USA .
| | - Kyungah Suh
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , USA .
| | - Ashley G Woolfork
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , USA .
| | - David S Hage
- Department of Chemistry , University of Nebraska-Lincoln , Lincoln , Nebraska 68588 , USA .
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA . ;
- Center for Structural Genomics of Infectious Diseases (CSGID) , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA . ;
- Center for Structural Genomics of Infectious Diseases (CSGID) , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , VA 22908 , USA
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15
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Czub MP, Zhang B, Chiarelli MP, Majorek KA, Joe L, Porebski PJ, Revilla A, Wu W, Becker DP, Minor W, Kuhn ML. A Gcn5-Related N-Acetyltransferase (GNAT) Capable of Acetylating Polymyxin B and Colistin Antibiotics in Vitro. Biochemistry 2018; 57:7011-7020. [PMID: 30499668 DOI: 10.1021/acs.biochem.8b00946] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Deeper exploration of uncharacterized Gcn5-related N-acetyltransferases has the potential to expand our knowledge of the types of molecules that can be acylated by this important superfamily of enzymes and may offer new opportunities for biotechnological applications. While determining native or biologically relevant in vivo functions of uncharacterized proteins is ideal, their alternative or promiscuous in vitro capabilities provide insight into key active site interactions. Additionally, this knowledge can be exploited to selectively modify complex molecules and reduce byproducts when synthetic routes become challenging. During our exploration of uncharacterized Gcn5-related N-acetyltransferases from Pseudomonas aeruginosa, we identified such an example. We found that the PA3944 enzyme acetylates both polymyxin B and colistin on a single diaminobutyric acid residue closest to the macrocyclic ring of the antimicrobial peptide and determined the PA3944 crystal structure. This finding is important for several reasons. (1) To the best of our knowledge, this is the first report of enzymatic acylation of polymyxins and thus reveals a new type of substrate that this enzyme family can use. (2) The enzymatic acetylation offers a controlled method for antibiotic modification compared to classical promiscuous chemical methods. (3) The site of acetylation would reduce the overall positive charge of the molecule, which is important for reducing nephrotoxic effects and may be a salvage strategy for this important class of antibiotics. While the physiological substrate for this enzyme remains unknown, our structural and functional characterization of PA3944 offers insight into its unique noncanonical substrate specificity.
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Affiliation(s)
- Mateusz P Czub
- Department of Molecular Physiology and Biological Physics , University of Virginia , Charlottesville , Virginia 22908 , United States.,Center for Structural Genomics of Infectious Diseases (CSGID) , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , Virginia 22908 , United States
| | - Brian Zhang
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - M Paul Chiarelli
- Department of Chemistry and Biochemistry , Loyola University Chicago , Chicago , Illinois 60660 , United States
| | - Karolina A Majorek
- Department of Molecular Physiology and Biological Physics , University of Virginia , Charlottesville , Virginia 22908 , United States.,Center for Structural Genomics of Infectious Diseases (CSGID) , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , Virginia 22908 , United States
| | - Layton Joe
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics , University of Virginia , Charlottesville , Virginia 22908 , United States.,Center for Structural Genomics of Infectious Diseases (CSGID) , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , Virginia 22908 , United States
| | - Alina Revilla
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - Weiming Wu
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - Daniel P Becker
- Department of Chemistry and Biochemistry , Loyola University Chicago , Chicago , Illinois 60660 , United States
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics , University of Virginia , Charlottesville , Virginia 22908 , United States.,Center for Structural Genomics of Infectious Diseases (CSGID) , University of Virginia , 1340 Jefferson Park Avenue , Charlottesville , Virginia 22908 , United States
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
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16
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Shabalin IG, Porebski PJ, Minor W. Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment. CRYSTALLOGR REV 2018; 24:236-262. [PMID: 30416256 DOI: 10.1080/0889311x.2018.1521805] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Refinement of macromolecular X-ray crystal structures involves using complex software with hundreds of different settings. The complexity of underlying concepts and the sheer amount sof instructions may make it difficult for less experienced crystallographers to achieve optimal results in their refinements. This tutorial review offers guidelines for choosing the best settings for the reciprocal-space refinement of macromolecular models and provides practical tips for manual model correction. To help aspiring crystallographers navigate the process, some of the most practically important concepts of protein structure refinement are described. Among the topics covered are the use and purpose of R-free, geometrical restraints, restraints on atomic displacement parameters (ADPs), refinement weights, various parametrizations of ADPs (full anisotropic refinement and TLS), and omit maps. We also give practical tips for manual model correction in Coot, modelling of side-chains with poor or missing density, and ligand identification, fitting, and refinement.
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Affiliation(s)
- Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
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17
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Kluza A, Niedzialkowska E, Kurpiewska K, Wojdyla Z, Quesne M, Kot E, Porebski PJ, Borowski T. Crystal structure of thebaine 6-O-demethylase from the morphine biosynthesis pathway. J Struct Biol 2018; 202:229-235. [PMID: 29408320 DOI: 10.1016/j.jsb.2018.01.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/24/2018] [Accepted: 01/28/2018] [Indexed: 11/17/2022]
Abstract
Thebaine 6-O-demethylase (T6ODM) from Papaver somniferum (opium poppy), which belongs to the non-heme 2-oxoglutarate/Fe(II)-dependent dioxygenases (ODD) family, is a key enzyme in the morphine biosynthesis pathway. Initially, T6ODM was characterized as an enzyme catalyzing O-demethylation of thebaine to neopinone and oripavine to morphinone. However, the substrate range of T6ODM was recently expanded to a number of various benzylisoquinoline alkaloids. Here, we present crystal structures of T6ODM in complexes with 2-oxoglutarate (T6ODM:2OG, PDB: 5O9W) and succinate (T6ODM:SIN, PDB: 5O7Y). Both metal and 2OG binding sites display similarity to other proteins from the ODD family, but T6ODM is characterized by an exceptionally large substrate binding cavity, whose volume can partially explain the promiscuity of this enzyme. Moreover, the size of the cavity allows for binding of multiple molecules at once, posing a question about the substrate-driven specificity of the enzyme.
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Affiliation(s)
- Anna Kluza
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Ewa Niedzialkowska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Katarzyna Kurpiewska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland; Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, PL-30387 Krakow, Poland
| | - Zuzanna Wojdyla
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Matthew Quesne
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Ewa Kot
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Przemyslaw J Porebski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.
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18
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Kutner J, Shabalin IG, Matelska D, Handing KB, Gasiorowska O, Sroka P, Gorna MW, Ginalski K, Wozniak K, Minor W. Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies. Biochemistry 2018; 57:963-977. [PMID: 29309127 PMCID: PMC6469932 DOI: 10.1021/acs.biochem.7b01137] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The d-2-hydroxyacid dehydrogenase (2HADH) family illustrates a complex evolutionary history with multiple lateral gene transfers and gene duplications and losses. As a result, the exact functional annotation of individual members can be extrapolated to a very limited extent. Here, we revise the previous simplified view on the classification of the 2HADH family; specifically, we show that the previously delineated glyoxylate/hydroxypyruvate reductase (GHPR) subfamily consists of two evolutionary separated GHRA and GHRB subfamilies. We compare two representatives of these subfamilies from Sinorhizobium meliloti (SmGhrA and SmGhrB), employing a combination of biochemical, structural, and bioinformatics approaches. Our kinetic results show that both enzymes reduce several 2-ketocarboxylic acids with overlapping, but not equivalent, substrate preferences. SmGhrA and SmGhrB show highest activity with glyoxylate and hydroxypyruvate, respectively; in addition, only SmGhrB reduces 2-keto-d-gluconate, and only SmGhrA reduces pyruvate (with low efficiency). We present nine crystal structures of both enzymes in apo forms and in complexes with cofactors and substrates/substrate analogues. In particular, we determined a crystal structure of SmGhrB with 2-keto-d-gluconate, which is the biggest substrate cocrystallized with a 2HADH member. The structures reveal significant differences between SmGhrA and SmGhrB, both in the overall structure and within the substrate-binding pocket, offering insight into the molecular basis for the observed substrate preferences and subfamily differences. In addition, we provide an overview of all GHRA and GHRB structures complexed with a ligand in the active site.
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Affiliation(s)
- Jan Kutner
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States,Laboratory for Structural and Biochemical Research, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Zwirki i Wigury, 02-089 Warsaw, Poland
| | - Ivan G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Dorota Matelska
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States,Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 93 Zwirki i Wigury, 02-089 Warsaw, Poland
| | - Katarzyna B. Handing
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Olga Gasiorowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Piotr Sroka
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Maria W. Gorna
- Laboratory for Structural and Biochemical Research, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Zwirki i Wigury, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 93 Zwirki i Wigury, 02-089 Warsaw, Poland,Corresponding Authors: (K.G.)., (K.W.)., . Phone: (434) 243-6865. Fax: (434) 243-2981 (W.M.)
| | - Krzysztof Wozniak
- Laboratory for Structural and Biochemical Research, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Zwirki i Wigury, 02-089 Warsaw, Poland,Corresponding Authors: (K.G.)., (K.W.)., . Phone: (434) 243-6865. Fax: (434) 243-2981 (W.M.)
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States,Department of Chemistry, University of Warsaw, 1 Ludwika Pasteura, 02-093 Warsaw, Poland,Corresponding Authors: (K.G.)., (K.W.)., . Phone: (434) 243-6865. Fax: (434) 243-2981 (W.M.)
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19
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Wlodawer A, Dauter Z, Porebski PJ, Minor W, Stanfield R, Jaskolski M, Pozharski E, Weichenberger CX, Rupp B. Detect, correct, retract: How to manage incorrect structural models. FEBS J 2018; 285:444-466. [PMID: 29113027 PMCID: PMC5799025 DOI: 10.1111/febs.14320] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 11/01/2017] [Indexed: 12/13/2022]
Abstract
The massive technical and computational progress of biomolecular crystallography has generated some adverse side effects. Most crystal structure models, produced by crystallographers or well-trained structural biologists, constitute useful sources of information, but occasional extreme outliers remind us that the process of structure determination is not fail-safe. The occurrence of severe errors or gross misinterpretations raises fundamental questions: Why do such aberrations emerge in the first place? How did they evade the sophisticated validation procedures which often produce clear and dire warnings, and why were severe errors not noticed by the depositors themselves, their supervisors, referees and editors? Once detected, what can be done to either correct, improve or eliminate such models? How do incorrect models affect the underlying claims or biomedical hypotheses they were intended, but failed, to support? What is the long-range effect of the propagation of such errors? And finally, what mechanisms can be envisioned to restore the validity of the scientific record and, if necessary, retract publications that are clearly invalidated by the lack of experimental evidence? We suggest that cognitive bias and flawed epistemology are likely at the root of the problem. By using examples from the published literature and from public repositories such as the Protein Data Bank, we provide case summaries to guide correction or improvement of structural models. When strong claims are unsustainable because of a deficient crystallographic model, removal of such a model and even retraction of the affected publication are necessary to restore the integrity of the scientific record.
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Affiliation(s)
- Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Przemyslaw J. Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Robyn Stanfield
- Department of Structural and Computational Biology, BCC206, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, Poznan, 61-614, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan, 61-704, Poland
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Bernhard Rupp
- CVMO, k.-k.Hofkristallamt, 991 Audrey Place, Vista, CA, 92084, USA
- Department of Genetic Epidemiology, Medical University Innsbruck, Schöpfstr. 41, Innsbruck, 6020, Austria
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20
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Zheng H, Porebski PJ, Grabowski M, Cooper DR, Minor W. Databases, Repositories, and Other Data Resources in Structural Biology. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1607:643-665. [PMID: 28573593 DOI: 10.1007/978-1-4939-7000-1_27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Structural biology, like many other areas of modern science, produces an enormous amount of primary, derived, and "meta" data with a high demand on data storage and manipulations. Primary data come from various steps of sample preparation, diffraction experiments, and functional studies. These data are not only used to obtain tangible results, like macromolecular structural models, but also to enrich and guide our analysis and interpretation of various biomedical problems. Herein we define several categories of data resources, (a) Archives, (b) Repositories, (c) Databases, and (d) Advanced Information Systems, that can accommodate primary, derived, or reference data. Data resources may be used either as web portals or internally by structural biology software. To be useful, each resource must be maintained, curated, as well as integrated with other resources. Ideally, the system of interconnected resources should evolve toward comprehensive "hubs", or Advanced Information Systems. Such systems, encompassing the PDB and UniProt, are indispensable not only for structural biology, but for many related fields of science. The categories of data resources described herein are applicable well beyond our usual scientific endeavors.
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Affiliation(s)
- Heping Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA, 22908, USA
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA, 22908, USA
| | - Marek Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA, 22908, USA
| | - David R Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA, 22908, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA, 22908, USA.
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21
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Krojer T, Talon R, Pearce N, Collins P, Douangamath A, Brandao-Neto J, Dias A, Marsden B, von Delft F. The XChemExplorer graphical workflow tool for routine or large-scale protein-ligand structure determination. Acta Crystallogr D Struct Biol 2017; 73:267-278. [PMID: 28291762 PMCID: PMC5349439 DOI: 10.1107/s2059798316020234] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/20/2016] [Indexed: 11/11/2022] Open
Abstract
XChemExplorer (XCE) is a data-management and workflow tool to support large-scale simultaneous analysis of protein-ligand complexes during structure-based ligand discovery (SBLD). The user interfaces of established crystallographic software packages such as CCP4 [Winn et al. (2011), Acta Cryst. D67, 235-242] or PHENIX [Adams et al. (2010), Acta Cryst. D66, 213-221] have entrenched the paradigm that a `project' is concerned with solving one structure. This does not hold for SBLD, where many almost identical structures need to be solved and analysed quickly in one batch of work. Functionality to track progress and annotate structures is essential. XCE provides an intuitive graphical user interface which guides the user from data processing, initial map calculation, ligand identification and refinement up until data dissemination. It provides multiple entry points depending on the need of each project, enables batch processing of multiple data sets and records metadata, progress and annotations in an SQLite database. XCE is freely available and works on any Linux and Mac OS X system, and the only dependency is to have the latest version of CCP4 installed. The design and usage of this tool are described here, and its usefulness is demonstrated in the context of fragment-screening campaigns at the Diamond Light Source. It is routinely used to analyse projects comprising 1000 data sets or more, and therefore scales well to even very large ligand-design projects.
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Affiliation(s)
- Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Romain Talon
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Nicholas Pearce
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Patrick Collins
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
| | - Alice Douangamath
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
| | - Jose Brandao-Neto
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
| | - Alexandre Dias
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
| | - Brian Marsden
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, England
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
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22
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Morales-Perez CL, Noviello CM, Hibbs RE. X-ray structure of the human α4β2 nicotinic receptor. Nature 2016; 538:411-415. [PMID: 27698419 PMCID: PMC5161573 DOI: 10.1038/nature19785] [Citation(s) in RCA: 305] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/22/2016] [Indexed: 02/07/2023]
Abstract
Nicotinic acetylcholine receptors are ligand-gated ion channels that mediate fast chemical neurotransmission at the neuromuscular junction and have diverse signalling roles in the central nervous system. The nicotinic receptor has been a model system for cell-surface receptors, and specifically for ligand-gated ion channels, for well over a century. In addition to the receptors' prominent roles in the development of the fields of pharmacology and neurobiology, nicotinic receptors are important therapeutic targets for neuromuscular disease, addiction, epilepsy and for neuromuscular blocking agents used during surgery. The overall architecture of the receptor was described in landmark studies of the nicotinic receptor isolated from the electric organ of Torpedo marmorata. Structures of a soluble ligand-binding domain have provided atomic-scale insights into receptor-ligand interactions, while high-resolution structures of other members of the pentameric receptor superfamily provide touchstones for an emerging allosteric gating mechanism. All available high-resolution structures are of homopentameric receptors. However, the vast majority of pentameric receptors (called Cys-loop receptors in eukaryotes) present physiologically are heteromeric. Here we present the X-ray crystallographic structure of the human α4β2 nicotinic receptor, the most abundant nicotinic subtype in the brain. This structure provides insights into the architectural principles governing ligand recognition, heteromer assembly, ion permeation and desensitization in this prototypical receptor class.
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Affiliation(s)
- Claudio L. Morales-Perez
- Departments of Neuroscience and Biophysics, University of Texas
Southwestern Medical Center, Dallas, TX 75390, USA
| | - Colleen M. Noviello
- Departments of Neuroscience and Biophysics, University of Texas
Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ryan E. Hibbs
- Departments of Neuroscience and Biophysics, University of Texas
Southwestern Medical Center, Dallas, TX 75390, USA
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23
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Hintze BJ, Lewis SM, Richardson JS, Richardson DC. Molprobity's ultimate rotamer-library distributions for model validation. Proteins 2016; 84:1177-89. [PMID: 27018641 DOI: 10.1002/prot.25039] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 03/16/2016] [Accepted: 03/18/2016] [Indexed: 12/22/2022]
Abstract
Here we describe the updated MolProbity rotamer-library distributions derived from an order-of-magnitude larger and more stringently quality-filtered dataset of about 8000 (vs. 500) protein chains, and we explain the resulting changes and improvements to model validation as seen by users. To include only side-chains with satisfactory justification for their given conformation, we added residue-specific filters for electron-density value and model-to-density fit. The combined new protocol retains a million residues of data, while cleaning up false-positive noise in the multi- χ datapoint distributions. It enables unambiguous characterization of conformational clusters nearly 1000-fold less frequent than the most common ones. We describe examples of local interactions that favor these rare conformations, including the role of authentic covalent bond-angle deviations in enabling presumably strained side-chain conformations. Further, along with favored and outlier, an allowed category (0.3-2.0% occurrence in reference data) has been added, analogous to Ramachandran validation categories. The new rotamer distributions are used for current rotamer validation in MolProbity and PHENIX, and for rotamer choice in PHENIX model-building and refinement. The multi-dimensional χ distributions and Top8000 reference dataset are freely available on GitHub. These rotamers are termed "ultimate" because data sampling and quality are now fully adequate for this task, and also because we believe the future of conformational validation should integrate side-chain with backbone criteria. Proteins 2016; 84:1177-1189. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Bradley J Hintze
- Department of Biochemistry, Duke University, Durham North Carolina 27710
| | - Steven M Lewis
- Department of Biochemistry, Duke University, Durham North Carolina 27710
| | - Jane S Richardson
- Department of Biochemistry, Duke University, Durham North Carolina 27710
| | - David C Richardson
- Department of Biochemistry, Duke University, Durham North Carolina 27710
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24
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Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-Grained Protein Models and Their Applications. Chem Rev 2016; 116:7898-936. [DOI: 10.1021/acs.chemrev.6b00163] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sebastian Kmiecik
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Dominik Gront
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics
Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Lukasz Wieteska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
- Department
of Medical Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland
| | | | - Andrzej Kolinski
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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25
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Niedzialkowska E, Gasiorowska O, Handing KB, Majorek KA, Porebski PJ, Shabalin IG, Zasadzinska E, Cymborowski M, Minor W. Protein purification and crystallization artifacts: The tale usually not told. Protein Sci 2016; 25:720-33. [PMID: 26660914 PMCID: PMC4815408 DOI: 10.1002/pro.2861] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/02/2015] [Accepted: 12/02/2015] [Indexed: 01/07/2023]
Abstract
The misidentification of a protein sample, or contamination of a sample with the wrong protein, may be a potential reason for the non-reproducibility of experiments. This problem may occur in the process of heterologous overexpression and purification of recombinant proteins, as well as purification of proteins from natural sources. If the contaminated or misidentified sample is used for crystallization, in many cases the problem may not be detected until structures are determined. In the case of functional studies, the problem may not be detected for years. Here several procedures that can be successfully used for the identification of crystallized protein contaminants, including: (i) a lattice parameter search against known structures, (ii) sequence or fold identification from partially built models, and (iii) molecular replacement with common contaminants as search templates have been presented. A list of common contaminant structures to be used as alternative search models was provided. These methods were used to identify four cases of purification and crystallization artifacts. This report provides troubleshooting pointers for researchers facing difficulties in phasing or model building.
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Affiliation(s)
- Ewa Niedzialkowska
- Department of Molecular Physiology and Biological PhysicsUniversity of Virginia School of Medicine1340 Jefferson Park Avenue, Jordan Hall, Room 4223CharlottesvilleVirginia22908
- Jerzy Haber Institute of Catalysis and Surface ChemistryPolish Academy of SciencesNiezapominajek 8Krakow30‐239Poland
- Midwest Center for Structural Genomics (MCSG)ArgonneIllinois60439
| | - Olga Gasiorowska
- Department of Molecular Physiology and Biological PhysicsUniversity of Virginia School of Medicine1340 Jefferson Park Avenue, Jordan Hall, Room 4223CharlottesvilleVirginia22908
- Midwest Center for Structural Genomics (MCSG)ArgonneIllinois60439
| | - Katarzyna B. Handing
- Department of Molecular Physiology and Biological PhysicsUniversity of Virginia School of Medicine1340 Jefferson Park Avenue, Jordan Hall, Room 4223CharlottesvilleVirginia22908
- Midwest Center for Structural Genomics (MCSG)ArgonneIllinois60439
| | - Karolina A. Majorek
- Department of Molecular Physiology and Biological PhysicsUniversity of Virginia School of Medicine1340 Jefferson Park Avenue, Jordan Hall, Room 4223CharlottesvilleVirginia22908
- Midwest Center for Structural Genomics (MCSG)ArgonneIllinois60439
- Center for Structural Genomics of Infectious Diseases (CSGID)ChicagoIllinois60611
| | - Przemyslaw J. Porebski
- Department of Molecular Physiology and Biological PhysicsUniversity of Virginia School of Medicine1340 Jefferson Park Avenue, Jordan Hall, Room 4223CharlottesvilleVirginia22908
- Midwest Center for Structural Genomics (MCSG)ArgonneIllinois60439
| | - Ivan G. Shabalin
- Department of Molecular Physiology and Biological PhysicsUniversity of Virginia School of Medicine1340 Jefferson Park Avenue, Jordan Hall, Room 4223CharlottesvilleVirginia22908
- Midwest Center for Structural Genomics (MCSG)ArgonneIllinois60439
- Center for Structural Genomics of Infectious Diseases (CSGID)ChicagoIllinois60611
- New York Structural Genomics Research Consortium (NYSGRC)BronxNew York10461
| | - Ewelina Zasadzinska
- Department of Biochemistry and Molecular GeneticsUniversity of Virginia School of Medicine1340 Jefferson Park Avenue, Jordan Hall, Room 6044CharlottesvilleVirginia22908
| | - Marcin Cymborowski
- Department of Molecular Physiology and Biological PhysicsUniversity of Virginia School of Medicine1340 Jefferson Park Avenue, Jordan Hall, Room 4223CharlottesvilleVirginia22908
- Midwest Center for Structural Genomics (MCSG)ArgonneIllinois60439
| | - Wladek Minor
- Department of Molecular Physiology and Biological PhysicsUniversity of Virginia School of Medicine1340 Jefferson Park Avenue, Jordan Hall, Room 4223CharlottesvilleVirginia22908
- Midwest Center for Structural Genomics (MCSG)ArgonneIllinois60439
- Center for Structural Genomics of Infectious Diseases (CSGID)ChicagoIllinois60611
- New York Structural Genomics Research Consortium (NYSGRC)BronxNew York10461
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