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Structure and Function of the T4 Spackle Protein Gp61.3. Viruses 2020; 12:v12101070. [PMID: 32987925 PMCID: PMC7650644 DOI: 10.3390/v12101070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 01/13/2023] Open
Abstract
The bacteriophage T4 genome contains two genes that code for proteins with lysozyme activity—e and 5. Gene e encodes the well-known T4 lysozyme (commonly called T4L) that functions to break the peptidoglycan layer late in the infection cycle, which is required for liberating newly assembled phage progeny. Gene product 5 (gp5) is the tail-associated lysozyme, a component of the phage particle. It forms a spike at the tip of the tail tube and functions to pierce the outer membrane of the Escherichia coli host cell after the phage has attached to the cell surface. Gp5 contains a T4L-like lysozyme domain that locally digests the peptidoglycan layer upon infection. The T4 Spackle protein (encoded by gene 61.3) has been thought to play a role in the inhibition of gp5 lysozyme activity and, as a consequence, in making cells infected by bacteriophage T4 resistant to later infection by T4 and closely related phages. Here we show that (1) gp61.3 is secreted into the periplasm where its N-terminal periplasm-targeting peptide is cleaved off; (2) gp61.3 forms a 1:1 complex with the lysozyme domain of gp5 (gp5Lys); (3) gp61.3 selectively inhibits the activity of gp5, but not that of T4L; (4) overexpression of gp5 causes cell lysis. We also report a crystal structure of the gp61.3-gp5Lys complex that demonstrates that unlike other known lysozyme inhibitors, gp61.3 does not interact with the active site cleft. Instead, it forms a “wall” that blocks access of an extended polysaccharide substrate to the cleft and, possibly, locks the enzyme in an “open-jaw”-like conformation making catalysis impossible.
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2
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Juan C, Torrens G, Barceló IM, Oliver A. Interplay between Peptidoglycan Biology and Virulence in Gram-Negative Pathogens. Microbiol Mol Biol Rev 2018; 82:e00033-18. [PMID: 30209071 PMCID: PMC6298613 DOI: 10.1128/mmbr.00033-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The clinical and epidemiological threat of the growing antimicrobial resistance in Gram-negative pathogens, particularly for β-lactams, the most frequently used and relevant antibiotics, urges research to find new therapeutic weapons to combat the infections caused by these microorganisms. An essential previous step in the development of these therapeutic solutions is to identify their potential targets in the biology of the pathogen. This is precisely what we sought to do in this review specifically regarding the barely exploited field analyzing the interplay among the biology of the peptidoglycan and related processes, such as β-lactamase regulation and virulence. Hence, here we gather, analyze, and integrate the knowledge derived from published works that provide information on the topic, starting with those dealing with the historically neglected essential role of the Gram-negative peptidoglycan in virulence, including structural, biogenesis, remodeling, and recycling aspects, in addition to proinflammatory and other interactions with the host. We also review the complex link between intrinsic β-lactamase production and peptidoglycan metabolism, as well as the biological costs potentially associated with the expression of horizontally acquired β-lactamases. Finally, we analyze the existing evidence from multiple perspectives to provide useful clues for identifying targets enabling the future development of therapeutic options attacking the peptidoglycan-virulence interconnection as a key weak point of the Gram-negative pathogens to be used, if not to kill the bacteria, to mitigate their capacity to produce severe infections.
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Affiliation(s)
- Carlos Juan
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Baleares (IdISBa), Palma, Spain
| | - Gabriel Torrens
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Baleares (IdISBa), Palma, Spain
| | - Isabel Maria Barceló
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Baleares (IdISBa), Palma, Spain
| | - Antonio Oliver
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Baleares (IdISBa), Palma, Spain
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3
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Liu Z, García-Díaz B, Catacchio B, Chiancone E, Vogel HJ. Protecting Gram-negative bacterial cell envelopes from human lysozyme: Interactions with Ivy inhibitor proteins from Escherichia coli and Pseudomonas aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:3032-46. [PMID: 25838125 DOI: 10.1016/j.bbamem.2015.03.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/16/2015] [Accepted: 03/24/2015] [Indexed: 11/15/2022]
Abstract
Lysozymes play an important role in host defense by degrading peptidoglycan in the cell envelopes of pathogenic bacteria. Several Gram-negative bacteria can evade this mechanism by producing periplasmic proteins that inhibit the enzymatic activity of lysozyme. The Escherichia coli inhibitor of vertebrate lysozyme, Ivyc and its Pseudomonas aeruginosa homolog, Ivyp1 have been shown to be potent inhibitors of hen egg white lysozyme (HEWL). Since human lysozyme (HL) plays an important role in the innate immune response, we have examined the binding of HL to Ivyc and Ivyp1. Our results show that Ivyp1 is a weaker inhibitor of HL than Ivyc even though they inhibit HEWL with similar potency. Calorimetry experiments confirm that Ivyp1 interacts more weakly with HL than HEWL. Analytical ultracentrifugation studies revealed that Ivyp1 in solution is a monomer and forms a 30kDa heterodimer with both HL and HEWL, while Ivyc is a homodimer that forms a tetramer with both enzymes. The interaction of Ivyp1 with HL was further characterized by NMR chemical shift perturbation experiments. In addition to the characteristic His-containing Ivy inhibitory loop that binds into the active site of lysozyme, an extended loop (P2) between the final two beta-strands also participates in forming protein-protein interactions. The P2 loop is not conserved in Ivyc and it constitutes a flexible region in Ivyp1 that becomes more rigid in the complex with HL. We conclude that differences in the electrostatic interactions at the binding interface between Ivy inhibitors and distinct lysozymes determine the strength of this interaction. This article is part of a Special Issue entitled: Bacterial Resistance to Antimicrobial Peptides.
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Affiliation(s)
- Zhihong Liu
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Beatriz García-Díaz
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Bruno Catacchio
- Dipartimento di Scienze Biochimiche, Istituto di Biologia e Patologia Molecolari CNR, Università Sapienza, P.le A. Moro, 5-00185 Roma, Italy
| | - Emilia Chiancone
- Dipartimento di Scienze Biochimiche, Istituto di Biologia e Patologia Molecolari CNR, Università Sapienza, P.le A. Moro, 5-00185 Roma, Italy
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
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4
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Leysen S, Van Herreweghe JM, Yoneda K, Ogata M, Usui T, Araki T, Michiels CW, Strelkov SV. The structure of the proteinaceous inhibitor PliI from Aeromonas hydrophila in complex with its target lysozyme. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:344-51. [PMID: 25664745 DOI: 10.1107/s1399004714025863] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 11/26/2014] [Indexed: 11/10/2022]
Abstract
Recent microbiological data have revealed that Gram-negative bacteria are able to protect themselves against the lytic action of host lysozymes by secreting proteinaceous inhibitors. Four distinct classes of such inhibitors have been discovered that specifically act against c-type, g-type and i-type lysozymes. Here, the 1.24 Å resolution crystal structure of the periplasmic i-type lysozyme inhibitor from Aeromonas hydrophila (PliI-Ah) in complex with the i-type lysozyme from Meretrix lusoria is reported. The structure is the first to explain the inhibitory mechanism of the PliI family at the atomic level. A distinct `ridge' formed by three exposed PliI loops inserts into the substrate-binding groove of the lysozyme, resulting in a complementary `key-lock' interface. The interface is principally stabilized by the interactions made by the PliI-Ah residues Ser104 and Tyr107 belonging to the conserved SGxY motif, as well as by the other conserved residues Ser46 and Asp76. The functional importance of these residues is confirmed by inhibition assays with the corresponding point mutants of PliI-Ah. The accumulated structural data on lysozyme-inhibitor complexes from several classes indicate that in all cases an extensive interface of either a single or a double `key-lock' type is formed, resulting in highly efficient inhibition. These data provide a basis for the rational development of a new class of antibacterial drugs.
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Affiliation(s)
- Seppe Leysen
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Joris M Van Herreweghe
- Laboratory of Food Microbiology, Leuven Food Science and Nutrition Research Centre, KU Leuven, 3000 Leuven, Belgium
| | - Kazunari Yoneda
- Department of Bioscience, School of Agriculture, Tokai University, Kawayo, Minamiaso, Kumamoto 869-1404, Japan
| | - Makoto Ogata
- Department of Chemistry and Biochemistry, Fukushima National College of Technology, 30 Nagao, Kamiarakawa, Taira, Iwaki, Fukushima 970-8034, Japan
| | - Taichi Usui
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga, Shizuoka 422-8529, Japan
| | - Tomohiro Araki
- Department of Bioscience, School of Agriculture, Tokai University, Kawayo, Minamiaso, Kumamoto 869-1404, Japan
| | - Christiaan W Michiels
- Laboratory of Food Microbiology, Leuven Food Science and Nutrition Research Centre, KU Leuven, 3000 Leuven, Belgium
| | - Sergei V Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
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5
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Lu D, Shang G, Zhang H, Yu Q, Cong X, Yuan J, He F, Zhu C, Zhao Y, Yin K, Chen Y, Hu J, Zhang X, Yuan Z, Xu S, Hu W, Cang H, Gu L. Structural insights into the T6SS effector protein Tse3 and the Tse3-Tsi3 complex fromPseudomonas aeruginosareveal a calcium-dependent membrane-binding mechanism. Mol Microbiol 2014; 92:1092-112. [DOI: 10.1111/mmi.12616] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Defen Lu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
- The Liver Centre of Fujian Province; MengChao Hepatobiliary Hospital of Fujian Medical University; Fuzhou 350025 Fujian China
| | - Guijun Shang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Heqiao Zhang
- Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
- School of Life Sciences; Tsinghua University; Beijing 100084 China
| | - Qian Yu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Xiaoyan Cong
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Jupeng Yuan
- Institute of Medical Genetics; Shandong University School of Medicine; Jinan 250012 Shandong China
| | - Fengjuan He
- Institute of Medical Genetics; Shandong University School of Medicine; Jinan 250012 Shandong China
| | - Chunyuan Zhu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Yanyu Zhao
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Kun Yin
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Yuanyuan Chen
- Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
| | - Junqiang Hu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Xiaodan Zhang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Zenglin Yuan
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Sujuan Xu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Wei Hu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Huaixing Cang
- Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
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6
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Tichy EM, Luisi BF, Salmond GPC. Crystal structure of the carbapenem intrinsic resistance protein CarG. J Mol Biol 2014; 426:1958-70. [PMID: 24583229 PMCID: PMC4361734 DOI: 10.1016/j.jmb.2014.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/15/2014] [Accepted: 02/20/2014] [Indexed: 10/25/2022]
Abstract
In the Gram-negative enterobacterium Erwinia (Pectobacterium) and Serratia sp. ATCC 39006, intrinsic resistance to the carbapenem antibiotic 1-carbapen-2-em-3-carboxylic acid is mediated by the CarF and CarG proteins, by an unknown mechanism. Here, we report a high-resolution crystal structure for the Serratia sp. ATCC 39006 carbapenem resistance protein CarG. This structure of CarG is the first in the carbapenem intrinsic resistance (CIR) family of resistance proteins from carbapenem-producing bacteria. The crystal structure shows the protein to form a homodimer, in agreement with results from analytical gel filtration. The structure of CarG does not show homology with any known antibiotic resistance proteins nor does it belong to any well-characterised protein structural family. However, it is a close structural homologue of the bacterial inhibitor of invertebrate lysozyme, PliI-Ah, with some interesting structural variations, including the absence of the catalytic site responsible for lysozyme inhibition. Both proteins show a unique β-sandwich fold with short terminal α-helices. The core of the protein is formed by stacked anti-parallel sheets that are individually very similar in the two proteins but differ in their packing interface, causing the splaying of the two sheets in CarG. Furthermore, a conserved cation binding site identified in CarG is absent from the homologue.
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Affiliation(s)
- E M Tichy
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB21QW, UK
| | - B F Luisi
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB21QW, UK
| | - G P C Salmond
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB21QW, UK
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7
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Huang SY, Yan C, Grinter SZ, Chang S, Jiang L, Zou X. Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in Critical Assessment of PRedicted Interactions (CAPRI). Proteins 2013; 81:2183-91. [PMID: 24227686 PMCID: PMC3916956 DOI: 10.1002/prot.24435] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/23/2013] [Accepted: 09/25/2013] [Indexed: 01/20/2023]
Abstract
Inclusion of entropy is important and challenging for protein-protein binding prediction. Here, we present a statistical mechanics-based approach to empirically consider the effect of orientational entropy. Specifically, we globally sample the possible binding orientations based on a simple shape-complementarity scoring function using an FFT-type docking method. Then, for each generated orientation, we calculate the probability through the partition function of the ensemble of accessible states, which are assumed to be represented by the set of nearby binding modes. For each mode, the interaction energy is calculated using our ITScorePP scoring function that was developed in our laboratory based on principles of statistical mechanics. Using the above protocol, we present the results of our participation in Rounds 22-27 of the Critical Assessment of PRedicted Interactions (CAPRI) experiment for 10 targets (T46-T58). Additional experimental information, such as low-resolution small-angle X-ray scattering data, was used when available. In the prediction (or docking) experiments of the 10 target complexes, we achieved correct binding modes for six targets: one with high accuracy (T47), two with medium accuracy (T48 and T57), and three with acceptable accuracy (T49, T50, and T58). In the scoring experiments of seven target complexes, we obtained correct binding modes for six targets: one with high accuracy (T47), two with medium accuracy (T49 and T50), and three with acceptable accuracy (T46, T51, and T53).
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Affiliation(s)
- Sheng-You Huang
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, MO 65211
| | | | | | - Shan Chang
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, MO 65211
| | - Lin Jiang
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, MO 65211
| | - Xiaoqin Zou
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, MO 65211
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8
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Kilambi KP, Pacella MS, Xu J, Labonte JW, Porter JR, Muthu P, Drew K, Kuroda D, Schueler-Furman O, Bonneau R, Gray JJ. Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27. Proteins 2013; 81:2201-9. [PMID: 24123494 PMCID: PMC4037910 DOI: 10.1002/prot.24425] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 09/12/2013] [Accepted: 09/13/2013] [Indexed: 11/09/2022]
Abstract
Rounds 20-27 of the Critical Assessment of PRotein Interactions (CAPRI) provided a testing platform for computational methods designed to address a wide range of challenges. The diverse targets drove the creation of and new combinations of computational tools. In this study, RosettaDock and other novel Rosetta protocols were used to successfully predict four of the 10 blind targets. For example, for DNase domain of Colicin E2-Im2 immunity protein, RosettaDock and RosettaLigand were used to predict the positions of water molecules at the interface, recovering 46% of the native water-mediated contacts. For α-repeat Rep4-Rep2 and g-type lysozyme-PliG inhibitor complexes, homology models were built and standard and pH-sensitive docking algorithms were used to generate structures with interface RMSD values of 3.3 Å and 2.0 Å, respectively. A novel flexible sugar-protein docking protocol was also developed and used for structure prediction of the BT4661-heparin-like saccharide complex, recovering 71% of the native contacts. Challenges remain in the generation of accurate homology models for protein mutants and sampling during global docking. On proteins designed to bind influenza hemagglutinin, only about half of the mutations were identified that affect binding (T55: 54%; T56: 48%). The prediction of the structure of the xylanase complex involving homology modeling and multidomain docking pushed the limits of global conformational sampling and did not result in any successful prediction. The diversity of problems at hand requires computational algorithms to be versatile; the recent additions to the Rosetta suite expand the capabilities to encompass more biologically realistic docking problems.
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Affiliation(s)
- Krishna Praneeth Kilambi
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Michael S. Pacella
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Jianqing Xu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Jason W. Labonte
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Justin R. Porter
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Pravin Muthu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Kevin Drew
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York
| | - Daisuke Kuroda
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
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9
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Qin S, Zhou HX. Using the concept of transient complex for affinity predictions in CAPRI rounds 20-27 and beyond. Proteins 2013; 81:2229-36. [PMID: 23873496 PMCID: PMC3842397 DOI: 10.1002/prot.24366] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/26/2013] [Accepted: 06/29/2013] [Indexed: 11/10/2022]
Abstract
Predictions of protein-protein binders and binding affinities have traditionally focused on features pertaining to the native complexes. In developing a computational method for predicting protein-protein association rate constants, we introduced the concept of transient complex after mapping the interaction energy surface. The transient complex is located at the outer boundary of the bound-state energy well, having near-native separation and relative orientation between the subunits but not yet formed most of the short-range native interactions. We found that the width of the binding funnel and the electrostatic interaction energy of the transient complex are among the features predictive of binders and binding affinities. These ideas were very promising for the five affinity-related targets (T43-45, 55, and 56) of CAPRI rounds 20-27. For T43, we ranked the single crystallographic complex as number 1 and were one of only two groups that clearly identified that complex as a true binder; for T44, we ranked the only design with measurable binding affinity as number 4. For the nine docking targets, continuing on our success in previous CAPRI rounds, we produced 10 medium-quality models for T47 and acceptable models for T48 and T49. We conclude that the interaction energy landscape and the transient complex in particular will complement existing features in leading to better prediction of binding affinities.
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Affiliation(s)
- Sanbo Qin
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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10
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Pallara C, Jiménez-García B, Pérez-Cano L, Romero-Durana M, Solernou A, Grosdidier S, Pons C, Moal IH, Fernandez-Recio J. Expanding the frontiers of protein-protein modeling: from docking and scoring to binding affinity predictions and other challenges. Proteins 2013; 81:2192-200. [PMID: 23934865 DOI: 10.1002/prot.24387] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/31/2013] [Accepted: 08/01/2013] [Indexed: 11/06/2022]
Abstract
In addition to protein-protein docking, this CAPRI edition included new challenges, like protein-water and protein-sugar interactions, or the prediction of binding affinities and ΔΔG changes upon mutation. Regarding the standard protein-protein docking cases, our approach, mostly based on the pyDock scheme, submitted correct models as predictors and as scorers for 67% and 57% of the evaluated targets, respectively. In this edition, available information on known interface residues hardly made any difference for our predictions. In one of the targets, the inclusion of available experimental small-angle X-ray scattering (SAXS) data using our pyDockSAXS approach slightly improved the predictions. In addition to the standard protein-protein docking assessment, new challenges were proposed. One of the new problems was predicting the position of the interface water molecules, for which we submitted models with 20% and 43% of the water-mediated native contacts predicted as predictors and scorers, respectively. Another new problem was the prediction of protein-carbohydrate binding, where our submitted model was very close to being acceptable. A set of targets were related to the prediction of binding affinities, in which our pyDock scheme was able to discriminate between natural and designed complexes with area under the curve = 83%. It was also proposed to estimate the effect of point mutations on binding affinity. Our approach, based on machine learning methods, showed high rates of correctly classified mutations for all cases. The overall results were highly rewarding, and show that the field is ready to move forward and face new interesting challenges in interactomics.
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Affiliation(s)
- Chiara Pallara
- Joint BSC-IRB Research Programme in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
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11
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Leysen S, Vanderkelen L, Weeks SD, Michiels CW, Strelkov SV. Structural basis of bacterial defense against g-type lysozyme-based innate immunity. Cell Mol Life Sci 2013; 70:1113-22. [PMID: 23086131 PMCID: PMC11113182 DOI: 10.1007/s00018-012-1184-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 09/21/2012] [Accepted: 09/27/2012] [Indexed: 10/27/2022]
Abstract
Gram-negative bacteria can produce specific proteinaceous inhibitors to defend themselves against the lytic action of host lysozymes. So far, four different lysozyme inhibitor families have been identified. Here, we report the crystal structure of the Escherichia coli periplasmic lysozyme inhibitor of g-type lysozyme (PliG-Ec) in complex with Atlantic salmon g-type lysozyme (SalG) at a resolution of 0.95 Å, which is exceptionally high for a complex of two proteins. The structure reveals for the first time the mechanism of g-type lysozyme inhibition by the PliG family. The latter contains two specific conserved regions that are essential for its inhibitory activity. The inhibitory complex formation is based on a double 'key-lock' mechanism. The first key-lock element is formed by the insertion of two conserved PliG regions into the active site of the lysozyme. The second element is defined by a distinct pocket of PliG accommodating a lysozyme loop. Computational analysis indicates that this pocket represents a suitable site for small molecule binding, which opens an avenue for the development of novel antibacterial agents that suppress the inhibitory activity of PliG.
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Affiliation(s)
- S. Leysen
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Herestraat 49 bus 822, 3000 Leuven, Belgium
| | - L. Vanderkelen
- Laboratory of Food Microbiology, Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - S. D. Weeks
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Herestraat 49 bus 822, 3000 Leuven, Belgium
| | - C. W. Michiels
- Laboratory of Food Microbiology, Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - S. V. Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Herestraat 49 bus 822, 3000 Leuven, Belgium
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12
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Callewaert L, Van Herreweghe JM, Vanderkelen L, Leysen S, Voet A, Michiels CW. Guards of the great wall: bacterial lysozyme inhibitors. Trends Microbiol 2012; 20:501-10. [DOI: 10.1016/j.tim.2012.06.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 06/22/2012] [Accepted: 06/29/2012] [Indexed: 10/28/2022]
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