1
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Iron-Sulfur Clusters: A Key Factor of Regulated Cell Death in Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:7449941. [PMID: 36338346 PMCID: PMC9629928 DOI: 10.1155/2022/7449941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/23/2022] [Accepted: 10/07/2022] [Indexed: 11/21/2022]
Abstract
Iron-sulfur clusters are ancient cofactors that play crucial roles in myriad cellular functions. Recent studies have shown that iron-sulfur clusters are closely related to the mechanisms of multiple cell death modalities. In addition, numerous previous studies have demonstrated that iron-sulfur clusters play an important role in the development and treatment of cancer. This review first summarizes the close association of iron-sulfur clusters with cell death modalities such as ferroptosis, cuprotosis, PANoptosis, and apoptosis and their potential role in cancer activation and drug resistance. This review hopes to generate new cancer therapy ideas and overcome drug resistance by modulating iron-sulfur clusters.
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2
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Yang L, He W, Yun Y, Gao Y, Zhu Z, Teng M, Liang Z, Niu L. Defining A Global Map of Functional Group-based 3D Ligand-binding Motifs. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:765-779. [PMID: 35288344 PMCID: PMC9881048 DOI: 10.1016/j.gpb.2021.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 06/30/2021] [Accepted: 09/27/2021] [Indexed: 01/31/2023]
Abstract
Uncovering conserved 3D protein-ligand binding patterns on the basis of functional groups (FGs) shared by a variety of small molecules can greatly expand our knowledge of protein-ligand interactions. Despite that conserved binding patterns for a few commonly used FGs have been reported in the literature, large-scale identification and evaluation of FG-based 3D binding motifs are still lacking. Here, we propose a computational method, Automatic FG-based Three-dimensional Motif Extractor (AFTME), for automatic mapping of 3D motifs to different FGs of a specific ligand. Applying our method to 233 naturally-occurring ligands, we define 481 FG-binding motifs that are highly conserved across different ligand-binding pockets. Systematic analysis further reveals four main classes of binding motifs corresponding to distinct sets of FGs. Combinations of FG-binding motifs facilitate the binding of proteins to a wide spectrum of ligands with various binding affinities. Finally, we show that our FG-motif map can be used to nominate FGs that potentially bind to specific drug targets, thus providing useful insights and guidance for rational design of small-molecule drugs.
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Affiliation(s)
- Liu Yang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Wei He
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China.
| | - Yuehui Yun
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Yongxiang Gao
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Zhongliang Zhu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Maikun Teng
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Zhi Liang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China.
| | - Liwen Niu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China.
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3
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So M, Stiban J, Ciesielski GL, Hovde SL, Kaguni LS. Implications of Membrane Binding by the Fe-S Cluster-Containing N-Terminal Domain in the Drosophila Mitochondrial Replicative DNA Helicase. Front Genet 2021; 12:790521. [PMID: 34950192 PMCID: PMC8688847 DOI: 10.3389/fgene.2021.790521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Recent evidence suggests that iron-sulfur clusters (ISCs) in DNA replicative proteins sense DNA-mediated charge transfer to modulate nuclear DNA replication. In the mitochondrial DNA replisome, only the replicative DNA helicase (mtDNA helicase) from Drosophila melanogaster (Dm) has been shown to contain an ISC in its N-terminal, primase-like domain (NTD). In this report, we confirm the presence of the ISC and demonstrate the importance of a metal cofactor in the structural stability of the Dm mtDNA helicase. Further, we show that the NTD also serves a role in membrane binding. We demonstrate that the NTD binds to asolectin liposomes, which mimic phospholipid membranes, through electrostatic interactions. Notably, membrane binding is more specific with increasing cardiolipin content, which is characteristically high in the mitochondrial inner membrane (MIM). We suggest that the N-terminal domain of the mtDNA helicase interacts with the MIM to recruit mtDNA and initiate mtDNA replication. Furthermore, Dm NUBPL, the known ISC donor for respiratory complex I and a putative donor for Dm mtDNA helicase, was identified as a peripheral membrane protein that is likely to execute membrane-mediated ISC delivery to its target proteins.
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Affiliation(s)
- Minyoung So
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States
| | - Johnny Stiban
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States.,Department of Biology and Biochemistry, Birzeit University, Birzeit, Palestine
| | - Grzegorz L Ciesielski
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States.,Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland.,Department of Chemistry, Auburn University at Montgomery, Montgomery, AL, United States
| | - Stacy L Hovde
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States.,Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland
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4
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Structural Modeling and Ligand-Binding Prediction for Analysis of Structure-Unknown and Function-Unknown Proteins Using FORTE Alignment and PoSSuM Pocket Search. Methods Mol Biol 2020. [PMID: 32621216 DOI: 10.1007/978-1-0716-0708-4_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Structural data of biomolecules, such as those of proteins and nucleic acids, provide much information for estimation of their functions. For structure-unknown proteins, structure information is obtainable by modeling their structures based on sequence similarity of proteins. Moreover, information related to ligands or ligand-binding sites is necessary to elucidate protein functions because the binding of ligands can engender not only the activation and inactivation of the proteins but also the modification of protein functions. This chapter presents methods using our profile-profile alignment server FORTE and the PoSSuM ligand-binding site database for prediction of the structure and potential ligand-binding sites of structure-unknown and function-unknown proteins, aimed at protein function prediction.
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5
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Sahu S, Sheet T, Banerjee R. Interaction landscape of a 'C αNN' motif with arsenate and arsenite: a potential peptide-based scavenger of arsenic. RSC Adv 2019; 9:1062-1074. [PMID: 35517606 PMCID: PMC9059529 DOI: 10.1039/c8ra08225a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/08/2018] [Indexed: 12/01/2022] Open
Abstract
Arsenic (As) is a toxic metalloid that has drawn immense attention from the scientific community recently due to its fatal effects through its unwanted occurrence in ground water around the globe. The presence of an excess amount of water soluble arsenate and/or arsenite salt (permissible limit 10 μg L-1 as recommended by the WHO) in water has been correlated with several human diseases. Although arsenate (HAsO4 2-) is a molecular analogue of phosphate (HPO4 2-), phosphate is indispensable for life, while arsenic and its salts are toxic. Therefore, it is worthwhile to focus on the removal of arsenic from water. Towards this end, the design of peptide-based scaffolds for the recognition of arsenate and arsenite would add a new dimension. Utilizing the stereochemical similarity between arsenate (HAsO4 2-) and phosphate (HPO4 2-), we successfully investigated the recognition of arsenate and arsenite with a naturally occurring novel phosphate binding 'CαNN' motif and its related designed analogues. Using computational as well as biophysical approaches, for the first time, we report here that a designed peptide-based scaffold based on the 'CαNN' motif can recognize anions of arsenic in a thermodynamically favorable manner in a context-free system. This peptide-based arsenic binding agent has the potential for future development as a scavenger of arsenic anions to obtain arsenic free water.
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Affiliation(s)
- Subhankar Sahu
- Department of Biotechnology and Head Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology) BF-142, Salt Lake Kolkata 700064 West Bengal India
| | - Tridip Sheet
- Department of Biotechnology and Head Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology) BF-142, Salt Lake Kolkata 700064 West Bengal India
| | - Raja Banerjee
- Department of Biotechnology and Head Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology) BF-142, Salt Lake Kolkata 700064 West Bengal India
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6
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Thieker DF, Xu Y, Chapla D, Nora C, Qiu H, Felix T, Wang L, Moremen KW, Liu J, Esko JD, Woods RJ. Downstream Products are Potent Inhibitors of the Heparan Sulfate 2-O-Sulfotransferase. Sci Rep 2018; 8:11832. [PMID: 30087361 PMCID: PMC6081452 DOI: 10.1038/s41598-018-29602-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/09/2018] [Indexed: 12/31/2022] Open
Abstract
Heparan Sulfate (HS) is a cell signaling molecule linked to pathological processes ranging from cancer to viral entry, yet fundamental aspects of its biosynthesis remain incompletely understood. Here, the binding preferences of the uronyl 2-O-sulfotransferase (HS2ST) are examined with variably-sulfated hexasaccharides. Surprisingly, heavily sulfated oligosaccharides formed by later-acting sulfotransferases bind more tightly to HS2ST than those corresponding to its natural substrate or product. Inhibition assays also indicate that the IC50 values correlate simply with degree of oligosaccharide sulfation. Structural analysis predicts a mode of inhibition in which 6-O-sulfate groups located on glucosamine residues present in highly-sulfated oligosaccharides occupy the canonical binding site of the nucleotide cofactor. The unexpected finding that oligosaccharides associated with later stages in HS biosynthesis inhibit HS2ST indicates that the enzyme must be separated temporally and/or spatially from downstream products during biosynthesis in vivo, and highlights a challenge for the enzymatic synthesis of lengthy HS chains in vitro.
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Affiliation(s)
- David F Thieker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Yongmei Xu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Rm 1044, Genetic Medicine Building, Chapel Hill, USA
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Chelsea Nora
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Hong Qiu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Thomas Felix
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Lianchun Wang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Rm 1044, Genetic Medicine Building, Chapel Hill, USA
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Robert J Woods
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
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7
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Cui P, Li RF, Zhang DP, Tang JL, Lu GT. HpaP, a novel regulatory protein with ATPase and phosphatase activity, contributes to full virulence in Xanthomonas campestris pv. campestris. Environ Microbiol 2018; 20:1389-1404. [PMID: 29345052 DOI: 10.1111/1462-2920.14046] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/10/2018] [Indexed: 11/30/2022]
Abstract
The ability of the bacterial phytopathogen Xanthomonas campestris pv. campestris (Xcc) to cause disease is dependent on the type III secretion system (T3SS). Proteins of the Xcc T3SS are encoded by hrp (hypersensitive response and pathogenicity) genes and whose expression is mainly controlled by the regulators HrpG and HrpX. Here, we describe the identification and characterization of a previously unknown regulatory protein (named HpaP), which plays important role in hrp gene expression and virulence in Xcc. Clean deletion of hpaP demonstrated reduced virulence and HR (hypersensitive response) induction of Xcc and alterations in cell motility and stress tolerance. Global transcriptome analyses revealed that most hrp genes were down regulated in the hpaP mutant, suggesting HpaP positively regulates hrp genes. GUS activity assays implied that HpaP regulates the expression of hrp genes via controlling the expression of hrpX. Biochemical analyses revealed that HpaP protein had both ATPase and phosphatase activity. While further site-directed mutagenesis of conserved residues in the PTP loop (a protein tyrosine phosphatase signature) of HpaP resulted in the loss of both phosphatase activity and regulatory activity in virulence and HR. Taken together, the findings identify a new regulatory protein that controls hrp gene expression and virulence in Xcc.
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Affiliation(s)
- Ping Cui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Rui-Fang Li
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, 174 Daxue Road, Nanning, Guangxi 530007, China
| | - Da-Pei Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Guang-Tao Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
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8
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Zheng H, Cooper DR, Porebski PJ, Shabalin IG, Handing KB, Minor W. CheckMyMetal: a macromolecular metal-binding validation tool. Acta Crystallogr D Struct Biol 2017; 73:223-233. [PMID: 28291757 PMCID: PMC5349434 DOI: 10.1107/s2059798317001061] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/21/2017] [Indexed: 12/19/2022] Open
Abstract
Metals are essential in many biological processes, and metal ions are modeled in roughly 40% of the macromolecular structures in the Protein Data Bank (PDB). However, a significant fraction of these structures contain poorly modeled metal-binding sites. CheckMyMetal (CMM) is an easy-to-use metal-binding site validation server for macromolecules that is freely available at http://csgid.org/csgid/metal_sites. The CMM server can detect incorrect metal assignments as well as geometrical and other irregularities in the metal-binding sites. Guidelines for metal-site modeling and validation in macromolecules are illustrated by several practical examples grouped by the type of metal. These examples show CMM users (and crystallographers in general) problems they may encounter during the modeling of a specific metal ion.
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Affiliation(s)
- Heping Zheng
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - David R. Cooper
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Przemyslaw J. Porebski
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Ivan G. Shabalin
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Katarzyna B. Handing
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Wladek Minor
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
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9
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Stiban J, So M, Kaguni LS. Iron-Sulfur Clusters in Mitochondrial Metabolism: Multifaceted Roles of a Simple Cofactor. BIOCHEMISTRY (MOSCOW) 2017; 81:1066-1080. [PMID: 27908232 DOI: 10.1134/s0006297916100059] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Iron-sulfur metabolism is essential for cellular function and is a key process in mitochondria. In this review, we focus on the structure and assembly of mitochondrial iron-sulfur clusters and their roles in various metabolic processes that occur in mitochondria. Iron-sulfur clusters are crucial in mitochondrial respiration, in which they are required for the assembly, stability, and function of respiratory complexes I, II, and III. They also serve important functions in the citric acid cycle, DNA metabolism, and apoptosis. Whereas the identification of iron-sulfur containing proteins and their roles in numerous aspects of cellular function has been a long-standing research area, that in mitochondria is comparatively recent, and it is likely that their roles within mitochondria have been only partially revealed. We review the status of the field and provide examples of other cellular iron-sulfur proteins to highlight their multifarious roles.
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Affiliation(s)
- Johnny Stiban
- Birzeit University, Department of Biology and Biochemistry, West Bank Birzeit, 627, Palestine.
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10
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He W, Liang Z, Teng M, Niu L. LibME-automatic extraction of 3D ligand-binding motifs for mechanistic analysis of protein-ligand recognition. FEBS Open Bio 2016; 6:1331-1340. [PMID: 28255540 PMCID: PMC5324770 DOI: 10.1002/2211-5463.12150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 11/23/2022] Open
Abstract
Identifying conserved binding motifs is an efficient way to study protein–ligand recognition. Most 3D binding motifs only contain information from the protein side, and so motifs that combine information from both protein and ligand sides are desired. Here, we propose an algorithm called LibME (Ligand‐binding Motif Extractor), which automatically extracts 3D binding motifs composed of the target ligand and surrounding conserved residues. We show that the motifs extracted by LibME for ATP and its analogs are highly similar to well‐known motifs reported by previous studies. The superiority of our method to handle flexible ligands was also demonstrated using isocitric acid as an example. Finally, we show that these motifs, together with their visual exhibition, permit better investigating and understanding of protein–ligand recognition process.
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Affiliation(s)
- Wei He
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences University of Science and Technology of China Anhui China
| | - Zhi Liang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences University of Science and Technology of China Anhui China
| | - MaiKun Teng
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences University of Science and Technology of China Anhui China
| | - LiWen Niu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences University of Science and Technology of China Anhui China
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11
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Schaeffer RD, Kinch LN, Liao Y, Grishin NV. Classification of proteins with shared motifs and internal repeats in the ECOD database. Protein Sci 2016; 25:1188-203. [PMID: 26833690 DOI: 10.1002/pro.2893] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/23/2016] [Accepted: 01/27/2016] [Indexed: 12/19/2022]
Abstract
Proteins and their domains evolve by a set of events commonly including the duplication and divergence of small motifs. The presence of short repetitive regions in domains has generally constituted a difficult case for structural domain classifications and their hierarchies. We developed the Evolutionary Classification Of protein Domains (ECOD) in part to implement a new schema for the classification of these types of proteins. Here we document the ways in which ECOD classifies proteins with small internal repeats, widespread functional motifs, and assemblies of small domain-like fragments in its evolutionary schema. We illustrate the ways in which the structural genomics project impacted the classification and characterization of new structural domains and sequence families over the decade.
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Affiliation(s)
- R Dustin Schaeffer
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9050
| | - Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9050
| | - Yuxing Liao
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9050
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9050.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9050
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12
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Sueldo DJ, Shimels M, Spiridon LN, Caldararu O, Petrescu AJ, Joosten MHAJ, Tameling WIL. Random mutagenesis of the nucleotide-binding domain of NRC1 (NB-LRR Required for Hypersensitive Response-Associated Cell Death-1), a downstream signalling nucleotide-binding, leucine-rich repeat (NB-LRR) protein, identifies gain-of-function mutations in the nucleotide-binding pocket. THE NEW PHYTOLOGIST 2015; 208:210-23. [PMID: 26009937 DOI: 10.1111/nph.13459] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/25/2015] [Indexed: 05/26/2023]
Abstract
Plant nucleotide-binding, leucine-rich repeat (NB-LRR) proteins confer immunity to pathogens possessing the corresponding avirulence proteins. Activation of NB-LRR proteins is often associated with induction of the hypersensitive response (HR), a form of programmed cell death. NRC1 (NB-LRR Required for HR-Associated Cell Death-1) is a tomato (Solanum lycopersicum) NB-LRR protein that participates in the signalling cascade leading to resistance to the pathogens Cladosporium fulvum and Verticillium dahliae. To identify mutations in NRC1 that cause increased signalling activity, we generated a random library of NRC1 variants mutated in their nucleotide-binding domain and screened them for the ability to induce an elicitor-independent HR in Nicotiana tabacum. Screening of 1920 clones retrieved 11 gain-of-function mutants, with 10 of them caused by a single amino acid substitution. All substitutions are located in or very close to highly conserved motifs within the nucleotide-binding domain, suggesting modulation of the signalling activity of NRC1. Three-dimensional modelling of the nucleotide-binding domain of NRC1 revealed that the targeted residues are centred around the bound nucleotide. Our mutational approach has generated a wide set of novel gain-of-function mutations in NRC1 and provides insight into how the activity of this NB-LRR is regulated.
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Affiliation(s)
- Daniela J Sueldo
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Mahdere Shimels
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Laurentiu N Spiridon
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060036, Bucharest, Romania
| | - Octav Caldararu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060036, Bucharest, Romania
| | - Andrei-Jose Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060036, Bucharest, Romania
| | - Matthieu H A J Joosten
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Wladimir I L Tameling
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
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13
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Gruber MF, Wood E, Truelsen S, Østergaard T, Hélix-Nielsen C. Computational Design of Biomimetic Phosphate Scavengers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:9469-9478. [PMID: 25920519 DOI: 10.1021/es506214c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Phosphorus has long been the target of much research, but in recent years the focus has shifted from being limited only to reducing its detrimental environmental impact, to also looking at how it is linked to the global food security. Therefore, the interest in finding novel techniques for phosphorus recovery, as well as improving existing techniques, has increased. In this study we apply a hybrid simulation approach of molecular dynamics and quantum mechanics to investigate the binding modes of phosphate anions by a small intrinsically disordered peptide. Our results confirm that the conformational ensemble of the peptide is significantly changed, or stabilized, by the binding of phosphate anions and that binding does not take place purely as a result of a stable P-loop binding nest, but rather that multiple binding modes may be involved. Such small synthetic peptides capable of binding phosphate could be the starting point of new novel technological approaches toward phosphorus recovery, and they represent an excellent model system for investigating the nature and dynamics of functional de novo designed intrinsically disordered proteins.
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Affiliation(s)
- Mathias F Gruber
- †The Biomimetic Membrane Group, Department of Environmental Engineering, Technical University of Denmark, DK 2800 Kgs. Lyngby Denmark
| | - Elizabeth Wood
- †The Biomimetic Membrane Group, Department of Environmental Engineering, Technical University of Denmark, DK 2800 Kgs. Lyngby Denmark
| | - Sigurd Truelsen
- †The Biomimetic Membrane Group, Department of Environmental Engineering, Technical University of Denmark, DK 2800 Kgs. Lyngby Denmark
| | - Thomas Østergaard
- †The Biomimetic Membrane Group, Department of Environmental Engineering, Technical University of Denmark, DK 2800 Kgs. Lyngby Denmark
| | - Claus Hélix-Nielsen
- †The Biomimetic Membrane Group, Department of Environmental Engineering, Technical University of Denmark, DK 2800 Kgs. Lyngby Denmark
- ‡University of Maribor, Faculty of Chemistry and Chemical Engineering, Smetanova ulica 17, SI-2000 Maribor, Slovenia
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TRAPPII regulates exocytic Golgi exit by mediating nucleotide exchange on the Ypt31 ortholog RabERAB11. Proc Natl Acad Sci U S A 2015; 112:4346-51. [PMID: 25831508 DOI: 10.1073/pnas.1419168112] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The oligomeric complex transport protein particle I (TRAPPI) mediates nucleotide exchange on the RAB GTPase RAB1/Ypt1. TRAPPII is composed of TRAPPI plus three additional subunits, Trs120, Trs130, and Trs65. Unclear is whether TRAPPII mediates nucleotide exchange on RAB1/Ypt1, RAB11/Ypt31, or both. In Aspergillus nidulans, RabO(RAB1) resides in the Golgi, RabE(RAB11) localizes to exocytic post-Golgi carriers undergoing transport to the apex, and hypA encodes Trs120. RabE(RAB11), but not RabO(RAB1), immunoprecipitates contain Trs120/Trs130/Trs65, demonstrating specific association of TRAPPII with RabE(RAB11) in vivo. hypA1(ts) rapidly shifts RabE(RAB11), but not RabO(RAB1), to the cytosol, consistent with HypA(Trs120) being specifically required for RabE(RAB11) activation. Missense mutations rescuing hypA1(ts) at 42 °C mapped to rabE, affecting seven residues. Substitutions in six, of which four resulted in 7- to 36-fold accelerated GDP release, rescued lethality associated to TRAPPII deficiency, whereas equivalent substitutions in RabO(RAB1) did not, establishing that the essential role of TRAPPII is facilitating RabE(RAB11) nucleotide exchange. In vitro, TRAPPII purified with HypA(Trs120)-S-tag accelerates nucleotide exchange on RabE(RAB11) and, paradoxically, to a lesser yet substantial extent, on RabO(RAB1). Evidence obtained by exploiting hypA1-mediated destabilization of HypA(Trs120)/HypC(Trs130)/Trs65 assembly onto the TRAPPI core indicates that these subunits sculpt a second RAB binding site on TRAPP apparently independent from that for RabO(RAB1), which would explain TRAPPII in vitro activity on two RABs. Using A. nidulans in vivo microscopy, we show that HypA(Trs120) colocalizes with RabE(RAB11), arriving at late Golgi cisternae as they dissipate into exocytic carriers. Thus, TRAPPII marks, and possibly determines, the Golgi-to-post-Golgi transition.
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15
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Salaemae W, Yap MY, Wegener KL, Booker GW, Wilce MCJ, Polyak SW. Nucleotide triphosphate promiscuity in Mycobacterium tuberculosis dethiobiotin synthetase. Tuberculosis (Edinb) 2015; 95:259-66. [PMID: 25801336 DOI: 10.1016/j.tube.2015.02.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 02/26/2015] [Indexed: 11/29/2022]
Abstract
Dethiobiotin synthetase (DTBS) plays a crucial role in biotin biosynthesis in microorganisms, fungi, and plants. Due to its importance in bacterial pathogenesis, and the absence of a human homologue, DTBS is a promising target for the development of new antibacterials desperately needed to combat antibiotic resistance. Here we report the first X-ray structure of DTBS from Mycobacterium tuberculosis (MtDTBS) bound to a nucleotide triphosphate (CTP). The nucleoside base is stabilized in its pocket through hydrogen-bonding interactions with the protein backbone, rather than amino acid side chains. This resulted in the unexpected finding that MtDTBS could utilise ATP, CTP, GTP, ITP, TTP, or UTP with similar Km and kcat values, although the enzyme had the highest affinity for CTP in competitive binding and surface plasmon resonance assays. This is in contrast to other DTBS homologues that preferentially bind ATP primarily through hydrogen-bonds between the purine base and the carboxamide side chain of a key asparagine. Mutational analysis performed alongside in silico experiments revealed a gate-keeper role for Asn175 in Escherichia coli DTBS that excludes binding of other nucleotide triphosphates. Here we provide evidence to show that MtDTBS has a broad nucleotide specificity due to the absence of the gate-keeper residue.
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Affiliation(s)
- Wanisa Salaemae
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Min Y Yap
- Department of Biochemistry and Molecular Biology, School of Biomedical Science, Monash University, Victoria, 3800, Australia
| | - Kate L Wegener
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Grant W Booker
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Matthew C J Wilce
- Department of Biochemistry and Molecular Biology, School of Biomedical Science, Monash University, Victoria, 3800, Australia
| | - Steven W Polyak
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia.
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16
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Song J, Kose S, Watanabe A, Son SY, Choi S, Hong H, Yamashita E, Park IY, Imamoto N, Lee SJ. Structural and functional analysis of Hikeshi, a new nuclear transport receptor of Hsp70s. ACTA ACUST UNITED AC 2015; 71:473-83. [PMID: 25760597 DOI: 10.1107/s1399004714026881] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/08/2014] [Indexed: 11/10/2022]
Abstract
Hikeshi is a nuclear transport receptor required for cell survival after stress. It mediates heat-shock-induced nuclear import of 70 kDa heat-shock proteins (Hsp70s) through interactions with FG-nucleoporins (FG-Nups), which are proteins in nuclear pore complexes (NPCs). Here, the crystal structure of human Hikeshi is presented at 1.8 Å resolution. Hikeshi forms an asymmetric homodimer that is responsible for the interaction with Hsp70s. The asymmetry of Hikeshi arises from the distinct conformation of the C-terminal domain (CTD) and the flexibility of the linker regions of each monomer. Structure-guided mutational analyses showed that both the flexible linker region and the CTD are important for nuclear import of Hsp70. Pull-down assays revealed that only full-length Hsp70s can interact with Hikeshi. The N-terminal domain (NTD) consists of a jelly-roll/β-sandwich fold structure which contains hydrophobic pockets involved in FG-Nup recognition. A unique extended loop (E-loop) in the NTD is likely to regulate the interactions of Hikeshi with FG-Nups. The crystal structure of Hikeshi explains how Hikeshi participates in the regulation of nuclear import through the recognition of FG-Nups and which part of Hikeshi affects its binding to Hsp70. This study is the first to yield structural insight into this highly unique import receptor.
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Affiliation(s)
- Jinsue Song
- College of Pharmacy, Chungbuk National University, 48 Gaeshin-dong, Heungduk-gu, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Shingo Kose
- Cellular Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ai Watanabe
- Cellular Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Se Young Son
- College of Pharmacy, Chungbuk National University, 48 Gaeshin-dong, Heungduk-gu, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Saehae Choi
- College of Pharmacy, Chungbuk National University, 48 Gaeshin-dong, Heungduk-gu, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Hyerim Hong
- College of Pharmacy, Chungbuk National University, 48 Gaeshin-dong, Heungduk-gu, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Il Yeong Park
- College of Pharmacy, Chungbuk National University, 48 Gaeshin-dong, Heungduk-gu, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Soo Jae Lee
- College of Pharmacy, Chungbuk National University, 48 Gaeshin-dong, Heungduk-gu, Cheongju, Chungbuk 361-763, Republic of Korea
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17
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Hernández-González M, Peñalva MA, Pantazopoulou A. Conditional inactivation ofAspergillus nidulans sarASAR1uncovers the morphogenetic potential of regulating endoplasmic reticulum (ER) exit. Mol Microbiol 2014; 95:491-508. [DOI: 10.1111/mmi.12880] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Miguel Hernández-González
- Departamento de Biología Celular y Molecular; Centro de Investigaciones Biológicas CSIC; Ramiro de Maeztu 9 Madrid 28040 Spain
| | - Miguel A. Peñalva
- Departamento de Biología Celular y Molecular; Centro de Investigaciones Biológicas CSIC; Ramiro de Maeztu 9 Madrid 28040 Spain
| | - Areti Pantazopoulou
- Departamento de Biología Celular y Molecular; Centro de Investigaciones Biológicas CSIC; Ramiro de Maeztu 9 Madrid 28040 Spain
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18
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Gong X, Chen X, Yu D, Zhang N, Zhu Z, Niu L, Mao Y, Ge H. Crystal structure of Legionella pneumophila dephospho-CoA kinase reveals a non-canonical conformation of P-loop. J Struct Biol 2014; 188:233-9. [PMID: 25449315 DOI: 10.1016/j.jsb.2014.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/30/2014] [Accepted: 10/20/2014] [Indexed: 11/19/2022]
Abstract
Dephospho-CoA kinase (DPCK; EC 2.7.1.24) catalyzes the final step in the coenzyme A biosynthetic pathway. DPCK transfers a phosphate group from ATP to the 3-hydroxyl group of the ribose of dephosphocoenzyme A (dCoA) to yield CoA and ADP. Upon the binding of ligands, large conformational changes is induced in DPCKs, as well as in many other kinases, to shield the bound ATP in their catalytic site from the futile hydrolysis by bulk water molecules. To investigate the molecular mechanisms underlying the phosphoryl transfer during DPCK catalytic cycle, we determined the crystal structures of the Legionellapneumophila DPCK (LpDPCK) both in its apo-form and in complex with ATP. The structures reveal that LpDPCK comprises of three domains, the classical core domain, the CoA domain, and the LID domain, which are packed together to create a central cavity for substrate-binding and enzymatic catalysis. The binding of ATP induces large conformational changes, including a hinge-bending motion of the CoA binding domain and the "helix to loop" conformational change of the P-loop. Finally, modeling of a dCoA molecule to the enzyme provides insights into the catalytic mechanism of DPCK.
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Affiliation(s)
- Xiaojian Gong
- Institute of Health Sciences and School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Xiaofang Chen
- Institute of Health Sciences and School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Dongmin Yu
- Institute of Health Sciences and School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Nannan Zhang
- Institute of Health Sciences and School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Zhongliang Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Liwen Niu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yuxin Mao
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Honghua Ge
- Institute of Health Sciences and School of Life Sciences, Anhui University, Hefei, Anhui 230601, China; Modern Experiment Technology Center, Anhui University, Hefei, Anhui 230601, China.
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19
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Parca L, Gherardini PF, Truglio M, Mangone I, Ferrè F, Helmer-Citterich M, Ausiello G. Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity. PLoS One 2012; 7:e50240. [PMID: 23209685 PMCID: PMC3507729 DOI: 10.1371/journal.pone.0050240] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 10/22/2012] [Indexed: 01/30/2023] Open
Abstract
Nucleotides are involved in several cellular processes, ranging from the transmission of genetic information, to energy transfer and storage. Both sequence and structure based methods have been developed to predict the location of nucleotide-binding sites in proteins. Here we propose a novel methodology that leverages the observation that nucleotide-binding sites have a modular structure. Nucleotides are composed of identifiable fragments, i.e. the phosphate, the nucleobase and the carbohydrate moieties. These fragments are bound by specific structural motifs that recur in proteins of different fold. Moreover these motifs behave as modules and are found in different combinations across fold space. Our method predicts binding sites for each nucleotide fragment by comparing a query protein with a database of templates extracted from proteins of known structure. Whenever a similarity is found the fragment bound by the template is transferred on the query protein, thus identifying a putative binding site. Predictions falling inside the surface of the protein are discarded, and the remaining ones are scored using clustering and conservation. The method is able to rank as first a correct prediction in the 48%, 48% and 68% of the analyzed proteins for the nucleobase, carbohydrate and phosphate respectively, while considering the first five predictions the performances change to 71%, 65% and 86% respectively. Furthermore we attempted to reconstruct the full structure of the binding site, starting from the predicted positions of the fragments. We calculated that in the 59% of the analyzed proteins the method ranks as first a reconstructed binding site or a part of it. Finally we tested the reliability of our method in a real world case in which it has to predict nucleotide-binding sites in unbound proteins. We analyzed proteins whose structure has been solved with and without the nucleotide and observed only little variations in the method performance.
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Affiliation(s)
- Luca Parca
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | | | - Mauro Truglio
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Iolanda Mangone
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Fabrizio Ferrè
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | | | - Gabriele Ausiello
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
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20
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Novel molecular fossils of bacteria: insights into hydrothermal origin of life. J Theor Biol 2012; 310:249-56. [PMID: 22796638 DOI: 10.1016/j.jtbi.2012.06.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 06/27/2012] [Accepted: 06/28/2012] [Indexed: 11/21/2022]
Abstract
Hydrothermal vents, in particular, alkaline submarine vents, are potential systems for the origin of life. Early hydrothermal vents may have imprinted on biochemical processes and housekeeping proteins of life and have hallmarked key molecules. This essay introduces new information to this discussion by focusing on newly identified sulfur-modified DNA and a heretofore ignored anhydro bond of the cell wall peptidoglycan in bacteria. It is suggested that they are novel molecular fossils that are relevant to the settings of alkaline submarine vents and harbor clues of early life. As DNA and the cell wall are bound up with genetic information and the integrity of cell, respectively, these two molecular fossils may provide insights into hydrothermal origin of life from a new angle.
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21
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Bianchi A, Giorgi C, Ruzza P, Toniolo C, Milner-White EJ. A synthetic hexapeptide designed to resemble a proteinaceous p-loop nest is shown to bind inorganic phosphate. Proteins 2012; 80:1418-24. [DOI: 10.1002/prot.24038] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 12/19/2011] [Accepted: 12/29/2011] [Indexed: 11/09/2022]
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22
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Porebski PJ, Klimecka M, Chruszcz M, Nicholls RA, Murzyn K, Cuff ME, Xu X, Cymborowski M, Murshudov GN, Savchenko A, Edwards A, Minor W. Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members. FEBS J 2012; 279:1093-105. [PMID: 22284390 PMCID: PMC3392494 DOI: 10.1111/j.1742-4658.2012.08506.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Dethiobiotin synthetase (DTBS) is involved in the biosynthesis of biotin in bacteria, fungi, and plants. As humans lack this pathway, DTBS is a promising antimicrobial drug target. We determined structures of DTBS from Helicobacter pylori (hpDTBS) bound with cofactors and a substrate analog, and described its unique characteristics relative to other DTBS proteins. Comparison with bacterial DTBS orthologs revealed considerable structural differences in nucleotide recognition. The C-terminal region of DTBS proteins, which contains two nucleotide-recognition motifs, differs greatly among DTBS proteins from different species. The structure of hpDTBS revealed that this protein is unique and does not contain a C-terminal region containing one of the motifs. The single nucleotide-binding motif in hpDTBS is similar to its counterpart in GTPases; however, isothermal titration calorimetry binding studies showed that hpDTBS has a strong preference for ATP. The structural determinants of ATP specificity were assessed with X-ray crystallographic studies of hpDTBS·ATP and hpDTBS·GTP complexes. The unique mode of nucleotide recognition in hpDTBS makes this protein a good target for H. pylori-specific inhibitors of the biotin synthesis pathway.
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Affiliation(s)
- Przemyslaw J. Porebski
- University of Virginia, Department of Molecular Physiology and Biological Physics, Charlottesville, VA 22908, USA
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, 30-387 Kraków, Poland
- Midwest Center for Structural Genomics
| | - Maria Klimecka
- University of Virginia, Department of Molecular Physiology and Biological Physics, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics
| | - Maksymilian Chruszcz
- University of Virginia, Department of Molecular Physiology and Biological Physics, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics
| | - Robert A. Nicholls
- University of Virginia, Department of Molecular Physiology and Biological Physics, Charlottesville, VA 22908, USA
- York Structural Biology Laboratory, Department of Chemistry, University of York, UK
- Midwest Center for Structural Genomics
| | - Krzysztof Murzyn
- University of Virginia, Department of Molecular Physiology and Biological Physics, Charlottesville, VA 22908, USA
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, 30-387 Kraków, Poland
- Midwest Center for Structural Genomics
| | - Marianne E. Cuff
- Structural Biology Center, Argonne National Laboratory, Argonne, IL 60439, USA
- Midwest Center for Structural Genomics
| | - Xiaohui Xu
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 1L6
- Midwest Center for Structural Genomics
| | - Marcin Cymborowski
- University of Virginia, Department of Molecular Physiology and Biological Physics, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics
| | - Garib N. Murshudov
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH UK
| | - Alexei Savchenko
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 1L6
- Midwest Center for Structural Genomics
| | - Aled Edwards
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 1L6
- Midwest Center for Structural Genomics
| | - Wladek Minor
- University of Virginia, Department of Molecular Physiology and Biological Physics, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics
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23
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Sehnal D, Vařeková RS, Huber HJ, Geidl S, Ionescu CM, Wimmerová M, Koča J. SiteBinder: an improved approach for comparing multiple protein structural motifs. J Chem Inf Model 2012; 52:343-59. [PMID: 22296449 DOI: 10.1021/ci200444d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
There is a paramount need to develop new techniques and tools that will extract as much information as possible from the ever growing repository of protein 3D structures. We report here on the development of a software tool for the multiple superimposition of large sets of protein structural motifs. Our superimposition methodology performs a systematic search for the atom pairing that provides the best fit. During this search, the RMSD values for all chemically relevant pairings are calculated by quaternion algebra. The number of evaluated pairings is markedly decreased by using PDB annotations for atoms. This approach guarantees that the best fit will be found and can be applied even when sequence similarity is low or does not exist at all. We have implemented this methodology in the Web application SiteBinder, which is able to process up to thousands of protein structural motifs in a very short time, and which provides an intuitive and user-friendly interface. Our benchmarking analysis has shown the robustness, efficiency, and versatility of our methodology and its implementation by the successful superimposition of 1000 experimentally determined structures for each of 32 eukaryotic linear motifs. We also demonstrate the applicability of SiteBinder using three case studies. We first compared the structures of 61 PA-IIL sugar binding sites containing nine different sugars, and we found that the sugar binding sites of PA-IIL and its mutants have a conserved structure despite their binding different sugars. We then superimposed over 300 zinc finger central motifs and revealed that the molecular structure in the vicinity of the Zn atom is highly conserved. Finally, we superimposed 12 BH3 domains from pro-apoptotic proteins. Our findings come to support the hypothesis that there is a structural basis for the functional segregation of BH3-only proteins into activators and enablers.
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Affiliation(s)
- David Sehnal
- National Centre for Biomolecular Research, Faculty of Science and CEITEC-Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 62500 Brno-Bohunice, Czech Republic
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24
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Kato G, Kondo H, Aoki T, Hirono I. A novel immune-related gene, microtubule aggregate protein homologue, is up-regulated during IFN-γ-related immune responses in Japanese flounder, Paralichthys olivaceus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2012; 36:349-358. [PMID: 21824491 DOI: 10.1016/j.dci.2011.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/02/2011] [Accepted: 06/02/2011] [Indexed: 05/31/2023]
Abstract
Delayed-type hypersensitivity (DTH) response mediated by antigen-specific Th1 cells is used as a test to detect exposure to tuberculosis in humans. Japanese flounder (Paralichthys olivaceus) microtubule aggregate protein homologue (PoMTAP) was identified as a gene strongly induced during fish DTH response. In this study, PoMTAP gene was cloned and its expression profile was analyzed. The PoMTAP gene has a transcriptional regulatory region that includes two interferon-stimulated response elements and two IFN-γ activated sites. Expressions of PoMTAP and IFN-γ genes were up-regulated at the same time points during the DTH response, Edwardsiella tarda infection and VHSV infection. Furthermore, PoMTAP gene expressing cells also expressed CD3ε, confirming that PoMTAP is expressed by T lymphocytes. These results suggest that PoMTAP is a novel immune-related gene expressed by T lymphocytes that is preferentially induced by IFN-γ and has a role in Th1-mediated immune responses in Japanese flounder.
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Affiliation(s)
- Goshi Kato
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Tokyo, Japan
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25
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Ito JI, Tabei Y, Shimizu K, Tomii K, Tsuda K. PDB-scale analysis of known and putative ligand-binding sites with structural sketches. Proteins 2011; 80:747-63. [PMID: 22113700 DOI: 10.1002/prot.23232] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 10/13/2011] [Accepted: 10/18/2011] [Indexed: 11/06/2022]
Abstract
Computational investigation of protein functions is one of the most urgent and demanding tasks in the field of structural bioinformatics. Exhaustive pairwise comparison of known and putative ligand-binding sites, across protein families and folds, is essential in elucidating the biological functions and evolutionary relationships of proteins. Given the vast amounts of data available now, existing 3D structural comparison methods are not adequate due to their computation time complexity. In this article, we propose a new bit string representation of binding sites called structural sketches, which is obtained by random projections of triplet descriptors. It allows us to use ultra-fast all-pair similarity search methods for strings with strictly controlled error rates. Exhaustive comparison of 1.2 million known and putative binding sites finished in ∼30 h on a single core to yield 88 million similar binding site pairs. Careful investigation of 3.5 million pairs verified by TM-align revealed several notable analogous sites across distinct protein families or folds. In particular, we succeeded in finding highly plausible functions of several pockets via strong structural analogies. These results indicate that our method is a promising tool for functional annotation of binding sites derived from structural genomics projects.
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Affiliation(s)
- Jun-Ichi Ito
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8568, Japan
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26
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Regad L, Martin J, Camproux AC. Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs. BMC Bioinformatics 2011; 12:247. [PMID: 21689388 PMCID: PMC3158783 DOI: 10.1186/1471-2105-12-247] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 06/20/2011] [Indexed: 12/24/2022] Open
Abstract
Background One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Results Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Conclusions Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.
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27
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Regad L, Saladin A, Maupetit J, Geneix C, Camproux AC. SA-Mot: a web server for the identification of motifs of interest extracted from protein loops. Nucleic Acids Res 2011; 39:W203-9. [PMID: 21665924 PMCID: PMC3125790 DOI: 10.1093/nar/gkr410] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The detection of functional motifs is an important step for the determination of protein functions. We present here a new web server SA-Mot (Structural Alphabet Motif) for the extraction and location of structural motifs of interest from protein loops. Contrary to other methods, SA-Mot does not focus only on functional motifs, but it extracts recurrent and conserved structural motifs involved in structural redundancy of loops. SA-Mot uses the structural word notion to extract all structural motifs from uni-dimensional sequences corresponding to loop structures. Then, SA-Mot provides a description of these structural motifs using statistics computed in the loop data set and in SCOP superfamily, sequence and structural parameters. SA-Mot results correspond to an interactive table listing all structural motifs extracted from a target structure and their associated descriptors. Using this information, the users can easily locate loop regions that are important for the protein folding and function. The SA-Mot web server is available at http://sa-mot.mti.univ-paris-diderot.fr.
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Affiliation(s)
- Leslie Regad
- INSERM, U973, Université Paris 7-Paris Diderot, UMR-S973, MTi F-75013 Paris, France.
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Gherardini PF, Ausiello G, Russell RB, Helmer-Citterich M. Modular architecture of nucleotide-binding pockets. Nucleic Acids Res 2010; 38:3809-16. [PMID: 20185567 PMCID: PMC2887960 DOI: 10.1093/nar/gkq090] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Recently, modularity has emerged as a general attribute of complex biological systems. This is probably because modular systems lend themselves readily to optimization via random mutation followed by natural selection. Although they are not traditionally considered to evolve by this process, biological ligands are also modular, being composed of recurring chemical fragments, and moreover they exhibit similarities reminiscent of mutations (e.g. the few atoms differentiating adenine and guanine). Many ligands are also promiscuous in the sense that they bind to many different protein folds. Here, we investigated whether ligand chemical modularity is reflected in an underlying modularity of binding sites across unrelated proteins. We chose nucleotides as paradigmatic ligands, because they can be described as composed of well-defined fragments (nucleobase, ribose and phosphates) and are quite abundant both in nature and in protein structure databases. We found that nucleotide-binding sites do indeed show a modular organization and are composed of fragment-specific protein structural motifs, which parallel the modular structure of their ligands. Through an analysis of the distribution of these motifs in different proteins and in different folds, we discuss the evolutionary implications of these findings and argue that the structural features we observed can arise both as a result of divergence from a common ancestor or convergent evolution.
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Affiliation(s)
- Pier Federico Gherardini
- Centre for Molecular Bioinformatics, Department of Biology, University of Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy
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Mining protein loops using a structural alphabet and statistical exceptionality. BMC Bioinformatics 2010; 11:75. [PMID: 20132552 PMCID: PMC2833150 DOI: 10.1186/1471-2105-11-75] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 02/04/2010] [Indexed: 12/21/2022] Open
Abstract
Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 Å). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. Conclusions We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/.
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Ausiello G, Gherardini PF, Gatti E, Incani O, Helmer-Citterich M. Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics 2009; 10:182. [PMID: 19527512 PMCID: PMC2704211 DOI: 10.1186/1471-2105-10-182] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Accepted: 06/15/2009] [Indexed: 12/11/2022] Open
Abstract
Background The structural analysis of protein ligand binding sites can provide information relevant for assigning functions to unknown proteins, to guide the drug discovery process and to infer relations among distant protein folds. Previous approaches to the comparative analysis of binding pockets have usually been focused either on the ligand or the protein component. Even though several useful observations have been made with these approaches they both have limitations. In the former case the analysis is restricted to binding pockets interacting with similar ligands, while in the latter it is difficult to systematically check whether the observed structural similarities have a functional significance. Results Here we propose a novel methodology that takes into account the structure of both the binding pocket and the ligand. We first look for local similarities in a set of binding pockets and then check whether the bound ligands, even if completely different, share a common fragment that can account for the presence of the structural motif. Thanks to this method we can identify structural motifs whose functional significance is explained by the presence of shared features in the interacting ligands. Conclusion The application of this method to a large dataset of binding pockets allows the identification of recurring protein motifs that bind specific ligand fragments, even in the context of molecules with a different overall structure. In addition some of these motifs are present in a high number of evolutionarily unrelated proteins.
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Affiliation(s)
- Gabriele Ausiello
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy.
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Characterization of YvcJ, a conserved P-loop-containing protein, and its implication in competence in Bacillus subtilis. J Bacteriol 2008; 191:1556-64. [PMID: 19074378 DOI: 10.1128/jb.01493-08] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The uncharacterized protein family UPF0042 of the Swiss-Prot database is predicted to be a member of the conserved group of bacterium-specific P-loop-containing proteins. Here we show that two of its members, YvcJ from Bacillus subtilis and YhbJ, its homologue from Escherichia coli, indeed bind and hydrolyze nucleotides. The cellular function of yvcJ was then addressed. In contrast to results recently obtained for E. coli, which indicated that yhbJ mutants strongly overproduced glucosamine-6-phosphate synthase (GlmS), comparison of the wild type with the yvcJ mutant of B. subtilis showed that GlmS expression was quite similar in the two strains. However, in mutants defective in yvcJ, the transformation efficiency and the fraction of cells that expressed competence were reduced. Furthermore, our data show that YvcJ positively controls the expression of late competence genes. The overexpression of comK or comS compensates for the decrease in competence of the yvcJ mutant. Our results show that even if YvcJ and YhbJ belong to the same family of P-loop-containing proteins, the deletion of corresponding genes has different consequences in B. subtilis and in E. coli.
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Gherardini PF, Helmer-Citterich M. Structure-based function prediction: approaches and applications. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 7:291-302. [PMID: 18599513 DOI: 10.1093/bfgp/eln030] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The ever increasing number of protein structures determined by structural genomic projects has spurred much interest in the development of methods for structure-based function prediction. Existing methods can be roughly classified in two groups: some use a comparative approach looking for the presence of structural motifs possibly associated with a known biochemical function. Other methods try to identify functional patches on the surface of a protein using only its physicochemical characteristics. This review will cover both kinds of approaches to structure-based function prediction as well as their use in real-world cases. The main issues and limitations in using protein structure to predict function will also be discussed. These are mainly: the assessment of the statistical significance of structural similarities and the extent to which these methods depend on the accuracy and availability of structural data.
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Affiliation(s)
- Pier Federico Gherardini
- Department of Biology, Centre for Molecular Bioinformatics, University of Tor Vergata, Rome, Italy.
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Ausiello G, Gherardini PF, Marcatili P, Tramontano A, Via A, Helmer-Citterich M. FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics 2008; 9 Suppl 2:S2. [PMID: 18387204 PMCID: PMC2323665 DOI: 10.1186/1471-2105-9-s2-s2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The occurrence of very similar structural motifs brought about by different parts of non homologous proteins is often indicative of a common function. Indeed, relatively small local structures can mediate binding to a common partner, be it a protein, a nucleic acid, a cofactor or a substrate. While it is relatively easy to identify short amino acid or nucleotide sequence motifs in a given set of proteins or genes, and many methods do exist for this purpose, much more challenging is the identification of common local substructures, especially if they are formed by non consecutive residues in the sequence. RESULTS Here we describe a publicly available tool, able to identify common structural motifs shared by different non homologous proteins in an unsupervised mode. The motifs can be as short as three residues and need not to be contiguous or even present in the same order in the sequence. Users can submit a set of protein structures deemed or not to share a common function (e.g. they bind similar ligands, or share a common epitope). The server finds and lists structural motifs composed of three or more spatially well conserved residues shared by at least three of the submitted structures. The method uses a local structural comparison algorithm to identify subsets of similar amino acids between each pair of input protein chains and a clustering procedure to group similarities shared among different structure pairs. CONCLUSIONS FunClust is fast, completely sequence independent, and does not need an a priori knowledge of the motif to be found. The output consists of a list of aligned structural matches displayed in both tabular and graphical form. We show here examples of its usefulness by searching for the largest common structural motifs in test sets of non homologous proteins and showing that the identified motifs correspond to a known common functional feature.
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Affiliation(s)
- Gabriele Ausiello
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome "Tor Vergata", Rome, Italy.
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Milner-White EJ, Russell MJ. Predicting the conformations of peptides and proteins in early evolution. A review article submitted to Biology Direct. Biol Direct 2008; 3:3. [PMID: 18226248 PMCID: PMC2241844 DOI: 10.1186/1745-6150-3-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Accepted: 01/28/2008] [Indexed: 01/26/2023] Open
Abstract
Considering that short, mainly heterochiral, polypeptides with a high glycine content are expected to have played a prominent role in evolution at the earliest stage of life before nucleic acids were available, we review recent knowledge about polypeptide three-dimensional structure to predict the types of conformations they would have adopted. The possible existence of such structures at this time leads to a consideration of their functional significance, and the consequences for the course of evolution. This article was reviewed by Bill Martin, Eugene Koonin and Nick Grishin.
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Sherrer RL, O'Donoghue P, Söll D. Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation. Nucleic Acids Res 2008; 36:1247-59. [PMID: 18174226 PMCID: PMC2275090 DOI: 10.1093/nar/gkm1134] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Selenocysteine (Sec)-decoding archaea and eukaryotes employ a unique route of Sec-tRNASec synthesis in which O-phosphoseryl-tRNASec kinase (PSTK) phosphorylates Ser-tRNASec to produce the O-phosphoseryl-tRNASec (Sep-tRNASec) substrate that Sep-tRNA:Sec-tRNA synthase (SepSecS) converts to Sec-tRNASec. This study presents a biochemical characterization of Methanocaldococcus jannaschii PSTK, including kinetics of Sep-tRNASec formation (Km for Ser-tRNASec of 40 nM and ATP of 2.6 mM). PSTK binds both Ser-tRNASec and tRNASec with high affinity (Kd values of 53 nM and 39 nM, respectively). The ATPase activity of PSTK may be activated via an induced fit mechanism in which binding of tRNASec specifically stimulates hydrolysis. Albeit with lower activity than ATP, PSTK utilizes GTP, CTP, UTP and dATP as phosphate-donors. Homology with related kinases allowed prediction of the ATPase active site, comprised of phosphate-binding loop (P-loop), Walker B and RxxxR motifs. Gly14, Lys17, Ser18, Asp41, Arg116 and Arg120 mutations resulted in enzymes with decreased activity highlighting the importance of these conserved motifs in PSTK catalysis both in vivo and in vitro. Phylogenetic analysis of PSTK in the context of its ‘DxTN’ kinase family shows that PSTK co-evolved precisely with SepSecS and indicates the presence of a previously unidentified PSTK in Plasmodium species.
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Affiliation(s)
- R Lynn Sherrer
- Department of Molecular Biophysics, Yale University, New Haven, CT 06520-8114, USA
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Via A, Peluso D, Gherardini PF, de Rinaldis E, Colombo T, Ausiello G, Helmer-Citterich M. 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. Nucleic Acids Res 2007; 35:W416-9. [PMID: 17488847 PMCID: PMC1933223 DOI: 10.1093/nar/gkm228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
3dLOGO is a web server for the identification and analysis of conserved protein 3D substructures. Given a set of residues in a PDB (Protein Data Bank) chain, the server detects the matching substructure(s) in a set of user-provided protein structures, generates a multiple structure alignment centered on the input substructures and highlights other residues whose structural conservation becomes evident after the defined superposition. Conserved residues are proposed to the user for highlighting functional areas, deriving refined structural motifs or building sequence patterns. Residue structural conservation can be visualized through an expressly designed Java application, 3dProLogo, which is a 3D implementation of a sequence logo. The 3dLOGO server, with related documentation, is available at http://3dlogo.uniroma2.it/
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Affiliation(s)
- Allegra Via
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy, Bioinformatics Group, I.R.B.M. P. Angeletti, MRL-Rome, Via Pontina Km, 30600 Pomezia, Italy, Center for Comparative Functional Genomics, Department of Biology, New York University, NY 10003, USA and Systems Biology Group - Max-Delbrück-Centrum für Molekulare Medizin, Berlin
- *To whom correspondence should be addressed. +39 067259 4324+39 067259 4314 Correspondence may also be addressed to Manuela Helmer-Citterich.
| | - Daniele Peluso
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy, Bioinformatics Group, I.R.B.M. P. Angeletti, MRL-Rome, Via Pontina Km, 30600 Pomezia, Italy, Center for Comparative Functional Genomics, Department of Biology, New York University, NY 10003, USA and Systems Biology Group - Max-Delbrück-Centrum für Molekulare Medizin, Berlin
| | - Pier Federico Gherardini
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy, Bioinformatics Group, I.R.B.M. P. Angeletti, MRL-Rome, Via Pontina Km, 30600 Pomezia, Italy, Center for Comparative Functional Genomics, Department of Biology, New York University, NY 10003, USA and Systems Biology Group - Max-Delbrück-Centrum für Molekulare Medizin, Berlin
| | - Emanuele de Rinaldis
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy, Bioinformatics Group, I.R.B.M. P. Angeletti, MRL-Rome, Via Pontina Km, 30600 Pomezia, Italy, Center for Comparative Functional Genomics, Department of Biology, New York University, NY 10003, USA and Systems Biology Group - Max-Delbrück-Centrum für Molekulare Medizin, Berlin
| | - Teresa Colombo
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy, Bioinformatics Group, I.R.B.M. P. Angeletti, MRL-Rome, Via Pontina Km, 30600 Pomezia, Italy, Center for Comparative Functional Genomics, Department of Biology, New York University, NY 10003, USA and Systems Biology Group - Max-Delbrück-Centrum für Molekulare Medizin, Berlin
| | - Gabriele Ausiello
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy, Bioinformatics Group, I.R.B.M. P. Angeletti, MRL-Rome, Via Pontina Km, 30600 Pomezia, Italy, Center for Comparative Functional Genomics, Department of Biology, New York University, NY 10003, USA and Systems Biology Group - Max-Delbrück-Centrum für Molekulare Medizin, Berlin
| | - Manuela Helmer-Citterich
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy, Bioinformatics Group, I.R.B.M. P. Angeletti, MRL-Rome, Via Pontina Km, 30600 Pomezia, Italy, Center for Comparative Functional Genomics, Department of Biology, New York University, NY 10003, USA and Systems Biology Group - Max-Delbrück-Centrum für Molekulare Medizin, Berlin
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Ausiello G, Peluso D, Via A, Helmer-Citterich M. Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites. BMC Bioinformatics 2007; 8 Suppl 1:S24. [PMID: 17430569 PMCID: PMC1885854 DOI: 10.1186/1471-2105-8-s1-s24] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background We performed an exhaustive search for local structural similarities in an ensemble of non-redundant protein functional sites. With the purpose of finding new examples of convergent evolution, we selected only those matching sites composed of structural regions whose residue order is inverted in the relative protein sequences. Results A novel case of local analogy was detected between members of the ABC transporter and of the HprK/P families in their ATP binding site. This case cannot be derived by events of circular permutation since the residues of one of the region pairs are located in reverse order in the sequence of the two protein families. One of the analogous binding sites, the one identified in HprK/P, is known to also bind pyrophosphate, which is used as preferred energy source in its kinase and phosphorylase activity. Conclusion The discovery of this striking molecular similarity, also associated to a functional similarity, may help in suggesting new experiments aimed at a deeper understanding of members of the ABC transporter family known to be involved in many serious human diseases.
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Affiliation(s)
- Gabriele Ausiello
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Daniele Peluso
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Allegra Via
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Manuela Helmer-Citterich
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome "Tor Vergata", Rome, Italy
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Bonet J, Caltabiano G, Khan AK, Johnston MA, Corbí C, Gómez A, Rovira X, Teyra J, Villà-Freixa J. The role of residue stability in transient protein-protein interactions involved in enzymatic phosphate hydrolysis. A computational study. Proteins 2006; 63:65-77. [PMID: 16374872 DOI: 10.1002/prot.20791] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Finding why protein-protein interactions (PPIs) are so specific can provide a valuable tool in a variety of fields. Statistical surveys of so-called transient complexes (like those relevant for signal transduction mechanisms) have shown a tendency of polar residues to participate in the interaction region. Following this scheme, residues in the unbound partners have to compete between interacting with water or interacting with other residues of the protein. On the other hand, several works have shown that the notion of active site electrostatic preorganization can be used to interpret the high efficiency in enzyme reactions. This preorganization can be related to the instability of the residues important for catalysis. In some enzymes, in addition, conformational changes upon binding to other proteins lead to an increase in the activity of the enzymatic partner. In this article the linear response approximation version of the semimacroscopic protein dipoles Langevin dipoles (PDLD/S-LRA) model is used to evaluate the stability of several residues in two phosphate hydrolysis enzymes upon complexation with their activating partners. In particular, the residues relevant for PPI and for phosphate hydrolysis in the CDK2/Cyclin A and Ras/GAP complexes are analyzed. We find that the evaluation of the stability of residues in these systems can be used to identify not only active site regions but it can also be used as a guide to locate "hot spots" for PPIs. We also show that conformational changes play a major role in positioning interfacing residues in a proper "energetic" orientation, ready to interact with the residues in the partner protein surface. Thus, we extend the preorganization theory to PPIs, extrapolating the results we obtained from the above-mentioned complexes to a more general case. We conclude that the correlation between stability of a residue in the surface and the likelihood that it participates in the interaction can be a general fact for transient PPIs.
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Affiliation(s)
- Jaume Bonet
- Computational Biochemistry and Biophysics Laboratory, Research Group on Biomedical Informatics (GRIB), IMIM/UPF, Barcelona, Spain
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Merelli I, Morra G, D'Agostino D, Clematis A, Milanesi L. High performance workflow implementation for protein surface characterization using grid technology. BMC Bioinformatics 2005; 6 Suppl 4:S19. [PMID: 16351745 PMCID: PMC1866389 DOI: 10.1186/1471-2105-6-s4-s19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background This study concerns the development of a high performance workflow that, using grid technology, correlates different kinds of Bioinformatics data, starting from the base pairs of the nucleotide sequence to the exposed residues of the protein surface. The implementation of this workflow is based on the Italian Grid.it project infrastructure, that is a network of several computational resources and storage facilities distributed at different grid sites. Methods Workflows are very common in Bioinformatics because they allow to process large quantities of data by delegating the management of resources to the information streaming. Grid technology optimizes the computational load during the different workflow steps, dividing the more expensive tasks into a set of small jobs. Results Grid technology allows efficient database management, a crucial problem for obtaining good results in Bioinformatics applications. The proposed workflow is implemented to integrate huge amounts of data and the results themselves must be stored into a relational database, which results as the added value to the global knowledge. Conclusion A web interface has been developed to make this technology accessible to grid users. Once the workflow has started, by means of the simplified interface, it is possible to follow all the different steps throughout the data processing. Eventually, when the workflow has been terminated, the different features of the protein, like the amino acids exposed on the protein surface, can be compared with the data present in the output database.
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Affiliation(s)
- Ivan Merelli
- Istituto di Tecnologie Biomediche (ITB – CNR), via F.lli Cervi, Segrate (Milano), Italy
| | - Giulia Morra
- Istituto di Tecnologie Biomediche (ITB – CNR), via F.lli Cervi, Segrate (Milano), Italy
| | - Daniele D'Agostino
- Istituto di Matematica Applicata e Tecnologie Informatiche (IMATI – CNR), via de Marini, Genova, Italy
| | - Andrea Clematis
- Istituto di Matematica Applicata e Tecnologie Informatiche (IMATI – CNR), via de Marini, Genova, Italy
| | - Luciano Milanesi
- Istituto di Tecnologie Biomediche (ITB – CNR), via F.lli Cervi, Segrate (Milano), Italy
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Li S, Zhang QR, Xu WH, Schooley DA. Juvenile hormone diol kinase, a calcium-binding protein with kinase activity, from the silkworm, Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2005; 35:1235-48. [PMID: 16203205 DOI: 10.1016/j.ibmb.2005.06.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Revised: 06/16/2005] [Accepted: 06/17/2005] [Indexed: 05/04/2023]
Abstract
Juvenile hormone (JH) diol kinase (JHDK) is an important enzyme involved in the JH degradation pathway. Bombyx mori (Bommo)-JHDK cDNA (637bp) contains an open reading frame encoding a 183-amino acid protein, which reveals a high degree of identity to the two previously reported JHDKs. JHDK is similar to GTP-binding proteins with three conserved sequence elements involved in purine nucleotide binding, contains eight alpha-helices and three EF-hand motifs, and resembles the three-dimensional model of 2SCP and some other calcium-binding proteins. The Bommo-JHDK gene has only a single copy in the silkworm haploid genome, contains only one exon, and its 5'-upstream sequence does not have a JH response element. Although Bommo-JHDK is highly expressed in the gut of the silkworm, its mRNA expression remains at a constant level during larval development suggesting this enzyme is constitutive and not regulated by JH, at least at the transcriptional level. Recombinant Bommo-JHDK catalyzed the conversion of 10S-JH diol into JH diol phosphate, confirming its enzymatic function. Recombinant enzyme formed a dimer and had biochemical characteristics similar to other JHDKs. Bommo-JHDK, a calcium-binding protein with kinase activity, provides unique insights on how JH levels are regulated in the silkworm.
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Affiliation(s)
- Sheng Li
- Institute of Plant Physiology and Ecology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, PR China.
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Miyazono KI, Sawano Y, Tanokura M. Crystal structure and structural stability of acylphosphatase from hyperthermophilic archaeon Pyrococcus horikoshii OT3. Proteins 2005; 61:196-205. [PMID: 16080154 DOI: 10.1002/prot.20535] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
To elucidate the structural basis for the high stability of acylphosphatase (AcP) from Pyrococcus horikoshii OT3, we determined its crystal structure at 1.72 A resolution. P. horikoshii AcP possesses high stability despite its approximately 30% sequence identity with eukaryotic enzymes that have moderate thermostability. The overall fold of P. horikoshii AcP was very similar to the structures of eukaryotic counterparts. The crystal structure of P. horikoshii AcP shows the same fold betaalphabetabetaalphabeta topology and the conserved putative catalytic residues as observed in eukaryotic enzymes. Comparison with the crystal structure of bovine common-type AcP and that of D. melanogaster AcP (AcPDro2) as representative of eukaryotic AcP revealed some significant characteristics in P. horikoshii AcP that likely play important roles in structural stability: (1) shortening of the flexible N-terminal region and long loop; (2) an increased number of ion pairs on the protein surface; (3) stabilization of the loop structure by hydrogen bonds. In P. horikoshii AcP, two ion pair networks were observed one located in the loop structure positioned near the C-terminus, and other on the beta-sheet. The importance of ion pairs for structural stability was confirmed by site-directed mutation and denaturation induced by guanidium chloride.
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Affiliation(s)
- Ken-ichi Miyazono
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
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Merdanovic M, Sauer E, Reidl J. Coupling of NAD+ biosynthesis and nicotinamide ribosyl transport: characterization of NadR ribonucleotide kinase mutants of Haemophilus influenzae. J Bacteriol 2005; 187:4410-20. [PMID: 15968050 PMCID: PMC1151767 DOI: 10.1128/jb.187.13.4410-4420.2005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previously, we characterized a pathway necessary for the processing of NAD+ and for uptake of nicotinamide riboside (NR) in Haemophilus influenzae. Here we report on the role of NadR, which is essential for NAD+ utilization in this organism. Different NadR variants with a deleted ribonucleotide kinase domain or with a single amino acid change were characterized in vitro and in vivo with respect to cell viability, ribonucleotide kinase activity, and NR transport. The ribonucleotide kinase mutants were viable only in a nadV+ (nicotinamide phosphoribosyltransferase) background, indicating that the ribonucleotide kinase domain is essential for cell viability in H. influenzae. Mutations located in the Walker A and B motifs and the LID region resulted in deficiencies in both NR phosphorylation and NR uptake. The ribonucleotide kinase function of NadR was found to be feedback controlled by NAD+ under in vitro conditions and by NAD+ utilization in vivo. Taken together, our data demonstrate that the NR phosphorylation step is essential for both NR uptake across the inner membrane and NAD+ synthesis and is also involved in controlling the NAD+ biosynthesis rate.
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Affiliation(s)
- Melisa Merdanovic
- Institut für Hygiene und Mikrobiologie, Universität Würzburg, Josef Schneider Str. 2, E1, 97080 Würzburg, Germany
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Ferrè F, Ausiello G, Zanzoni A, Helmer-Citterich M. Functional annotation by identification of local surface similarities: a novel tool for structural genomics. BMC Bioinformatics 2005; 6:194. [PMID: 16076399 PMCID: PMC1190158 DOI: 10.1186/1471-2105-6-194] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Accepted: 08/02/2005] [Indexed: 12/03/2022] Open
Abstract
Background Protein function is often dependent on subsets of solvent-exposed residues that may exist in a similar three-dimensional configuration in non homologous proteins thus having different order and/or spacing in the sequence. Hence, functional annotation by means of sequence or fold similarity is not adequate for such cases. Results We describe a method for the function-related annotation of protein structures by means of the detection of local structural similarity with a library of annotated functional sites. An automatic procedure was used to annotate the function of local surface regions. Next, we employed a sequence-independent algorithm to compare exhaustively these functional patches with a larger collection of protein surface cavities. After tuning and validating the algorithm on a dataset of well annotated structures, we applied it to a list of protein structures that are classified as being of unknown function in the Protein Data Bank. By this strategy, we were able to provide functional clues to proteins that do not show any significant sequence or global structural similarity with proteins in the current databases. Conclusion This method is able to spot structural similarities associated to function-related similarities, independently on sequence or fold resemblance, therefore is a valuable tool for the functional analysis of uncharacterized proteins. Results are available at
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Affiliation(s)
- Fabrizio Ferrè
- Boston College, Biology Department, Chestnut Hill MA, USA
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Italy
| | - Gabriele Ausiello
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Italy
| | - Andreas Zanzoni
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Italy
| | - Manuela Helmer-Citterich
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Italy
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Fernandez-Fuentes N, Hermoso A, Espadaler J, Querol E, Aviles FX, Oliva B. Classification of common functional loops of kinase super-families. Proteins 2004; 56:539-55. [PMID: 15229886 DOI: 10.1002/prot.20136] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A structural classification of loops has been obtained from a set of 141 protein structures classified as kinases. A total of 1813 loops was classified into 133 subclasses (9 betabeta(links), 15 betabeta(hairpins), 31 alpha-alpha, 46 alpha-beta and 32 beta-alpha). Functional information and specific features relating subclasses and function were included in the classification. Functional loops such as the P-loop (shared by different folds) or the Gly-rich-loop, among others, were classified into structural motifs. As a result, a common mechanism of catalysis and substrate binding was proved for most kinases. Additionally, the multiple-alignment of loop sequences made within each subclass was shown to be useful for comparative modeling of kinase loops. The classification is summarized in a kinase loop database located at http://sbi.imim.es/archki.
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Affiliation(s)
- Narcis Fernandez-Fuentes
- Institut de Biotecnologia i Biomedicina and Department de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
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45
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Brakoulias A, Jackson RM. Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching. Proteins 2004; 56:250-60. [PMID: 15211509 DOI: 10.1002/prot.20123] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A method is described for the rapid comparison of protein binding sites using geometric matching to detect similar three-dimensional structure. The geometric matching detects common atomic features through identification of the maximum common sub-graph or clique. These features are not necessarily evident from sequence or from global structural similarity giving additional insight into molecular recognition not evident from current sequence or structural classification schemes. Here we use the method to produce an all-against-all comparison of phosphate binding sites in a number of different nucleotide phosphate-binding proteins. The similarity search is combined with clustering of similar sites to allow a preliminary structural classification. Clustering by site similarity produces a classification of binding sites for the 476 representative local environments producing ten main clusters representing half of the representative environments. The similarities make sense in terms of both structural and functional classification schemes. The ten main clusters represent a very limited number of unique structural binding motifs for phosphate. These are the structural P-loop, di-nucleotide binding motif [FAD/NAD(P)-binding and Rossman-like fold] and FAD-binding motif. Similar classification schemes for nucleotide binding proteins have also been arrived at independently by others using different methods.
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Affiliation(s)
- Andreas Brakoulias
- Department of Biochemistry & Molecular Biology, University College London, Gower Street, London, England
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46
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Sodhi JS, Bryson K, McGuffin LJ, Ward JJ, Wernisch L, Jones DT. Predicting metal-binding site residues in low-resolution structural models. J Mol Biol 2004; 342:307-20. [PMID: 15313626 DOI: 10.1016/j.jmb.2004.07.019] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2004] [Revised: 07/06/2004] [Accepted: 07/08/2004] [Indexed: 11/26/2022]
Abstract
The accurate prediction of the biochemical function of a protein is becoming increasingly important, given the unprecedented growth of both structural and sequence databanks. Consequently, computational methods are required to analyse such data in an automated manner to ensure genomes are annotated accurately. Protein structure prediction methods, for example, are capable of generating approximate structural models on a genome-wide scale. However, the detection of functionally important regions in such crude models, as well as structural genomics targets, remains an extremely important problem. The method described in the current study, MetSite, represents a fully automatic approach for the detection of metal-binding residue clusters applicable to protein models of moderate quality. The method involves using sequence profile information in combination with approximate structural data. Several neural network classifiers are shown to be able to distinguish metal sites from non-sites with a mean accuracy of 94.5%. The method was demonstrated to identify metal-binding sites correctly in LiveBench targets where no obvious metal-binding sequence motifs were detectable using InterPro. Accurate detection of metal sites was shown to be feasible for low-resolution predicted structures generated using mGenTHREADER where no side-chain information was available. High-scoring predictions were observed for a recently solved hypothetical protein from Haemophilus influenzae, indicating a putative metal-binding site.
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Affiliation(s)
- Jaspreet Singh Sodhi
- Bioinformatics Unit, Department of Computer Science, University College London, Gower Street, WC1E 6BT, UK
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47
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Hou Y, Pazour GJ, Witman GB. A dynein light intermediate chain, D1bLIC, is required for retrograde intraflagellar transport. Mol Biol Cell 2004; 15:4382-94. [PMID: 15269286 PMCID: PMC519134 DOI: 10.1091/mbc.e04-05-0377] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2004] [Revised: 07/09/2004] [Accepted: 07/12/2004] [Indexed: 11/11/2022] Open
Abstract
Intraflagellar transport (IFT), the bidirectional movement of particles along flagella, is essential for flagellar assembly. The motor for retrograde IFT in Chlamydomonas is cytoplasmic dynein 1b, which contains the dynein heavy chain DHC1b and the light intermediate chain (LIC) D1bLIC. To investigate a possible role for the LIC in IFT, we identified a d1blic mutant. DHC1b is reduced in the mutant, indicating that D1bLIC is important for stabilizing dynein 1b. The mutant has variable length flagella that accumulate IFT-particle proteins, indicative of a defect in retrograde IFT. Interestingly, the remaining DHC1b is normally distributed in the mutant flagella, strongly suggesting that the defect is in binding of cargo to the retrograde motor rather than in motor activity per se. Cell growth and Golgi apparatus localization and morphology are normal in the mutant, indicating that D1bLIC is involved mainly in retrograde IFT. Like mammalian LICs, D1bLIC has a phosphate-binding domain (P-loop) at its N-terminus. To investigate the function of this conserved domain, d1blic mutant cells were transformed with constructs designed to express D1bLIC proteins with mutated P-loops. The constructs rescued the mutant cells to a wild-type phenotype, indicating that the function of D1bLIC in IFT is independent of its P-loop.
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Affiliation(s)
- Yuqing Hou
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655,USA
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Modarressi MH, Cheng M, Tarnasky HA, Lamarche-Vane N, de Rooij DG, Ruan Y, van der Hoorn FA. A novel testicular RhoGAP-domain protein induces apoptosis. Biol Reprod 2004; 71:1980-90. [PMID: 15306557 PMCID: PMC3158803 DOI: 10.1095/biolreprod.104.032805] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The GTPase-activating proteins (GAPs) accelerate the hydrolysis of GTP to GDP by small GTPases. The GTPases play diverse roles in many cellular processes, including proliferation, cell motility, endocytosis, nuclear import/export, and nuclear membrane formation. Little is known about GAP-domain proteins in spermatogenesis. We isolated a novel RhoGAP domain-containing tGAP1 protein from male germ cells that exhibits unusual properties. The tGAP1 is expressed at low levels in early spermatogonia. Robust transcription initiates in midpachytene spermatocytes and continues after meiosis. The 175-kDa tGAP1 protein localizes to the cytoplasm of spermatocytes and to the cytoplasm and nucleus in spermatids. The protein contains four GAP domain-related sequences, in contrast to all other GAP proteins that harbor one such domain. No activity toward RhoA, Rac1, or Cdc42 could be detected. Results of transfection studies in various somatic cells indicated that low-level tGAP1 expression significantly slows down the cell cycle. Expression of higher levels of tGAP1 by infection of somatic cells with recombinant adenoviruses demonstrated that tGAP1 efficiently induces apoptosis, which to our knowledge is the first such demonstration for a RhoGAP protein. Based on its subcellular location in spermatids and its activity, tGAP1 may play a role in nuclear import/export.
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Affiliation(s)
- M. Hossein Modarressi
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Min Cheng
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Heide A. Tarnasky
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Nathalie Lamarche-Vane
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada H3A 2T5
| | - Dirk G. de Rooij
- Departments Endocrinology, Faculty of Biology and of Cell Biology, UMCU, Utrecht University, Utrecht, The Netherlands
| | - Yibing Ruan
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Frans A. van der Hoorn
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- Correspondence: Frans A. van der Hoorn, Department of Biochemistry & Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 4N1. FAX: 403 210 8109;
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Via A, Helmer-Citterich M. A structural study for the optimisation of functional motifs encoded in protein sequences. BMC Bioinformatics 2004; 5:50. [PMID: 15119965 PMCID: PMC420233 DOI: 10.1186/1471-2105-5-50] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Accepted: 04/30/2004] [Indexed: 11/23/2022] Open
Abstract
Background A large number of PROSITE patterns select false positives and/or miss known true positives. It is possible that – at least in some cases – the weak specificity and/or sensitivity of a pattern is due to the fact that one, or maybe more, functional and/or structural key residues are not represented in the pattern. Multiple sequence alignments are commonly used to build functional sequence patterns. If residues structurally conserved in proteins sharing a function cannot be aligned in a multiple sequence alignment, they are likely to be missed in a standard pattern construction procedure. Results Here we present a new procedure aimed at improving the sensitivity and/ or specificity of poorly-performing patterns. The procedure can be summarised as follows: 1. residues structurally conserved in different proteins, that are true positives for a pattern, are identified by means of a computational technique and by visual inspection. 2. the sequence positions of the structurally conserved residues falling outside the pattern are used to build extended sequence patterns. 3. the extended patterns are optimised on the SWISS-PROT database for their sensitivity and specificity. The method was applied to eight PROSITE patterns. Whenever structurally conserved residues are found in the surface region close to the pattern (seven out of eight cases), the addition of information inferred from structural analysis is shown to improve pattern selectivity and in some cases selectivity and sensitivity as well. In some of the cases considered the procedure allowed the identification of functionally interesting residues, whose biological role is also discussed. Conclusion Our method can be applied to any type of functional motif or pattern (not only PROSITE ones) which is not able to select all and only the true positive hits and for which at least two true positive structures are available. The computational technique for the identification of structurally conserved residues is already available on request and will be soon accessible on our web server. The procedure is intended for the use of pattern database curators and of scientists interested in a specific protein family for which no specific or selective patterns are yet available.
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Affiliation(s)
- Allegra Via
- Centre for Molecular Bioinformatics, Dept. of Biology, University of Rome Tor Vergata, Rome (Italy)
| | - Manuela Helmer-Citterich
- Centre for Molecular Bioinformatics, Dept. of Biology, University of Rome Tor Vergata, Rome (Italy)
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50
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Focia PJ, Alam H, Lu T, Ramirez UD, Freymann DM. Novel protein and Mg2+ configurations in the Mg2+GDP complex of the SRP GTPase ffh. Proteins 2004; 54:222-30. [PMID: 14696184 PMCID: PMC3540803 DOI: 10.1002/prot.10598] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Ffh is the signal sequence recognition and targeting subunit of the prokaryotic signal recognition particle (SRP). Previous structural studies of the NG GTPase domain of Ffh demonstrated magnesium-dependent and magnesium-independent binding conformations for GDP and GMPPNP that are believed to reflect novel mechanisms for exchange and activation in this member of the GTPase superfamily. The current study of the NG GTPase bound to Mg(2+)GDP reveals two new binding conformations-in the first the magnesium interactions are similar to those seen previously, however, the protein undergoes a conformational change that brings a conserved aspartate into its second coordination sphere. In the second, the protein conformation is similar to that seen previously, but the magnesium coordination sphere is disrupted so that only five oxygen ligands are present. The loss of the coordinating water molecule, at the position that would be occupied by the oxygen of the gamma-phosphate of GTP, is consistent with that position being privileged for exchange during phosphate release. The available structures of the GDP-bound protein provide a series of structural snapshots that illuminate steps along the pathway of GDP release following GTP hydrolysis.
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Affiliation(s)
| | | | | | | | - Douglas M. Freymann
- Correspondence to: Douglas M. Freymann, Department of Molecular Pharmacology & Biological Chemistry, Northwestern University Medical School, 303 E. Chicago Avenue, Chicago, Illinois 60611.
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