1
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Jones AA, Snow CD. Porous protein crystals: synthesis and applications. Chem Commun (Camb) 2024. [PMID: 38756076 DOI: 10.1039/d4cc00183d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Large-pore protein crystals (LPCs) are an emerging class of biomaterials. The inherent diversity of proteins translates to a diversity of crystal lattice structures, many of which display large pores and solvent channels. These pores can, in turn, be functionalized via directed evolution and rational redesign based on the known crystal structures. LPCs possess extremely high solvent content, as well as extremely high surface area to volume ratios. Because of these characteristics, LPCs continue to be explored in diverse applications including catalysis, targeted therapeutic delivery, templating of nanostructures, structural biology. This Feature review article will describe several of the existing platforms in detail, with particular focus on LPC synthesis approaches and reported applications.
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Affiliation(s)
- Alec Arthur Jones
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523-1301, USA.
| | - Christopher D Snow
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523-1301, USA.
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523-1301, USA
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2
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Meng Q, Moinuddin SGA, Celoy RM, Smith CA, Young RP, Costa MA, Freeman RA, Fukaya M, Kim DN, Cort JR, Hawes MC, van Etten HD, Pandey P, Chittiboyina AG, Ferreira D, Davin LB, Lewis NG. Dirigent isoflavene-forming PsPTS2: 3D structure, stereochemical, and kinetic characterization comparison with pterocarpan-forming PsPTS1 homolog in pea. J Biol Chem 2024; 300:105647. [PMID: 38219818 PMCID: PMC10882141 DOI: 10.1016/j.jbc.2024.105647] [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: 08/03/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 01/16/2024] Open
Abstract
Pea phytoalexins (-)-maackiain and (+)-pisatin have opposite C6a/C11a configurations, but biosynthetically how this occurs is unknown. Pea dirigent-protein (DP) PsPTS2 generates 7,2'-dihydroxy-4',5'-methylenedioxyisoflav-3-ene (DMDIF), and stereoselectivity toward four possible 7,2'-dihydroxy-4',5'-methylenedioxyisoflavan-4-ol (DMDI) stereoisomers was investigated. Stereoisomer configurations were determined using NMR spectroscopy, electronic circular dichroism, and molecular orbital analyses. PsPTS2 efficiently converted cis-(3R,4R)-DMDI into DMDIF 20-fold faster than the trans-(3R,4S)-isomer. The 4R-configured substrate's near β-axial OH orientation significantly enhanced its leaving group abilities in generating A-ring mono-quinone methide (QM), whereas 4S-isomer's α-equatorial-OH was a poorer leaving group. Docking simulations indicated that the 4R-configured β-axial OH was closest to Asp51, whereas 4S-isomer's α-equatorial OH was further away. Neither cis-(3S,4S)- nor trans-(3S,4R)-DMDIs were substrates, even with the former having C3/C4 stereochemistry as in (+)-pisatin. PsPTS2 used cis-(3R,4R)-7,2'-dihydroxy-4'-methoxyisoflavan-4-ol [cis-(3R,4R)-DMI] and C3/C4 stereoisomers to give 2',7-dihydroxy-4'-methoxyisoflav-3-ene (DMIF). DP homologs may exist in licorice (Glycyrrhiza pallidiflora) and tree legume Bolusanthus speciosus, as DMIF occurs in both species. PsPTS1 utilized cis-(3R,4R)-DMDI to give (-)-maackiain 2200-fold more efficiently than with cis-(3R,4R)-DMI to give (-)-medicarpin. PsPTS1 also slowly converted trans-(3S,4R)-DMDI into (+)-maackiain, reflecting the better 4R configured OH leaving group. PsPTS2 and PsPTS1 provisionally provide the means to enable differing C6a and C11a configurations in (+)-pisatin and (-)-maackiain, via identical DP-engendered mono-QM bound intermediate generation, which PsPTS2 either re-aromatizes to give DMDIF or PsPTS1 intramolecularly cyclizes to afford (-)-maackiain. Substrate docking simulations using PsPTS2 and PsPTS1 indicate cis-(3R,4R)-DMDI binds in the anti-configuration in PsPTS2 to afford DMDIF, and the syn-configuration in PsPTS1 to give maackiain.
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Affiliation(s)
- Qingyan Meng
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Syed G A Moinuddin
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Rhodesia M Celoy
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Clyde A Smith
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California, USA
| | - Robert P Young
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Michael A Costa
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Rachel A Freeman
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Masashi Fukaya
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Doo Nam Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - John R Cort
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Martha C Hawes
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Hans D van Etten
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Pankaj Pandey
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA
| | - Amar G Chittiboyina
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA
| | - Daneel Ferreira
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA; Division of Pharmacognosy, Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, Mississippi, USA
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA.
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3
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Hong S, Choe J. Crystallization and biochemical studies of the NYN domain of human KHNYN. Acta Crystallogr F Struct Biol Commun 2024; 80:67-72. [PMID: 38376822 PMCID: PMC10910534 DOI: 10.1107/s2053230x24000943] [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: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/21/2024] Open
Abstract
KHNYN is composed of an N-terminal KH-like RNA-binding domain and a C-terminal PIN/NYN endoribonuclease domain. It forms a complex with zinc-finger antiviral protein (ZAP), leading to the degradation of viral or cellular RNAs depending on the ZAP isoform. Here, the production, crystallization and biochemical analysis of the NYN domain (residues 477-636) of human KHNYN are presented. The NYN domain was crystallized with a heptameric single-stranded RNA from the AU-rich elements of the 3'-UTR of interferon lambda 3. The crystal belonged to space group P4132, with unit-cell parameters a = b = c = 111.3 Å, and diffacted to 1.72 Å resolution. The RNase activity of the NYN domain was demonstrated using different single-stranded RNAs, together with the binding between the NYN domain of KHNYN and the zinc-finger domain of ZAP.
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Affiliation(s)
- Sunho Hong
- Department of Life Science, University of Seoul, 163 Seoulsiripdaero, Seoul 02504, Republic of Korea
| | - Jungwoo Choe
- Department of Life Science, University of Seoul, 163 Seoulsiripdaero, Seoul 02504, Republic of Korea
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4
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Guerrero L, Ebrahim A, Riley BT, Kim M, Huang Q, Finke AD, Keedy DA. Pushed to extremes: distinct effects of high temperature versus pressure on the structure of STEP. Commun Biol 2024; 7:59. [PMID: 38216663 PMCID: PMC10786866 DOI: 10.1038/s42003-023-05609-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/20/2023] [Indexed: 01/14/2024] Open
Abstract
Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature versus. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Altogether, our work indicates that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.
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Affiliation(s)
- Liliana Guerrero
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
- PhD Program in Biochemistry, CUNY Graduate Center, New York, NY, 10016, USA
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Blake T Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Minyoung Kim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, 14853, USA
| | - Aaron D Finke
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, 14853, USA
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA.
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA.
- PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY, 10016, USA.
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5
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Snajdarova K, Marques SM, Damborsky J, Bednar D, Marek M. Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum. Acta Crystallogr D Struct Biol 2023; 79:956-970. [PMID: 37860958 PMCID: PMC10619424 DOI: 10.1107/s2059798323006642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/31/2023] [Indexed: 10/21/2023] Open
Abstract
Haloalkane dehalogenases (HLDs) are a family of α/β-hydrolase fold enzymes that employ SN2 nucleophilic substitution to cleave the carbon-halogen bond in diverse chemical structures, the biological role of which is still poorly understood. Atomic-level knowledge of both the inner organization and supramolecular complexation of HLDs is thus crucial to understand their catalytic and noncatalytic functions. Here, crystallographic structures of the (S)-enantioselective haloalkane dehalogenase DmmarA from the waterborne pathogenic microbe Mycobacterium marinum were determined at 1.6 and 1.85 Å resolution. The structures show a canonical αβα-sandwich HLD fold with several unusual structural features. Mechanistically, the atypical composition of the proton-relay catalytic triad (aspartate-histidine-aspartate) and uncommon active-site pocket reveal the molecular specificities of a catalytic apparatus that exhibits a rare (S)-enantiopreference. Additionally, the structures reveal a previously unobserved mode of symmetric homodimerization, which is predominantly mediated through unusual L5-to-L5 loop interactions. This homodimeric association in solution is confirmed experimentally by data obtained from small-angle X-ray scattering. Utilizing the newly determined structures of DmmarA, molecular modelling techniques were employed to elucidate the underlying mechanism behind its uncommon enantioselectivity. The (S)-preference can be attributed to the presence of a distinct binding pocket and variance in the activation barrier for nucleophilic substitution.
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Affiliation(s)
- Karolina Snajdarova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Building A13, 625 00 Brno, Czech Republic
| | - Sérgio M. Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Building A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Building A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Building A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Martin Marek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Building A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
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6
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Schroeder GM, Kiliushik D, Jenkins JL, Wedekind JE. Structure and function analysis of a type III preQ 1-I riboswitch from Escherichia coli reveals direct metabolite sensing by the Shine-Dalgarno sequence. J Biol Chem 2023; 299:105208. [PMID: 37660906 PMCID: PMC10622847 DOI: 10.1016/j.jbc.2023.105208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023] Open
Abstract
Riboswitches are small noncoding RNAs found primarily in the 5' leader regions of bacterial messenger RNAs where they regulate expression of downstream genes in response to binding one or more cellular metabolites. Such noncoding RNAs are often regulated at the translation level, which is thought to be mediated by the accessibility of the Shine-Dalgarno sequence (SDS) ribosome-binding site. Three classes (I-III) of prequeuosine1 (preQ1)-sensing riboswitches are known that control translation. Class I is divided into three subtypes (types I-III) that have diverse mechanisms of sensing preQ1, which is involved in queuosine biosynthesis. To provide insight into translation control, we determined a 2.30 Å-resolution cocrystal structure of a class I type III preQ1-sensing riboswitch identified in Escherichia coli (Eco) by bioinformatic searches. The Eco riboswitch structure differs from previous preQ1 riboswitch structures because it has the smallest naturally occurring aptamer and the SDS directly contacts the preQ1 metabolite. We validated structural observations using surface plasmon resonance and in vivo gene-expression assays, which showed strong switching in live E. coli. Our results demonstrate that the Eco riboswitch is relatively sensitive to mutations that disrupt noncanonical interactions that form the pseudoknot. In contrast to type II preQ1 riboswitches, a kinetic analysis showed that the type III Eco riboswitch strongly prefers preQ1 over the chemically similar metabolic precursor preQ0. Our results reveal the importance of noncanonical interactions in riboswitch-driven gene regulation and the versatility of the class I preQ1 riboswitch pseudoknot as a metabolite-sensing platform that supports SDS sequestration.
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Affiliation(s)
- Griffin M Schroeder
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Daniil Kiliushik
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Jermaine L Jenkins
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Joseph E Wedekind
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA; Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.
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7
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Stegmann DP, Steuber J, Fritz G, Wojdyla JA, Sharpe ME. Fast fragment and compound screening pipeline at the Swiss Light Source. Methods Enzymol 2023; 690:235-284. [PMID: 37858531 DOI: 10.1016/bs.mie.2023.08.005] [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] [Indexed: 10/21/2023]
Abstract
Crystallography-based fragment screening is a highly effective technique employed in structure-based drug discovery to expand the range of lead development opportunities. It allows screening and sorting of weakly binding, low molecular mass fragments, which can be developed into larger high-affinity lead compounds. Technical improvements at synchrotron beamlines, design of innovative libraries mapping chemical space efficiently, effective soaking methods and enhanced data analysis have enabled the implementation of high-throughput fragment screening pipelines at multiple synchrotron facilities. This widened access to CBFS beyond the pharma industry has allowed academic users to rapidly screen large quantities of fragment-soaked protein crystals. The positive outcome of a CBFS campaign is a set of structures that present the three-dimensional arrangement of fragment-protein complexes in detail, thereby providing information on the location and the mode of interaction of bound fragments. Through this review, we provide users with a comprehensive guide that sets clear expectations before embarking on a crystallography-based fragment screening campaign. We present a list of essential pre-requirements that must be assessed, including the suitability of your current crystal system for a fragment screening campaign. Furthermore, we extensively discuss the available methodological options, addressing their limitations and providing strategies to overcome them. Additionally, we provide a brief perspective on how to proceed once hits are obtained. Notably, we emphasize the solutions we have implemented for instrumentation and software development within our Fast Fragment and Compound Screening pipeline. We also highlight third-party software options that can be utilized for rapid refinement and hit assessment.
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Affiliation(s)
| | - Julia Steuber
- Institute of Biology, Department of Cellular Microbiology, University of Hohenheim, Stuttgart, Germany
| | - Günter Fritz
- Institute of Biology, Department of Cellular Microbiology, University of Hohenheim, Stuttgart, Germany.
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8
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Pletzer-Zelgert J, Ehrt C, Fender I, Griewel A, Flachsenberg F, Klebe G, Rarey M. LifeSoaks: a tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments. Acta Crystallogr D Struct Biol 2023; 79:837-856. [PMID: 37561404 PMCID: PMC10478636 DOI: 10.1107/s205979832300582x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Due to the structural complexity of proteins, their corresponding crystal arrangements generally contain a significant amount of solvent-occupied space. These areas allow a certain degree of intracrystalline protein flexibility and mobility of solutes. Therefore, knowledge of the geometry of solvent-filled channels and cavities is essential whenever the dynamics inside a crystal are of interest. Especially in soaking experiments for structure-based drug design, ligands must be able to traverse the crystal solvent channels and reach the corresponding binding pockets. Unsuccessful screenings are sometimes attributed to the geometry of the crystal packing, but the underlying causes are often difficult to understand. This work presents LifeSoaks, a novel tool for analyzing and visualizing solvent channels in protein crystals. LifeSoaks uses a Voronoi diagram-based periodic channel representation which can be efficiently computed. The size and location of channel bottlenecks, which might hinder molecular diffusion, can be directly derived from this representation. This work presents the calculated bottleneck radii for all crystal structures in the PDB and the analysis of a new, hand-curated data set of structures obtained by soaking experiments. The results indicate that the consideration of bottleneck radii and the visual inspection of channels are beneficial for planning soaking experiments.
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Affiliation(s)
| | - Christiane Ehrt
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Inken Fender
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Axel Griewel
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Florian Flachsenberg
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Universität Marburg, Marbacher Weg 6-10, 35032 Marburg, Germany
| | - Matthias Rarey
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
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9
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Moody JD, Hill S, Lundahl MN, Saxton AJ, Galambas A, Broderick WE, Lawrence CM, Broderick JB. Computational engineering of previously crystallized pyruvate formate-lyase activating enzyme reveals insights into SAM binding and reductive cleavage. J Biol Chem 2023:104791. [PMID: 37156396 DOI: 10.1016/j.jbc.2023.104791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 05/10/2023] Open
Abstract
Radical S-adenosyl-l-methionine (SAM) enzymes are ubiquitous in nature and carry out a broad variety of difficult chemical transformations initiated by hydrogen atom abstraction. Although numerous radical SAM (RS) enzymes have been structurally characterized, many prove recalcitrant to crystallization needed for atomic-level structure determination using X-ray crystallography, and even those that have been crystallized for an initial study can be difficult to recrystallize for further structural work. We present here a method for computationally engineering previously observed crystallographic contacts and employ it to obtain more reproducible crystallization of the RS enzyme pyruvate formate-lyase activating enzyme (PFL-AE). We show that the computationally engineered variant binds a typical RS [4Fe-4S]2+/+ cluster that binds SAM, with electron paramagnetic resonance (EPR) properties indistinguishable from the native PFL-AE. The variant also retains the typical PFL-AE catalytic activity, as evidenced by the characteristic glycyl radical EPR signal observed upon incubation of the PFL-AE variant with reducing agent, SAM, and PFL. The PFL-AE variant was also crystallized in the [4Fe-4S]2+ state with SAM bound, providing a new high-resolution structure of the SAM complex in the absence of substrate. Finally, by incubating such a crystal in a solution of sodium dithionite, the reductive cleavage of SAM is triggered, providing us with a structure in which the SAM cleavage products 5'-deoxyadenosine and methionine are bound in the active site. We propose that the methods described herein may be useful in the structural characterization of other difficult-to-resolve proteins.
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Affiliation(s)
- James D Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA; Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Sarah Hill
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Maike N Lundahl
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Aubrianna J Saxton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Amanda Galambas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - William E Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - C Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.
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10
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Kingston RL, Millane RP. A general method for directly phasing diffraction data from high-solvent-content protein crystals. IUCRJ 2022; 9:648-665. [PMID: 36071801 PMCID: PMC9438493 DOI: 10.1107/s2052252522006996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
A procedure is described for direct phase determination in protein crystallography, applicable to crystals with high solvent content. The procedure requires only the diffraction data and an estimate of the solvent content as input. Direct phase determination is treated as a constraint satisfaction problem, in which an image is sought that is consistent with both the diffraction data and generic constraints on the density distribution in the crystal. The problem is solved using an iterative projection algorithm, the Difference Map algorithm, which has good global convergence properties, and can locate the correct solution without any initial phase information. Computational efficiency is improved by breaking the problem down into two stages; initial approximation of the molecular envelope at low resolution, followed by subsequent phase determination using all of the data. The molecular envelope is continually updated during the phase determination step. At both stages, the algorithm is initiated with many different and random phase sets, which are evolved subject to the constraints. A clustering procedure is used to identify consistent results across multiple runs, which are then averaged to generate consensus envelopes or phase sets. The emergence of highly consistent phase sets is diagnostic of success. The effectiveness of the procedure is demonstrated by application to 42 known structures of solvent fraction 0.60-0.85. The procedure works robustly at intermediate resolutions (1.9-3.5 Å) but is strongly dependent on crystal solvent content, only working routinely with solvent fractions greater than 0.70.
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Affiliation(s)
- Richard Lawrence Kingston
- School of Biological Sciences, University of Auckland, 3a Symonds St, Auckland City, Auckland 1010, New Zealand
| | - Rick P. Millane
- Computational Imaging Group, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
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11
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Mahoney BJ, Takayesu A, Zhou A, Cascio D, Clubb RT. The structure of the Clostridium thermocellum RsgI9 ectodomain provides insight into the mechanism of biomass sensing. Proteins 2022; 90:1457-1467. [PMID: 35194841 PMCID: PMC9177573 DOI: 10.1002/prot.26326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/10/2022] [Indexed: 01/03/2023]
Abstract
Clostridium thermocellum is actively being developed as a microbial platform to produce biofuels and chemicals from renewable plant biomass. An attractive feature of this bacterium is its ability to efficiently degrade lignocellulose using surface-displayed cellulosomes, large multi-protein complexes that house different types of cellulase enzymes. Clostridium thermocellum tailors the enzyme composition of its cellulosome using nine membrane-embedded anti-σ factors (RsgI1-9), which are thought to sense different types of extracellular carbohydrates and then elicit distinct gene expression programs via cytoplasmic σ factors. Here we show that the RsgI9 anti-σ factor interacts with cellulose via a C-terminal bi-domain unit. A 2.0 Å crystal structure reveals that the unit is constructed from S1C peptidase and NTF2-like protein domains that contain a potential binding site for cellulose. Small-angle X-ray scattering experiments of the intact ectodomain indicate that it adopts a bi-lobed, elongated conformation. In the structure, a conserved RsgI extracellular (CRE) domain is connected to the bi-domain via a proline-rich linker, which is expected to project the carbohydrate-binding unit ~160 Å from the cell surface. The CRE and proline-rich elements are conserved in several other C. thermocellum anti-σ factors, suggesting that they will also form extended structures that sense carbohydrates.
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Affiliation(s)
- Brendan J. Mahoney
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA.,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Allen Takayesu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Anqi Zhou
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Duilio Cascio
- UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Robert T. Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA.,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA.,To whom correspondence should be addressed: Prof. Robert T. Clubb, Department of Chemistry and Biochemistry, University of California, Los Angeles, 602 Boyer Hall, Los Angeles, CA 90095
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12
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Krivacic C, Kundert K, Pan X, Pache RA, Liu L, Conchúir SO, Jeliazkov JR, Gray JJ, Thompson MC, Fraser JS, Kortemme T. Accurate positioning of functional residues with robotics-inspired computational protein design. Proc Natl Acad Sci U S A 2022; 119:e2115480119. [PMID: 35254891 PMCID: PMC8931229 DOI: 10.1073/pnas.2115480119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/27/2022] [Indexed: 11/18/2022] Open
Abstract
SignificanceComputational protein design promises to advance applications in medicine and biotechnology by creating proteins with many new and useful functions. However, new functions require the design of specific and often irregular atom-level geometries, which remains a major challenge. Here, we develop computational methods that design and predict local protein geometries with greater accuracy than existing methods. Then, as a proof of concept, we leverage these methods to design new protein conformations in the enzyme ketosteroid isomerase that change the protein's preference for a key functional residue. Our computational methods are openly accessible and can be applied to the design of other intricate geometries customized for new user-defined protein functions.
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Affiliation(s)
- Cody Krivacic
- UC Berkeley–UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94158
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Kale Kundert
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
- Biophysics Graduate Program, University of California, San Francisco, CA 94158
| | - Xingjie Pan
- UC Berkeley–UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94158
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Roland A. Pache
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Lin Liu
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Shane O Conchúir
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | | | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Michael C. Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - James S. Fraser
- UC Berkeley–UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94158
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
- Biophysics Graduate Program, University of California, San Francisco, CA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94158
| | - Tanja Kortemme
- UC Berkeley–UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA 94158
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
- Biophysics Graduate Program, University of California, San Francisco, CA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94158
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13
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Legault S, Fraser-Halberg DP, McAnelly RL, Eason MG, Thompson MC, Chica RA. Generation of bright monomeric red fluorescent proteins via computational design of enhanced chromophore packing. Chem Sci 2022; 13:1408-1418. [PMID: 35222925 PMCID: PMC8809391 DOI: 10.1039/d1sc05088e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/07/2022] [Indexed: 12/11/2022] Open
Abstract
Red fluorescent proteins (RFPs) have found widespread application in chemical and biological research due to their longer emission wavelengths. Here, we use computational protein design to increase the quantum yield and thereby brightness of a dim monomeric RFP (mRojoA, quantum yield = 0.02) by optimizing chromophore packing with aliphatic residues, which we hypothesized would reduce torsional motions causing non-radiative decay. Experimental characterization of the top 10 designed sequences yielded mSandy1 (λ em = 609 nm, quantum yield = 0.26), a variant with equivalent brightness to mCherry, a widely used RFP. We next used directed evolution to further increase brightness, resulting in mSandy2 (λ em = 606 nm, quantum yield = 0.35), the brightest Discosoma sp. derived monomeric RFP with an emission maximum above 600 nm reported to date. Crystallographic analysis of mSandy2 showed that the chromophore p-hydroxybenzylidene moiety is sandwiched between the side chains of Leu63 and Ile197, a structural motif that has not previously been observed in RFPs, and confirms that aliphatic packing leads to chromophore rigidification. Our results demonstrate that computational protein design can be used to generate bright monomeric RFPs, which can serve as templates for the evolution of novel far-red fluorescent proteins.
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Affiliation(s)
- Sandrine Legault
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
| | - Derek P Fraser-Halberg
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
| | - Ralph L McAnelly
- Department of Chemistry and Biochemistry, University of California, Merced Merced California 95343 USA
| | - Matthew G Eason
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
| | - Michael C Thompson
- Department of Chemistry and Biochemistry, University of California, Merced Merced California 95343 USA
| | - Roberto A Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada
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14
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Spiliopoulou M, Valmas A, Triandafillidis DP, Fili S, Christopoulou M, Filopoulou AJ, Piskopou A, Papadea P, Fitch AN, Beckers D, Degen T, Gozzo F, Morin M, Reinle-Schmitt ML, Karavassili F, Rosmaraki E, Chasapis CT, Margiolaki I. High-throughput macromolecular polymorph screening via an NMR and X-ray powder diffraction synergistic approach: the case of human insulin co-crystallized with resorcinol derivatives. J Appl Crystallogr 2021. [DOI: 10.1107/s160057672100426x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Regular injections of insulin provide life-saving benefits to millions of diabetics. Apart from native insulin and insulin analogue formulations, microcrystalline insulin suspensions are also commercially available. The onset of action of the currently available basal insulins relies on the slow dissociation of insulin hexamers in the subcutaneous space due to the strong binding of small organic ligands. With the aim of identifying insulin–ligand complexes with enhanced pharmacokinetic and pharmacodynamic profiles, the binding affinity of two resorcinol-based molecules (4-chlororesorcinol and 4-bromoresorcinol) and the structural characteristics of insulin upon co-crystallization with them were investigated in the present study. `In solution' measurements were performed via saturation transfer difference (STD) NMR. Co-crystallization upon pH variation resulted in the production of polycrystalline precipitates, whose structural characteristics (i.e. unit-cell symmetry and dimension) were assessed. In both cases, different polymorphs (four and three, respectively) of monoclinic symmetry (P21 and C2 space groups) were identified via X-ray powder diffraction. The results demonstrate the efficiency of a new approach that combines spectroscopy and diffraction techniques and provides an innovative alternative for high-throughput examination of insulin and other therapeutic proteins.
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15
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Sprenger J, Carey J, Schulz A, Drouard F, Lawson CL, von Wachenfeldt C, Linse S, Lo Leggio L. Guest-protein incorporation into solvent channels of a protein host crystal (hostal). Acta Crystallogr D Struct Biol 2021; 77:471-485. [PMID: 33825708 PMCID: PMC8025882 DOI: 10.1107/s2059798321001078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/29/2021] [Indexed: 11/10/2022] Open
Abstract
Soaking small molecules into the solvent channels of protein crystals is the most common method of obtaining crystalline complexes with ligands such as substrates or inhibitors. The solvent channels of some protein crystals are large enough to allow the incorporation of macromolecules, but soaking of protein guests into protein crystals has not been reported. Such protein host crystals (here given the name hostals) incorporating guest proteins may be useful for a wide range of applications in biotechnology, for example as cargo systems or for diffraction studies analogous to the crystal sponge method. The present study takes advantage of crystals of the Escherichia coli tryptophan repressor protein (ds-TrpR) that are extensively domain-swapped and suitable for incorporating guest proteins by diffusion, as they are robust and have large solvent channels. Confocal fluorescence microscopy is used to follow the migration of cytochrome c and fluorophore-labeled calmodulin into the solvent channels of ds-TrpR crystals. The guest proteins become uniformly distributed in the crystal within weeks and enriched within the solvent channels. X-ray diffraction studies on host crystals with high concentrations of incorporated guests demonstrate that diffraction limits of ∼2.5 Å can still be achieved. Weak electron density is observed in the solvent channels, but the guest-protein structures could not be determined by conventional crystallographic methods. Additional approaches that increase the ordering of guests in the host crystal are discussed that may support protein structure determination using the hostal system in the future. This host system may also be useful for biotechnological applications where crystallographic order of the guest is not required.
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Affiliation(s)
- Janina Sprenger
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Center for Molecular Protein Science, Lund University, SE-221 00 Lund, Sweden
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Jannette Carey
- Chemistry Department, Princeton University, Princeton, NJ 08544, USA
| | - Alexander Schulz
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg, Denmark
| | - Fleur Drouard
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Catherine L. Lawson
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA
| | | | - Sara Linse
- Center for Molecular Protein Science, Lund University, SE-221 00 Lund, Sweden
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
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16
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Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing. CRYSTALS 2021; 11. [PMID: 33777416 PMCID: PMC7996396 DOI: 10.3390/cryst11030273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
RNA plays a central role in all organisms and can fold into complex structures to orchestrate function. Visualization of such structures often requires crystallization, which can be a bottleneck in the structure-determination process. To promote crystallization, an RNA-recognition motif (RRM) of the U1A spliceosomal protein has been co-opted as a crystallization module. Specifically, the U1-snRNA hairpin II (hpII) single-stranded loop recognized by U1A can be transplanted into an RNA target to promote crystal contacts and to attain phase information via molecular replacement or anomalous diffraction methods using selenomethionine. Herein, we produced the F37M/F77M mutant of U1A to augment the phasing capability of this powerful crystallization module. Selenomethionine-substituted U1A(F37M/F77M) retains high affinity for hpII (K D of 59.7 ± 11.4 nM). The 2.20 Å resolution crystal structure reveals that the mutated sidechains make new S-π interactions in the hydrophobic core and are useful for single-wavelength anomalous diffraction. Crystals were also attained of U1A(F37M/F77M) in complex with a bacterial preQ1-II riboswitch. The F34M/F37M/F77M mutant was introduced similarly into a lab-evolved U1A variant (TBP6.9) that recognizes the internal bulged loop of HIV-1 TAR RNA. We envision that this short RNA sequence can be placed into non-essential duplex regions to promote crystallization and phasing of target RNAs. We show that selenomethionine-substituted TBP6.9(F34M/F37M/F77M) binds a TAR variant wherein the apical loop was replaced with a GNRA tetraloop (K D of 69.8 ± 2.9 nM), laying the groundwork for use of TBP6.9(F34M/F37M/F77M) as a crystallization module. These new tools are available to the research community.
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17
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Giddings LA, Lountos GT, Kim KW, Brockley M, Needle D, Cherry S, Tropea JE, Waugh DS. Characterization of a broadly specific cadaverine N-hydroxylase involved in desferrioxamine B biosynthesis in Streptomyces sviceus. PLoS One 2021; 16:e0248385. [PMID: 33784308 PMCID: PMC8009421 DOI: 10.1371/journal.pone.0248385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
N-hydroxylating flavin-dependent monooxygenases (FMOs) are involved in the biosynthesis of hydroxamate siderophores, playing a key role in microbial virulence. Herein, we report the first structural and kinetic characterization of a novel alkyl diamine N-hydroxylase DesB from Streptomyces sviceus (SsDesB). This enzyme catalyzes the first committed step in the biosynthesis of desferrioxamine B, a clinical drug used to treat iron overload disorders. X-ray crystal structures of the SsDesB holoenzyme with FAD and the ternary complex with bound NADP+ were solved at 2.86 Å and 2.37 Å resolution, respectively, providing a structural view of the active site environment. SsDesB crystallized as a tetramer and the structure of the individual protomers closely resembles the structures of homologous N-hydroxylating FMOs from Erwinia amylovora (DfoA), Pseudomonas aeruginosa (PvdA), and Aspergillus fumigatus (SidA). Using NADPH oxidation, oxygen consumption, and product formation assays, kinetic parameters were determined for various substrates with SsDesB. SsDesB exhibited typical saturation kinetics with substrate inhibition at high concentrations of NAD(P)H as well as cadaverine. The apparent kcat values for NADPH in steady-state NADPH oxidation and oxygen consumption assays were 0.28 ± 0.01 s-1 and 0.24 ± 0.01 s-1, respectively. However, in product formation assays used to measure the rate of N-hydroxylation, the apparent kcat for NADPH (0.034 ± 0.008 s-1) was almost 10-fold lower under saturating FAD and cadaverine concentrations, reflecting an uncoupled reaction, and the apparent NADPH KM was 33 ± 24 μM. Under saturating FAD and NADPH concentrations, the apparent kcat and KM for cadaverine in Csaky assays were 0.048 ± 0.004 s-1 and 19 ± 9 μM, respectively. SsDesB also N-hydroxylated putrescine, spermidine, and L-lysine substrates but not alkyl (di)amines that were branched or had fewer than four methylene units in an alkyl chain. These data demonstrate that SsDesB has wider substrate scope compared to other well-studied ornithine and lysine N-hydroxylases, making it an amenable biocatalyst for the production of desferrioxamine B, derivatives, and other N-substituted products.
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Affiliation(s)
- Lesley-Ann Giddings
- Department of Chemistry, Smith College, Northampton, MA, United States of America
- Department of Chemistry & Biochemistry, Middlebury College, Middlebury, VT, United States of America
| | - George T. Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - Kang Woo Kim
- Department of Chemistry & Biochemistry, Middlebury College, Middlebury, VT, United States of America
| | - Matthew Brockley
- Department of Chemistry & Biochemistry, Middlebury College, Middlebury, VT, United States of America
| | - Danielle Needle
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States of America
| | - Scott Cherry
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States of America
| | - Joseph E. Tropea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States of America
| | - David S. Waugh
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States of America
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18
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Jaskolski M, Dauter Z, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Rupp B, Wlodawer A. Crystallographic models of SARS-CoV-2 3CL pro: in-depth assessment of structure quality and validation. IUCRJ 2021; 8:238-256. [PMID: 33708401 PMCID: PMC7924243 DOI: 10.1107/s2052252521001159] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/01/2021] [Indexed: 05/26/2023]
Abstract
The appearance at the end of 2019 of the new SARS-CoV-2 coronavirus led to an unprecedented response by the structural biology community, resulting in the rapid determination of many hundreds of structures of proteins encoded by the virus. As part of an effort to analyze and, if necessary, remediate these structures as deposited in the Protein Data Bank (PDB), this work presents a detailed analysis of 81 crystal structures of the main protease 3CLpro, an important target for the design of drugs against COVID-19. The structures of the unliganded enzyme and its complexes with a number of inhibitors were determined by multiple research groups using different experimental approaches and conditions; the resulting structures span 13 different polymorphs representing seven space groups. The structures of the enzyme itself, all determined by molecular replacement, are highly similar, with the exception of one polymorph with a different inter-domain orientation. However, a number of complexes with bound inhibitors were found to pose significant problems. Some of these could be traced to faulty definitions of geometrical restraints for ligands and to the general problem of a lack of such information in the PDB depositions. Several problems with ligand definition in the PDB itself were also noted. In several cases extensive corrections to the models were necessary to adhere to the evidence of the electron-density maps. Taken together, this analysis of a large number of structures of a single, medically important protein, all determined within less than a year using modern experimental tools, should be useful in future studies of other systems of high interest to the biomedical community.
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Affiliation(s)
- Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Zbigniew Dauter
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Ivan G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Miroslaw Gilski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Dariusz Brzezinski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Marcin Kowiel
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Bernhard Rupp
- k.-k Hofkristallamt, San Diego, CA 92084, USA
- Institute of Genetic Epidemiology, Medical University Innsbruck, A-6020 Innsbruck, Austria
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
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19
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Pan X, Thompson MC, Zhang Y, Liu L, Fraser JS, Kelly MJS, Kortemme T. Expanding the space of protein geometries by computational design of de novo fold families. Science 2020; 369:1132-1136. [PMID: 32855341 DOI: 10.1126/science.abc0881] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/14/2020] [Indexed: 01/03/2023]
Abstract
Naturally occurring proteins vary the precise geometries of structural elements to create distinct shapes optimal for function. We present a computational design method, loop-helix-loop unit combinatorial sampling (LUCS), that mimics nature's ability to create families of proteins with the same overall fold but precisely tunable geometries. Through near-exhaustive sampling of loop-helix-loop elements, LUCS generates highly diverse geometries encompassing those found in nature but also surpassing known structure space. Biophysical characterization showed that 17 (38%) of 45 tested LUCS designs encompassing two different structural topologies were well folded, including 16 with designed non-native geometries. Four experimentally solved structures closely matched the designs. LUCS greatly expands the designable structure space and offers a new paradigm for designing proteins with tunable geometries that may be customizable for novel functions.
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Affiliation(s)
- Xingjie Pan
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA. .,UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, USA
| | - Michael C Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Yang Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Lin Liu
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA. .,UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
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20
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Glasgow AA, Huang YM, Mandell DJ, Thompson M, Ritterson R, Loshbaugh AL, Pellegrino J, Krivacic C, Pache RA, Barlow KA, Ollikainen N, Jeon D, Kelly MJS, Fraser JS, Kortemme T. Computational design of a modular protein sense-response system. Science 2020; 366:1024-1028. [PMID: 31754004 DOI: 10.1126/science.aax8780] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/07/2019] [Indexed: 12/28/2022]
Abstract
Sensing and responding to signals is a fundamental ability of living systems, but despite substantial progress in the computational design of new protein structures, there is no general approach for engineering arbitrary new protein sensors. Here, we describe a generalizable computational strategy for designing sensor-actuator proteins by building binding sites de novo into heterodimeric protein-protein interfaces and coupling ligand sensing to modular actuation through split reporters. Using this approach, we designed protein sensors that respond to farnesyl pyrophosphate, a metabolic intermediate in the production of valuable compounds. The sensors are functional in vitro and in cells, and the crystal structure of the engineered binding site closely matches the design model. Our computational design strategy opens broad avenues to link biological outputs to new signals.
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Affiliation(s)
- Anum A Glasgow
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Yao-Ming Huang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel J Mandell
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Bioinformatics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Michael Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ryan Ritterson
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Amanda L Loshbaugh
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Jenna Pellegrino
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Cody Krivacic
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Roland A Pache
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kyle A Barlow
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Bioinformatics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Noah Ollikainen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Bioinformatics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Deborah Jeon
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA. .,Bioinformatics Graduate Program, University of California San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA.,UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
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21
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Karade SS, Ansari A, Srivastava VK, Nayak AR, Pratap JV. Molecular and structural analysis of a mechanical transition of helices in the L. donovani coronin coiled-coil domain. Int J Biol Macromol 2020; 143:785-796. [PMID: 31778699 DOI: 10.1016/j.ijbiomac.2019.09.138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 09/04/2019] [Accepted: 09/18/2019] [Indexed: 11/30/2022]
Abstract
Protein-protein interactions of cellular importance are mediated by coiled coils (CCs), the ubiquitous structural motif formed by the association of two or more α-helices in a knobs into holes manner. Coronins, actin-associated multi-functional proteins that possess distinct cytoskeleton-dependent and independent functions, oligomerize through their C-terminal CC domain. The structure of the L. donovani coronin CC domain (LdCoroCC; PDB ID 5CX2) revealed, in addition to a novel topology and architecture, an inherent asymmetry, with one of the helices of the 4-helix bundle axially shifted (~2 turns). The structural analysis identified that steric hindrance by Ile 486, Leu 493 and Met 500 as the cause for this asymmetry. To experimentally validate this hypothesis and to better understand the sequence-structure relationship in CCs, these amino acids have been mutated (I486A, L493A, M500V and the double mutant I486A-L493A) and characterized. Thermal CD studies suggest that the I486A and M500V mutants have comparable Tm values to LdCoroCC, while the other mutants have lower melting temperatures. The mutant crystal structures (I486A, M500V and the double mutant) retain the 'ade' core packing as LdcoroCC. While the M500V structure is similar to LdCoroCC, the I486A and the I486A-L493A structures show an asymmetry to symmetry transition. This study reveals crucial role of residues at position 'a' in coiled-coil domain play an important role in stabilizing the asymmetry in LdCoroCC, which might be necessary pursue specific biological function(s) inside the Leishmania.
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Affiliation(s)
- Sharanbasappa Shrimant Karade
- Molecular and Structural Biology Division, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Ahmadullah Ansari
- Molecular and Structural Biology Division, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Vijay Kumar Srivastava
- Molecular and Structural Biology Division, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Ashok Ranjan Nayak
- Molecular and Structural Biology Division, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - J Venkatesh Pratap
- Molecular and Structural Biology Division, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India.
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22
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Li C, Vavra JW, Carr CE, Huang HT, Maroney MJ, Wilmot CM. Complexation of the nickel and cobalt transcriptional regulator RcnR with DNA. Acta Crystallogr F Struct Biol Commun 2020; 76:25-30. [PMID: 31929183 PMCID: PMC6957110 DOI: 10.1107/s2053230x19017084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/20/2019] [Indexed: 11/10/2022] Open
Abstract
RcnR is a transcription factor that regulates the homeostasis of cobalt and nickel in bacterial cells. Escherichia coli RcnR was crystallized with DNA that encompasses the DNA-binding site. X-ray diffraction data were collected to 2.9 Å resolution. The crystal belonged to space group P6122 or P6522, with unit-cell parameters a = b = 73.59, c = 157.66 Å, α = β = 90, γ = 120°.
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Affiliation(s)
- Chao Li
- Department of Biochemistry, Molecular Biology, and Biophysics and the BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St Paul, MN 55108, USA
| | - Joseph W. Vavra
- Department of Biochemistry, Molecular Biology, and Biophysics and the BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St Paul, MN 55108, USA
| | - Carolyn E. Carr
- Department of Chemistry, University of Massachusetts, N373 Life Science Laboratory, Amherst, MA 01003, USA
| | - Hsin-Ting Huang
- Department of Chemistry, University of Massachusetts, N373 Life Science Laboratory, Amherst, MA 01003, USA
| | - Michael J. Maroney
- Department of Chemistry, University of Massachusetts, N373 Life Science Laboratory, Amherst, MA 01003, USA
| | - Carrie M. Wilmot
- Department of Biochemistry, Molecular Biology, and Biophysics and the BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St Paul, MN 55108, USA
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23
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Lovelace JJ, Borgstahl GEO. Characterizing pathological imperfections in macromolecular crystals: lattice disorders and modulations. CRYSTALLOGR REV 2019; 26:3-50. [PMID: 33041501 DOI: 10.1080/0889311x.2019.1692341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jeffrey J Lovelace
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Gloria E O Borgstahl
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
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24
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Svensson O, Gilski M, Nurizzo D, Bowler MW. A comparative anatomy of protein crystals: lessons from the automatic processing of 56 000 samples. IUCRJ 2019; 6:822-831. [PMID: 31576216 PMCID: PMC6760449 DOI: 10.1107/s2052252519008017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/04/2019] [Indexed: 05/12/2023]
Abstract
The fully automatic processing of crystals of macromolecules has presented a unique opportunity to gather information on the samples that is not usually recorded. This has proved invaluable in improving sample-location, characterization and data-collection algorithms. After operating for four years, MASSIF-1 has now processed over 56 000 samples, gathering information at each stage, from the volume of the crystal to the unit-cell dimensions, the space group, the quality of the data collected and the reasoning behind the decisions made in data collection. This provides an unprecedented opportunity to analyse these data together, providing a detailed landscape of macromolecular crystals, intimate details of their contents and, importantly, how the two are related. The data show that mosaic spread is unrelated to the size or shape of crystals and demonstrate experimentally that diffraction intensities scale in proportion to crystal volume and molecular weight. It is also shown that crystal volume scales inversely with molecular weight. The results set the scene for the development of X-ray crystallography in a changing environment for structural biology.
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Affiliation(s)
- Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Maciej Gilski
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
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25
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Gibbs ME, Lountos GT, Gumpena R, Waugh DS. Crystal structure of UDP-glucose pyrophosphorylase from Yersinia pestis, a potential therapeutic target against plague. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2019; 75:608-615. [PMID: 31475928 DOI: 10.1107/s2053230x19011154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/09/2019] [Indexed: 11/10/2022]
Abstract
Yersinia pestis, the causative agent of bubonic plague, is one of the most lethal pathogens in recorded human history. Today, the concern is the possible misuse of Y. pestis as an agent in bioweapons and bioterrorism. Current therapies for the treatment of plague include the use of a small number of antibiotics, but clinical cases of antibiotic resistance have been reported in some areas of the world. Therefore, the discovery of new drugs is required to combat potential Y. pestis infection. Here, the crystal structure of the Y. pestis UDP-glucose pyrophosphorylase (UGP), a metabolic enzyme implicated in the survival of Y. pestis in mouse macrophages, is described at 2.17 Å resolution. The structure provides a foundation that may enable the rational design of inhibitors and open new avenues for the development of antiplague therapeutics.
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Affiliation(s)
- Morgan E Gibbs
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - George T Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Rajesh Gumpena
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - David S Waugh
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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26
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Jones JA, Hevener KE. Crystal structure of the 65-kilodalton amino-terminal fragment of DNA topoisomerase I from the gram-positive model organism Streptococcus mutans. Biochem Biophys Res Commun 2019; 516:333-338. [PMID: 31204053 DOI: 10.1016/j.bbrc.2019.06.034] [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: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 01/06/2023]
Abstract
Herein we report the first structure of topoisomerase I determined from the gram-positive bacterium, S. mutans. Bacterial topoisomerase I is an ATP-independent type 1A topoisomerase that uses the inherent torsional strain within hyper-negatively supercoiled DNA as an energy source for its critical function of DNA relaxation. Interest in the enzyme has gained momentum as it has proven to be essential in various bacterial organisms. In order to aid in further biochemical characterization, the apo 65-kDa amino-terminal fragment of DNA topoisomerase I from the gram-positive model organism Streptococcus mutans was crystalized and a three-dimensional structure was determined to 2.06 Å resolution via x-ray crystallography. The overall structure illustrates the four classic major domains that create the traditional topoisomerase I "lock" formation comprised of a sizable toroidal aperture atop what is considered to be a highly dynamic body. A catalytic tyrosine residue resides at the interface between two domains and is known to form a 5' phosphotyrosine DNA-enzyme intermediate during transient single-stranded cleavage required for enzymatic relaxation of hyper negative DNA supercoils. Surrounding the catalytic tyrosine residue is the remainder of the highly conserved active site. Within 5 Å from the catalytic center, only one dissimilar residue is observed between topoisomerase I from S. mutans and the gram-negative model organism E. coli. Immediately adjacent to the conserved active site, however, S. mutans topoisomerase I displays a somewhat unique nine residue loop extension not present in any bacterial topoisomerase I structures previously determined other than that of an extremophile.
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Affiliation(s)
- Jesse A Jones
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, 38163, United States
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, 38163, United States.
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27
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Shao C, Liu Z, Yang H, Wang S, Burley SK. Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach. Sci Data 2018; 5:180293. [PMID: 30532050 PMCID: PMC6289109 DOI: 10.1038/sdata.2018.293] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/12/2018] [Indexed: 02/02/2023] Open
Abstract
Outlier analyses are central to scientific data assessments. Conventional outlier identification methods do not work effectively for Protein Data Bank (PDB) data, which are characterized by heavy skewness and the presence of bounds and/or long tails. We have developed a data-driven nonparametric method to identify outliers in PDB data based on kernel probability density estimation. Unlike conventional outlier analyses based on location and scale, Probability Density Ranking can be used for robust assessments of distance from other observations. Analyzing PDB data from the vantage points of probability and frequency enables proper outlier identification, which is important for quality control during deposition-validation-biocuration of new three-dimensional structure data. Ranking of Probability Density also permits use of Most Probable Range as a robust measure of data dispersion that is more compact than Interquartile Range. The Probability-Density-Ranking approach can be employed to analyze outliers and data-spread on any large data set with continuous distribution.
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Affiliation(s)
- Chenghua Shao
- RCSB Protein Data Bank, Rutgers, The State University of New
Jersey, Piscataway,
NJ
08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State
University of New Jersey, Piscataway, NJ
08854, USA
| | - Zonghong Liu
- Department of Statistics and Biostatistics, Rutgers, The State
University of New Jersey, New
Brunswick, NJ,
08903, USA
| | - Huanwang Yang
- RCSB Protein Data Bank, Rutgers, The State University of New
Jersey, Piscataway,
NJ
08854, USA
| | - Sijian Wang
- Institute for Quantitative Biomedicine, Rutgers, The State
University of New Jersey, Piscataway, NJ
08854, USA
- Department of Statistics and Biostatistics, Rutgers, The State
University of New Jersey, New
Brunswick, NJ,
08903, USA
| | - Stephen K. Burley
- RCSB Protein Data Bank, Rutgers, The State University of New
Jersey, Piscataway,
NJ
08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State
University of New Jersey, Piscataway, NJ
08854, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State
University of New Jersey, New
Brunswick, NJ,
08903, USA
- RCSB Protein Data Bank, San Diego Supercomputer Center and
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California
San Diego, La Jolla,
CA
92093, USA
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28
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The 2.1 Å structure of protein F9 and its comparison to L1, two components of the conserved poxvirus entry-fusion complex. Sci Rep 2018; 8:16807. [PMID: 30429486 PMCID: PMC6235832 DOI: 10.1038/s41598-018-34244-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/12/2018] [Indexed: 11/18/2022] Open
Abstract
The poxvirus F9 protein is a component of the vaccinia virus entry fusion complex (EFC) which consists of 11 proteins. The EFC forms a unique apparatus among viral fusion proteins and complexes. We solved the atomic structure of the F9 ectodomain at 2.10 Å. A structural comparison to the ectodomain of the EFC protein L1 indicated a similar fold and organization, in which a bundle of five α-helices is packed against two pairs of β-strands. However, instead of the L1 myristoylation site and hydrophobic cavity, F9 possesses a protruding loop between α-helices α3 and α4 starting at Gly90. Gly90 is conserved in all poxviruses except Salmon gill poxvirus (SGPV) and Diachasmimorpha longicaudata entomopoxvirus. Phylogenetic sequence analysis of all Poxviridae F9 and L1 orthologs revealed the SGPV genome to contain the most distantly related F9 and L1 sequences compared to the vaccinia proteins studied here. The structural differences between F9 and L1 suggest functional adaptations during evolution from a common precursor that underlie the present requirement for each protein.
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29
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Moyo T, Ereño-Orbea J, Jacob RA, Pavillet CE, Kariuki SM, Tangie EN, Julien JP, Dorfman JR. Molecular Basis of Unusually High Neutralization Resistance in Tier 3 HIV-1 Strain 253-11. J Virol 2018; 92:e02261-17. [PMID: 29618644 PMCID: PMC6026760 DOI: 10.1128/jvi.02261-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 02/26/2018] [Indexed: 01/06/2023] Open
Abstract
Understanding the mechanisms used by HIV-1 to evade antibody neutralization may contribute to the design of a high-coverage vaccine. The tier 3 virus 253-11 is poorly neutralized by subtype-matched and subtype C sera, even compared to other tier 3 viruses, and is also recognized poorly by V3/glycan-targeting monoclonal antibodies (MAbs). We found that sequence polymorphisms in the V3 loop and N-linked glycosylation sites contribute only minimally to the high neutralization resistance of 253-11. Interestingly, the 253-11 membrane-proximal external region (MPER) is rarely recognized by sera in the context of the wild-type virus but is commonly recognized in the context of an HIV-2 chimera, suggesting steric or kinetic hindrance of binding to MPER in the native envelope (Env). Mutations in the 253-11 MPER, which were previously reported to increase the lifetime of the prefusion Env conformation, affected the resistance of 253-11 to antibodies targeting various epitopes on HIV-1 Env, presumably destabilizing its otherwise stable, closed trimer structure. To gain insight into the structure of 253-11, we constructed and crystallized a recombinant 253-11 SOSIP trimer. The resulting structure revealed that the heptad repeat helices in gp41 are drawn in close proximity to the trimer axis and that gp120 protomers also showed a relatively compact disposition around the trimer axis. These observations give substantial insight into the molecular features of an envelope spike from a tier 3 virus and into possible mechanisms that may contribute to its unusually high neutralization resistance.IMPORTANCE HIV-1 isolates that are highly resistant to broadly neutralizing antibodies could limit the efficacy of an antibody-based vaccine. We studied 253-11, which is highly resistant to commonly elicited neutralizing antibodies. To further understand its resistance, we made mutations that are known to delay fusion and thus increase the time that the virus spends in the open conformation following CD4 binding. Interestingly, we found that these mutations affect the 253-11 envelope (Env) spike before CD4 binding, presumably by destabilizing the trimer structure. To gain further information about the structure of the 253-11 Env trimer, we generated a recombinant 253-11 SOSIP trimer. The crystal structure of the SOSIP trimer revealed that the gp41 helices and the gp120 protomers were drawn in toward the center of the molecule compared to most solved HIV-1 Env structures. These observations provide insight into the distinct molecular features of a tier 3 envelope spike.
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Affiliation(s)
- Thandeka Moyo
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - June Ereño-Orbea
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Rajesh Abraham Jacob
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Clara E Pavillet
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Samuel Mundia Kariuki
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
- Department of Biological Science, University of Eldoret, Eldoret, Kenya
| | - Emily N Tangie
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey R Dorfman
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Division of Immunology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
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30
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Altan I, Fusco D, Afonine PV, Charbonneau P. Learning about Biomolecular Solvation from Water in Protein Crystals. J Phys Chem B 2018; 122:2475-2486. [DOI: 10.1021/acs.jpcb.7b09898] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Diana Fusco
- Department of Physics, University of California, Berkeley, California 94720, United States
| | - Pavel V. Afonine
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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31
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Identification and Crystallographic Analysis of a New Carbohydrate Acetylesterase (SmAcE1) from Sinorhizobium meliloti. CRYSTALS 2018. [DOI: 10.3390/cryst8010012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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32
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Ereño-Orbea J, Sicard T, Cui H, Mazhab-Jafari MT, Benlekbir S, Guarné A, Rubinstein JL, Julien JP. Molecular basis of human CD22 function and therapeutic targeting. Nat Commun 2017; 8:764. [PMID: 28970495 PMCID: PMC5624926 DOI: 10.1038/s41467-017-00836-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/28/2017] [Indexed: 12/13/2022] Open
Abstract
CD22 maintains a baseline level of B-cell inhibition to keep humoral immunity in check. As a B-cell-restricted antigen, CD22 is targeted in therapies against dysregulated B cells that cause autoimmune diseases and blood cancers. Here we report the crystal structure of human CD22 at 2.1 Å resolution, which reveals that specificity for α2-6 sialic acid ligands is dictated by a pre-formed β-hairpin as a unique mode of recognition across sialic acid-binding immunoglobulin-type lectins. The CD22 ectodomain adopts an extended conformation that facilitates concomitant CD22 nanocluster formation on B cells and binding to trans ligands to avert autoimmunity in mammals. We structurally delineate the CD22 site targeted by the therapeutic antibody epratuzumab at 3.1 Å resolution and determine a critical role for CD22 N-linked glycosylation in antibody engagement. Our studies provide molecular insights into mechanisms governing B-cell inhibition and valuable clues for the design of immune modulators in B-cell dysfunction.The B-cell-specific co-receptor CD22 is a therapeutic target for depleting dysregulated B cells. Here the authors structurally characterize the ectodomain of CD22 and present its crystal structure with the bound therapeutic antibody epratuzumab, which gives insights into the mechanism of inhibition of B-cell activation.
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Affiliation(s)
- June Ereño-Orbea
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada, M5G 0A4
| | - Taylor Sicard
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada, M5G 0A4
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada, M5S 1A8
| | - Hong Cui
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada, M5G 0A4
| | - Mohammad T Mazhab-Jafari
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada, M5G 0A4
| | - Samir Benlekbir
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada, M5G 0A4
| | - Alba Guarné
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, ON, Canada, L8S 4L8
| | - John L Rubinstein
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada, M5G 0A4
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada, M5S 1A8
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada, M5G 1L7
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada, M5G 0A4.
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada, M5S 1A8.
- Department of Immunology, University of Toronto, Toronto, ON, Canada, M5S 1A8.
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33
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Deyaert E, Kortholt A, Versées W. The LRR-Roc-COR module of the Chlorobium tepidum Roco protein: crystallization and X-ray crystallographic analysis. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2017; 73:520-524. [PMID: 28876231 DOI: 10.1107/s2053230x17011955] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/17/2017] [Indexed: 01/08/2023]
Abstract
Roco proteins are characterized by the presence of a Roc-COR supradomain harbouring GTPase activity, which is often preceded by an LRR domain. The most notorious member of the Roco protein family is the Parkinson's disease-associated LRRK2. The Roco protein from the bacterium Chlorobium tepidum has been used as a model system to investigate the structure and mechanism of this class of enzymes. Here, the crystallization and crystallographic analysis of the LRR-Roc-COR construct of the C. tepidum Roco protein is reported. The LRR-Roc-COR crystals belonged to space group P212121, with unit-cell parameters a = 95.6, b = 129.8, c = 179.5 Å, α = β = γ = 90°, and diffracted to a resolution of 3.3 Å. Based on the calculated Matthews coefficient, Patterson map analysis and an initial molecular-replacement analysis, one protein dimer is present in the asymmetric unit. The crystal structure of this protein will provide valuable insights into the interaction between the Roc-COR and LRR domains within Roco proteins.
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Affiliation(s)
- Egon Deyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Wim Versées
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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34
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Giegé R. What macromolecular crystallogenesis tells us - what is needed in the future. IUCRJ 2017; 4:340-349. [PMID: 28875021 PMCID: PMC5571797 DOI: 10.1107/s2052252517006595] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/02/2017] [Indexed: 05/05/2023]
Abstract
Crystallogenesis is a longstanding topic that has transformed into a discipline that is mainly focused on the preparation of crystals for practising crystallo-graphers. Although the idiosyncratic features of proteins have to be taken into account, the crystallization of proteins is governed by the same physics as the crystallization of inorganic materials. At present, a diversified panel of crystallization methods adapted to proteins has been validated, and although only a few methods are in current practice, the success rate of crystallization has increased constantly, leading to the determination of ∼105 X-ray structures. These structures reveal a huge repertoire of protein folds, but they only cover a restricted part of macromolecular diversity across the tree of life. In the future, crystals representative of missing structures or that will better document the structural dynamics and functional steps underlying biological processes need to be grown. For the pertinent choice of biologically relevant targets, computer-guided analysis of structural databases is needed. From another perspective, crystallization is a self-assembly process that can occur in the bulk of crowded fluids, with crystals being supramolecular assemblies. Life also uses self-assembly and supramolecular processes leading to transient, or less often stable, complexes. An integrated view of supramolecularity implies that proteins crystallizing either in vitro or in vivo or participating in cellular processes share common attributes, notably determinants and antideterminants that favour or disfavour their correct or incorrect associations. As a result, under in vivo conditions proteins show a balance between features that favour or disfavour association. If this balance is broken, disorders/diseases occur. Understanding crystallization under in vivo conditions is a challenge for the future. In this quest, the analysis of packing contacts and contacts within oligomers will be crucial in order to decipher the rules governing protein self-assembly and will guide the engineering of novel biomaterials. In a wider perspective, understanding such contacts will open the route towards supramolecular biology and generalized crystallogenesis.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l’ARN, UPR 9002, Université de Strasbourg and CNRS, F-67084 Strasbourg, France
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35
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Rechlin C, Scheer F, Terwesten F, Wulsdorf T, Pol E, Fridh V, Toth P, Diederich WE, Heine A, Klebe G. Price for Opening the Transient Specificity Pocket in Human Aldose Reductase upon Ligand Binding: Structural, Thermodynamic, Kinetic, and Computational Analysis. ACS Chem Biol 2017; 12:1397-1415. [PMID: 28287700 DOI: 10.1021/acschembio.7b00062] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Insights into the thermodynamic and kinetic signature of the transient opening of a protein-binding pocket resulting from accommodation of suitable substituents attached to a given parent ligand scaffold are presented. As a target, we selected human aldose reductase, an enzyme involved in the development of late-stage diabetic complications. To recognize a large scope of substrate molecules, this reductase opens a transient specificity pocket. The pocket-opening step was studied by X-ray crystallography, microcalorimetry, and surface plasmon resonance using a narrow series of 2-carbamoyl-phenoxy-acetic acid derivatives. Molecular dynamics simulations suggest that pocket opening occurs only once an appropriate substituent is attached to the parent scaffold. Transient pocket opening of the uncomplexed protein is hardly recorded. Hydration-site analysis suggests that up to five water molecules entering the opened pocket cannot stabilize this state. Sole substitution with a benzyl group stabilizes the opened state, and the energetic barrier for opening is estimated to be ∼5 kJ/mol. Additional decoration of the pocket-opening benzyl substituent with a nitro group results in a huge enthalpy-driven potency increase; on the other hand, an isosteric carboxylic acid group reduces the potency 1000-fold, and binding occurs without pocket opening. We suggest a ligand induced-fit mechanism for the pocket-opening step, which, however, does not represent the rate-determining step in binding kinetics.
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Affiliation(s)
- Chris Rechlin
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Frithjof Scheer
- Institut
für Pharmazeutische Chemie, Zentrum für Tumor- und Immunbiologie (ZTI), Philipps-Universität Marburg, Hans-Meerwein-Straße
3, 35043 Marburg, Germany
| | - Felix Terwesten
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Tobias Wulsdorf
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Ewa Pol
- GE Healthcare Bio-Sciences AB, Björkgatan 30, SE-751 84 Uppsala, Sweden
| | - Veronica Fridh
- GE Healthcare Bio-Sciences AB, Björkgatan 30, SE-751 84 Uppsala, Sweden
| | - Philipp Toth
- Institut
für Pharmazeutische Chemie, Zentrum für Tumor- und Immunbiologie (ZTI), Philipps-Universität Marburg, Hans-Meerwein-Straße
3, 35043 Marburg, Germany
| | - Wibke E. Diederich
- Institut
für Pharmazeutische Chemie, Zentrum für Tumor- und Immunbiologie (ZTI), Philipps-Universität Marburg, Hans-Meerwein-Straße
3, 35043 Marburg, Germany
- Core
Facility Medicinal Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 3, 35043 Marburg, Germany
| | - Andreas Heine
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Gerhard Klebe
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
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36
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Heilingloh CS, Klingl S, Egerer-Sieber C, Schmid B, Weiler S, Mühl-Zürbes P, Hofmann J, Stump JD, Sticht H, Kummer M, Steinkasserer A, Muller YA. Crystal Structure of the Extracellular Domain of the Human Dendritic Cell Surface Marker CD83. J Mol Biol 2017; 429:1227-1243. [PMID: 28315353 DOI: 10.1016/j.jmb.2017.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 02/10/2017] [Accepted: 03/05/2017] [Indexed: 11/27/2022]
Abstract
CD83 is a type-I membrane protein and an efficient marker for identifying mature dendritic cells. Whereas membrane-bound, full-length CD83 co-stimulates the immune system, a soluble variant (sCD83), consisting of the extracellular domain only, displays strong immune-suppressive activities. Besides a prediction that sCD83 adopts a V-set Ig-like fold, however, little is known about the molecular architecture of CD83 and the mechanism by which CD83 exerts its function on dendritic cells and additional immune cells. Here, we report the crystal structure of human sCD83 up to a resolution of 1.7Å solved in three different crystal forms. Interestingly, β-strands C', C″, and D that are typical for V-set Ig-domains could not be traced in sCD83. Mass spectrometry analyses, limited proteolysis experiments, and bioinformatics studies show that the corresponding segment displays enhanced main-chain accessibility, extraordinary low sequence conservation, and a predicted high disorder propensity. Chimeric proteins with amino acid swaps in this segment show unaltered immune-suppressive activities in a TNF-α assay when compared to wild-type sCD83. This strongly indicates that this segment does not participate in the biological activity of CD83. The crystal structure of CD83 shows the recurrent formation of dimers and trimers in the various crystal forms and reveals strong structural similarities between sCD83 and B7 family members and CD48, a signaling lymphocyte activation molecule family member. This suggests that CD83 exerts its immunological activity by mixed homotypic and heterotypic interactions as typically observed for proteins present in the immunological synapse.
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Affiliation(s)
- Christiane S Heilingloh
- Department of Immune Modulation, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Hartmannstr. 14, D-91052 Erlangen, Germany
| | - Stefan Klingl
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Henkestr. 91, D-91052 Erlangen, Germany
| | - Claudia Egerer-Sieber
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Henkestr. 91, D-91052 Erlangen, Germany
| | - Benedikt Schmid
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Henkestr. 91, D-91052 Erlangen, Germany
| | - Sigrid Weiler
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Henkestr. 91, D-91052 Erlangen, Germany
| | - Petra Mühl-Zürbes
- Department of Immune Modulation, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Hartmannstr. 14, D-91052 Erlangen, Germany
| | - Jörg Hofmann
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstr. 5, D-91058 Erlangen, Germany
| | - Joachim D Stump
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Fahrstraße 17, D-91054 Erlangen, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Fahrstraße 17, D-91054 Erlangen, Germany
| | - Mirko Kummer
- Department of Immune Modulation, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Hartmannstr. 14, D-91052 Erlangen, Germany
| | - Alexander Steinkasserer
- Department of Immune Modulation, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Hartmannstr. 14, D-91052 Erlangen, Germany
| | - Yves A Muller
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Henkestr. 91, D-91052 Erlangen, Germany.
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37
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Abstract
Molecular replacement is a method for solving the crystallographic phase problem using an atomic model for the target structure. State-of-the-art methods have moved the field significantly from when it was first envisaged as a method for solving cases of high homology and completeness between a model and target structure. Improvements brought about by application of maximum likelihood statistics mean that various errors in the model and pathologies in the data can be accounted for, so that cases hitherto thought to be intractable are standardly solvable. As a result, molecular replacement phasing now accounts for the lion's share of structures deposited in the Protein Data Bank. However, there will always be cases at the fringes of solvability. I discuss here the approaches that will help tackle challenging molecular replacement cases.
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Affiliation(s)
- Airlie J McCoy
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.
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38
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Montemayor EJ, Didychuk AL, Liao H, Hu P, Brow DA, Butcher SE. Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core. Acta Crystallogr D Struct Biol 2017; 73:1-8. [PMID: 28045380 PMCID: PMC5331471 DOI: 10.1107/s2059798316018222] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/14/2016] [Indexed: 11/10/2022] Open
Abstract
U6 small nuclear RNA (snRNA) is a key component of the active site of the spliceosome, a large ribonucleoprotein complex that catalyzes the splicing of precursor messenger RNA. Prior to its incorporation into the spliceosome, U6 is bound by the protein Prp24, which facilitates unwinding of the U6 internal stem-loop (ISL) so that it can pair with U4 snRNA. A previously reported crystal structure of the `core' of the U6 small nuclear ribonucleoprotein (snRNP) contained an ISL-stabilized A62G mutant of U6 bound to all four RNA-recognition motif (RRM) domains of Prp24 [Montemayor et al. (2014), Nature Struct. Mol. Biol. 21, 544-551]. The structure revealed a novel topology containing interlocked rings of protein and RNA that was not predicted by prior biochemical and genetic data. Here, the crystal structure of the U6 snRNP core with a wild-type ISL is reported. This complex crystallized in a new space group, apparently owing in part to the presence of an intramolecular cross-link in RRM1 that was not observed in the previously reported U6-A62G structure. The structure exhibits the same protein-RNA interface and maintains the unique interlocked topology. However, the orientation of the wild-type ISL is altered relative to the A62G mutant structure, suggesting inherent structural dynamics that may facilitate its pairing with U4. Consistent with their similar architectures in the crystalline state, the wild-type and A62G variants of U6 exhibit similar Prp24-binding affinities and electrophoretic mobilities when analyzed by gel-shift assay.
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Affiliation(s)
- Eric J. Montemayor
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Allison L. Didychuk
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Honghong Liao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Panzhou Hu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David A. Brow
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Samuel E. Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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39
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Guerra Y, Valiente PA, Pons T, Berry C, Rudiño-Piñera E. Structures of a bi-functional Kunitz-type STI family inhibitor of serine and aspartic proteases: Could the aspartic protease inhibition have evolved from a canonical serine protease-binding loop? J Struct Biol 2016; 195:259-271. [PMID: 27329566 DOI: 10.1016/j.jsb.2016.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 06/14/2016] [Accepted: 06/18/2016] [Indexed: 01/06/2023]
Abstract
Bi-functional inhibitors from the Kunitz-type soybean trypsin inhibitor (STI) family are glycosylated proteins able to inhibit serine and aspartic proteases. Here we report six crystal structures of the wild-type and a non-glycosylated mutant of the bifunctional inhibitor E3Ad obtained at different pH values and space groups. The crystal structures show that E3Ad adopts the typical β-trefoil fold of the STI family exhibiting some conformational changes due to pH variations and crystal packing. Despite the high sequence identity with a recently reported potato cathepsin D inhibitor (PDI), three-dimensional structures obtained in this work show a significant conformational change in the protease-binding loop proposed for aspartic protease inhibition. The E3Ad binding loop for serine protease inhibition is also proposed, based on structural similarity with a novel non-canonical conformation described for the double-headed inhibitor API-A from the Kunitz-type STI family. In addition, structural and sequence analyses suggest that bifunctional inhibitors of serine and aspartic proteases from the Kunitz-type STI family are more similar to double-headed inhibitor API-A than other inhibitors with a canonical protease-binding loop.
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Affiliation(s)
- Yasel Guerra
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos CP 62210, Mexico.
| | - Pedro A Valiente
- Laboratorio de Biología Computacional y Diseño de Proteínas, Centro de Estudios de Proteínas (CEP), Facultad de Biología, Universidad de La Habana, Cuba
| | - Tirso Pons
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), C/Melchor Fernández Almagro 3, Madrid 28029, Spain
| | - Colin Berry
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos CP 62210, Mexico.
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40
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Terwilliger TC, Bunkóczi G, Hung LW, Zwart PH, Smith JL, Akey DL, Adams PD. Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal. Acta Crystallogr D Struct Biol 2016; 72:359-74. [PMID: 26960123 PMCID: PMC4784667 DOI: 10.1107/s2059798315019403] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 10/13/2015] [Indexed: 01/15/2023] Open
Abstract
A key challenge in the SAD phasing method is solving a structure when the anomalous signal-to-noise ratio is low. Here, algorithms and tools for evaluating and optimizing the useful anomalous correlation and the anomalous signal in a SAD experiment are described. A simple theoretical framework [Terwilliger et al. (2016), Acta Cryst. D72, 346-358] is used to develop methods for planning a SAD experiment, scaling SAD data sets and estimating the useful anomalous correlation and anomalous signal in a SAD data set. The phenix.plan_sad_experiment tool uses a database of solved and unsolved SAD data sets and the expected characteristics of a SAD data set to estimate the probability that the anomalous substructure will be found in the SAD experiment and the expected map quality that would be obtained if the substructure were found. The phenix.scale_and_merge tool scales unmerged SAD data from one or more crystals using local scaling and optimizes the anomalous signal by identifying the systematic differences among data sets, and the phenix.anomalous_signal tool estimates the useful anomalous correlation and anomalous signal after collecting SAD data and estimates the probability that the data set can be solved and the likely figure of merit of phasing.
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Affiliation(s)
- Thomas C. Terwilliger
- Bioscience Division, Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545, USA
| | - Gábor Bunkóczi
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Li-Wei Hung
- Physics Division, Los Alamos National Laboratory, Mail Stop D454, Los Alamos, NM 87545, USA
| | - Peter H. Zwart
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Janet L. Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - David L. Akey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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41
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Carminati M, Cecatiello V, Mapelli M. Crystallization and X-ray diffraction of LGN in complex with the actin-binding protein afadin. Acta Crystallogr F Struct Biol Commun 2016; 72:145-51. [PMID: 26841766 PMCID: PMC4741196 DOI: 10.1107/s2053230x16000807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 01/15/2016] [Indexed: 11/10/2022] Open
Abstract
Asymmetric stem-cell divisions are fundamental for morphogenesis and tissue homeostasis. They rely on the coordination between cortical polarity and the orientation of the mitotic spindle, which is orchestrated by microtubule pulling motors recruited at the cortex by NuMA-LGN-Gαi complexes. LGN has emerged as a central component of the spindle-orientation pathway that is conserved throughout species. Its domain structure consists of an N-terminal TPR domain associating with NuMA, followed by four GoLoco motifs binding to Gαi subunits. The LGN(TPR) region is also involved in interactions with other membrane-associated proteins ensuring the correct cortical localization of microtubule motors, among which is the junctional protein afadin. To investigate the architecture of LGN(TPR) in complex with afadin, a chimeric fusion protein with a native linker derived from the region of afadin upstream of the LGN-binding domain was generated. The fusion protein behaves as a globular monomer in solution and readily crystallizes in the presence of sulfate-containing reservoirs. The crystals diffracted to 3.0 Å resolution and belonged to the cubic space group P213, with unit-cell parameter a = 170.3 Å. The structure of the engineered protein revealed that the crystal packing is promoted by the coordination of sulfate ions by residues of the afadin linker region and LGN(TPR).
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Affiliation(s)
- Manuel Carminati
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Valentina Cecatiello
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
- IFOM, The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Marina Mapelli
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
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42
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Lunin VY, Lunina NL, Petrova TE, Baumstark MW, Urzhumtsev AG. Mask-based approach to phasing of single-particle diffraction data. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:147-57. [DOI: 10.1107/s2059798315022652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/25/2015] [Indexed: 11/10/2022]
Abstract
A Monte Carlo-type approach for low- and medium-resolution phasing of single-particle diffraction data is suggested. Firstly, the single-particle phase problem is substituted with the phase problem for an imaginary crystal. A unit cell of this crystal contains a single isolated particle surrounded by a large volume of bulk solvent. The developed phasing procedure then generates a large number of connected and finite molecular masks, calculates their Fourier coefficients, selects the sets with magnitudes that are highly correlated with the experimental values and finally aligns the selected phase sets and calculates the averaged phase values. A test with the known structure of monomeric photosystem II resulted in phases that have 97% correlation with the exact phases in the full 25 Å resolution shell (1054 structure factors) and correlations of 99, 94, 81 and 79% for the resolution shells ∞–60, 60–40, 40–30 and 30–25 Å, respectively. The same procedure may be used for crystallographicab initiophasing.
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43
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Millane RP, Arnal RD. Uniqueness of the macromolecular crystallographic phase problem. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2015; 71:592-8. [PMID: 26522408 DOI: 10.1107/s2053273315015387] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 08/17/2015] [Indexed: 11/11/2022]
Abstract
Uniqueness of the phase problem in macromolecular crystallography, and its relationship to the case of single particle imaging, is considered. The crystallographic problem is characterized by a constraint ratio that depends only on the size and symmetry of the molecule and the unit cell. The results are used to evaluate the effect of various real-space constraints. The case of an unknown molecular envelope is considered in detail. The results indicate the quite wide circumstances under which ab initio phasing should be possible.
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Affiliation(s)
- Rick P Millane
- Computational Imaging Group, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
| | - Romain D Arnal
- Computational Imaging Group, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
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44
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Gógl G, Alexa A, Kiss B, Katona G, Kovács M, Bodor A, Reményi A, Nyitray L. Structural Basis of Ribosomal S6 Kinase 1 (RSK1) Inhibition by S100B Protein: MODULATION OF THE EXTRACELLULAR SIGNAL-REGULATED KINASE (ERK) SIGNALING CASCADE IN A CALCIUM-DEPENDENT WAY. J Biol Chem 2015; 291:11-27. [PMID: 26527685 DOI: 10.1074/jbc.m115.684928] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Indexed: 12/31/2022] Open
Abstract
Mitogen-activated protein kinases (MAPK) promote MAPK-activated protein kinase activation. In the MAPK pathway responsible for cell growth, ERK2 initiates the first phosphorylation event on RSK1, which is inhibited by Ca(2+)-binding S100 proteins in malignant melanomas. Here, we present a detailed in vitro biochemical and structural characterization of the S100B-RSK1 interaction. The Ca(2+)-dependent binding of S100B to the calcium/calmodulin-dependent protein kinase (CaMK)-type domain of RSK1 is reminiscent of the better known binding of calmodulin to CaMKII. Although S100B-RSK1 and the calmodulin-CAMKII system are clearly distinct functionally, they demonstrate how unrelated intracellular Ca(2+)-binding proteins could influence the activity of the CaMK domain-containing protein kinases. Our crystallographic, small angle x-ray scattering, and NMR analysis revealed that S100B forms a "fuzzy" complex with RSK1 peptide ligands. Based on fast-kinetics experiments, we conclude that the binding involves both conformation selection and induced fit steps. Knowledge of the structural basis of this interaction could facilitate therapeutic targeting of melanomas.
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Affiliation(s)
| | - Anita Alexa
- the "Momentum" Protein Interaction Group, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Hungary, and
| | | | - Gergely Katona
- the Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Mihály Kovács
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, and
| | - Andrea Bodor
- Institute of Chemistry Eötvös Loránd University, 1117 Budapest, Hungary
| | - Attila Reményi
- the "Momentum" Protein Interaction Group, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Hungary, and
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45
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Deller MC, Rupp B. Models of protein-ligand crystal structures: trust, but verify. J Comput Aided Mol Des 2015; 29:817-36. [PMID: 25665575 PMCID: PMC4531100 DOI: 10.1007/s10822-015-9833-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/29/2015] [Indexed: 11/26/2022]
Abstract
X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.
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Affiliation(s)
- Marc C Deller
- The Joint Center for Structural Genomics, San Diego, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Bernhard Rupp
- , k.-k. Hofkristallamt 991 Audrey Place, Vista, CA, 92084, USA.
- Department of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstr. 41, 6020, Innsbruck, Austria.
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46
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X-ray structure determination using low-resolution electron microscopy maps for molecular replacement. Nat Protoc 2015; 10:1275-84. [PMID: 26226459 DOI: 10.1038/nprot.2015.069] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Structures of multisubunit macromolecular machines are primarily determined either by electron microscopy (EM) or by X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at a higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for the generation of atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the 'phase' information that is missing from an X-ray crystallography experiment; however, integration of EM and X-ray diffraction data has been technically challenging. Here we present a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over noncrystallographic symmetry. As the resolution gap between EM and X-ray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.
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47
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Lo VL, Kingston RL, Millane RP. Iterative projection algorithms in protein crystallography. II. Application. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2015; 71:451-9. [PMID: 26131900 DOI: 10.1107/s2053273315005574] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/18/2015] [Indexed: 11/10/2022]
Abstract
Iterative projection algorithms (IPAs) are a promising tool for protein crystallographic phase determination. Although related to traditional density-modification algorithms, IPAs have better convergence properties, and, as a result, can effectively overcome the phase problem given modest levels of structural redundancy. This is illustrated by applying IPAs to determine the electron densities of two protein crystals with fourfold non-crystallographic symmetry, starting with only the experimental diffraction amplitudes, a low-resolution molecular envelope and the position of the non-crystallographic axes. The algorithm returns electron densities that are sufficiently accurate for model building, allowing automated recovery of the known structures. This study indicates that IPAs should find routine application in protein crystallography, being capable of reconstructing electron densities starting with very little initial phase information.
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Affiliation(s)
- Victor L Lo
- Computational Imaging Group, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
| | - Richard L Kingston
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Rick P Millane
- Computational Imaging Group, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
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48
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Mooers BHM. Fusion RNAs in crystallographic studies of double-stranded RNA from trypanosome RNA editing. Methods Mol Biol 2015; 1240:191-216. [PMID: 25352146 DOI: 10.1007/978-1-4939-1896-6_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Head-to-head fusions of two identical double-stranded fragments of RNA can be designed to self-assemble from a single RNA species and form a double-stranded helix with a twofold rotation axis relating the two strands. These symmetrical RNA molecules are more likely to crystallize without end-on-end statistical packing disorder because the two halves of the molecule are identical. This approach can be used to study many fragments of double-stranded RNA or many isolated helical domains from large single-stranded RNAs that may not yet be amenable to high-resolution studies by crystallography or NMR. We used fusion RNAs to study one (the U-helix) of three functional domains formed when guide RNA binds to its cognate pre-edited mRNA from the trypanosome RNA editing system. The U-helix forms when the 3' oligo(U) tail of the guide RNA (gRNA) binds to the purine-rich, pre-edited mRNA upstream from the current RNA editing site. Fusion RNAs 16-and 32-base pairs in length formed crystals that gave diffraction to 1.37 and 1.05 Å respectively. We provide the composition of a fusion RNA crystallization screen and describe the X-ray data collection, structure determination, and refinement of the crystal structures of fusion RNAs.
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Affiliation(s)
- Blaine H M Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, 975 NE 10th St., Stanton L. Young Biomedical Research Center Rm. 466, Oklahoma City, OK, 73104-5419, USA,
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Weichenberger CX, Afonine PV, Kantardjieff K, Rupp B. The solvent component of macromolecular crystals. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1023-38. [PMID: 25945568 PMCID: PMC4427195 DOI: 10.1107/s1399004715006045] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 03/25/2015] [Indexed: 11/10/2022]
Abstract
The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initial phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.
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Affiliation(s)
- Christian X. Weichenberger
- Center for Biomedicine, European Academy of Bozen/Bolzano (EURAC), Viale Druso 1, Bozen/Bolzano, I-39100 Südtirol/Alto Adige, Italy
| | - Pavel V. Afonine
- Physical Biosciences Division, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Mail Stop 64R0121, Berkeley, CA 94720, USA
| | - Katherine Kantardjieff
- College of Science and Mathematics, California State University, San Marcos, CA 92078, USA
| | - Bernhard Rupp
- Department of Forensic Crystallography, k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084, USA
- Department of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck, Austria
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Ravera E, Schubeis T, Martelli T, Fragai M, Parigi G, Luchinat C. NMR of sedimented, fibrillized, silica-entrapped and microcrystalline (metallo)proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:60-70. [PMID: 25797005 DOI: 10.1016/j.jmr.2014.12.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/06/2014] [Accepted: 12/17/2014] [Indexed: 06/04/2023]
Abstract
Resolution and sensitivity in solid state NMR (SSNMR) can rival the results achieved by solution NMR, and even outperform them in the case of large systems. However, several factors affect the spectral quality in SSNMR samples, and not all systems turn out to be equally amenable for this methodology. In this review we attempt at analyzing the causes of this variable behavior and at providing hints to increase the chances of experimental success.
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Affiliation(s)
- Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Tobias Schubeis
- Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Tommaso Martelli
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy; Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
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