51
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Singh A, Singh A, Grover S, Pandey B, Kumari A, Grover A. Wild-type catalase peroxidase vs G279D mutant type: Molecular basis of Isoniazid drug resistance in Mycobacterium tuberculosis. Gene 2018; 641:226-234. [DOI: 10.1016/j.gene.2017.10.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/16/2017] [Indexed: 11/29/2022]
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52
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Aggarwal M, Singh A, Grover S, Pandey B, Kumari A, Grover A. Role of pncA gene mutations W68R and W68G in pyrazinamide resistance. J Cell Biochem 2017; 119:2567-2578. [PMID: 28980723 DOI: 10.1002/jcb.26420] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/03/2017] [Indexed: 12/12/2022]
Abstract
Mycobacterium tuberculosis (Mtb) resistance toward anti-tuberculosis drugs is a widespread problem. Pyrazinamide (PZA) is a first line antitubercular drug that kills semi-dormant bacilli when converted into its activated form, that is, pyrazinoic acid (POA) by Pyrazinamidase (PZase) enzyme coded by pncA gene. In this study, we conducted several analyses on native and mutant structures (W68R, W68G) of PZase before and after docking with the PZA drug to explore the molecular mechanism behind PZA resistance caused due to pncA mutations. Structural changes caused by mutations were studied with respect to their effects on functionality of protein. Docking was performed to analyze the protein-drug binding and comparative analysis was done to observe how the mutations affect drug binding affinity and binding site on protein. Native PZase protein was observed to have the maximum binding affinity in terms of docking score as well as shape complementarity in comparison to the mutant forms. Molecular dynamics simulation analyses showed that mutation in the 68th residue of protein results in a structural change at its active site which further affects the biological function of protein, that is, conversion of PZA to POA. Mutations in the protein thereby led to PZA resistance in the bacterium due to the inefficient binding.
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Affiliation(s)
- Mansi Aggarwal
- Ami, ty Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Aditi Singh
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Department of Biotechnology, TERI University, Vasant Kunj, New Delhi, India
| | - Sonam Grover
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Bharati Pandey
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Anchala Kumari
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Department of Biotechnology, TERI University, Vasant Kunj, New Delhi, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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53
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García-Castellanos R, Nielsen NS, Runager K, Thøgersen IB, Lukassen MV, Poulsen ET, Goulas T, Enghild JJ, Gomis-Rüth FX. Structural and Functional Implications of Human Transforming Growth Factor β-Induced Protein, TGFBIp, in Corneal Dystrophies. Structure 2017; 25:1740-1750.e2. [PMID: 28988748 DOI: 10.1016/j.str.2017.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/02/2017] [Accepted: 09/01/2017] [Indexed: 12/31/2022]
Abstract
A major cause of visual impairment, corneal dystrophies result from accumulation of protein deposits in the cornea. One of the proteins involved is transforming growth factor β-induced protein (TGFBIp), an extracellular matrix component that interacts with integrins but also produces corneal deposits when mutated. Human TGFBIp is a multi-domain 683-residue protein, which contains one CROPT domain and four FAS1 domains. Its structure spans ∼120 Å and reveals that vicinal domains FAS1-1/FAS1-2 and FAS1-3/FAS1-4 tightly interact in an equivalent manner. The FAS1 domains are sandwiches of two orthogonal four-stranded β sheets decorated with two three-helix insertions. The N-terminal FAS1 dimer forms a compact moiety with the structurally novel CROPT domain, which is a five-stranded all-β cysteine-knot solely found in TGFBIp and periostin. The overall TGFBIp architecture discloses regions for integrin binding and that most dystrophic mutations cluster at both molecule ends, within domains FAS1-1 and FAS1-4.
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Affiliation(s)
- Raquel García-Castellanos
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence), Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, c/Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain
| | - Nadia Sukusu Nielsen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej, 10, 8000 Aarhus C, Denmark
| | - Kasper Runager
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej, 10, 8000 Aarhus C, Denmark
| | - Ida B Thøgersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej, 10, 8000 Aarhus C, Denmark
| | - Marie V Lukassen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej, 10, 8000 Aarhus C, Denmark
| | - Ebbe T Poulsen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej, 10, 8000 Aarhus C, Denmark
| | - Theodoros Goulas
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence), Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, c/Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej, 10, 8000 Aarhus C, Denmark
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence), Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, c/Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain.
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54
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Ka D, Hong S, Jeong U, Jeong M, Suh N, Suh JY, Bae E. Structural and dynamic insights into the role of conformational switching in the nuclease activity of the Xanthomonas albilineans Cas2 in CRISPR-mediated adaptive immunity. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:054701. [PMID: 28612041 PMCID: PMC5438308 DOI: 10.1063/1.4984052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/11/2017] [Indexed: 06/07/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins constitute a microbial, adaptive immune system countering invading nucleic acids. Cas2 is a universal Cas protein found in all types of CRISPR-Cas systems, and its role is implicated in new spacer acquisition into CRISPR loci. In subtype I-C CRISPR-Cas systems, Cas2 proteins are metal-dependent double-stranded DNA (dsDNA) nucleases, and a pH-dependent conformational transition has been proposed as a prerequisite for catalytic action. Here, we report the crystal structure of Xanthomonas albilineans Cas2 (XaCas2) and provide experimental evidence of a pH-dependent conformational change during functional activation. XaCas2 crystallized at an acidic pH represented a catalytically inactive conformational state in which two Asp8 residues were too far apart to coordinate a single catalytic metal ion. Consistently, XaCas2 exhibited dsDNA nuclease activity only under neutral and basic conditions. Despite the overall structural similarity of the two protomers, significant conformational heterogeneity was evident in the putative hinge regions, suggesting that XaCas2 engages in hinge-bending conformational switching. The presence of a Trp residue in the hinge region enabled the investigation of hinge dynamics by fluorescence spectroscopy. The pH dependence of the fluorescence intensity overlapped precisely with that of nuclease activity. Mutational analyses further suggested that conformational activation proceeded via a rigid-body hinge-bending motion as both D8E and hinge mutations significantly reduced nuclease activity. Together, our results reveal strong correlations between the conformational states, catalytic activity, and hinge dynamics of XaCas2, and provide structural and dynamic insights into the conformational activation of the nuclease function of Cas2.
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Affiliation(s)
- Donghyun Ka
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Suji Hong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Ugeene Jeong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Migyeong Jeong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Nayoung Suh
- Department of Pharmaceutical Engineering, Soon Chun Hyang University, Asan 31538, South Korea
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55
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Lv D, Gong W, Zhang Y, Liu Y, Li C. A coarse-grained method to predict the open-to-closed behavior of glutamine binding protein. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.05.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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56
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Parker ML, Ramaswamy R, van Gordon K, Powell CJ, Bosch J, Boulanger MJ. The structure of Plasmodium falciparum 3D7_0606800 reveals a bi-lobed architecture that supports re-annotation as a Venus Flytrap protein. Protein Sci 2017; 26:1878-1885. [PMID: 28681555 DOI: 10.1002/pro.3218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/20/2017] [Accepted: 06/29/2017] [Indexed: 12/11/2022]
Abstract
Plasmodium falciparum, the causative agent of malaria, employs a diverse array of surface displayed proteins to promote dissemination and establish infection in the human host. Of these, Pf3D7_0606800 is highly immunogenic and has been designated a potential top 10 candidate for inclusion in a multicomponent malarial vaccine. The role of Pf3D7_0606800 in parasite biology, however, is unknown and its characterization has been complicated by a lack of sequence identity with proteins of known structure or function. Towards elucidating Pf3D7_0606800 function, we determined its structure to a resolution of 2.35 Å using selenium single wavelength anomalous dispersion. A bi-lobed architecture displays the core structural hallmarks of Venus Flytrap (VFT) proteins prompting us to re-annotate Pf3D7_0606800 as PfVFT1. Structural analysis further revealed an extended inter-lobe groove that, when interrogated by molecular docking, appears well suited to bind peptide-based ligands. Collectively, our structural characterization of the highly antigenic P. falciparum surface protein PfVFT1 provides intriguing functional insight and establishes a structural template that could prove valuable for malaria vaccine engineering studies.
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Affiliation(s)
- Michelle L Parker
- Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, V8W 3P6, Canada
| | - Raghavendran Ramaswamy
- Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, V8W 3P6, Canada
| | - Kyle van Gordon
- Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, V8W 3P6, Canada
| | - Cameron J Powell
- Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, V8W 3P6, Canada
| | - Jürgen Bosch
- Pediatric Pulmonology Division, Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio.,InterRayBio, LLC, Baltimore, Maryland
| | - Martin J Boulanger
- Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, V8W 3P6, Canada
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57
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Goulas T, Ksiazek M, Garcia-Ferrer I, Sochaj-Gregorczyk AM, Waligorska I, Wasylewski M, Potempa J, Gomis-Rüth FX. A structure-derived snap-trap mechanism of a multispecific serpin from the dysbiotic human oral microbiome. J Biol Chem 2017; 292:10883-10898. [PMID: 28512127 PMCID: PMC5491774 DOI: 10.1074/jbc.m117.786533] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/04/2017] [Indexed: 10/19/2022] Open
Abstract
Enduring host-microbiome relationships are based on adaptive strategies within a particular ecological niche. Tannerella forsythia is a dysbiotic member of the human oral microbiome that inhabits periodontal pockets and contributes to chronic periodontitis. To counteract endopeptidases from the host or microbial competitors, T. forsythia possesses a serpin-type proteinase inhibitor called miropin. Although serpins from animals, plants, and viruses have been widely studied, those from prokaryotes have received only limited attention. Here we show that miropin uses the serpin-type suicidal mechanism. We found that, similar to a snap trap, the protein transits from a metastable native form to a relaxed triggered or induced form after cleavage of a reactive-site target bond in an exposed reactive-center loop. The prey peptidase becomes covalently attached to the inhibitor, is dragged 75 Å apart, and is irreversibly inhibited. This coincides with a large conformational rearrangement of miropin, which inserts the segment upstream of the cleavage site as an extra β-strand in a central β-sheet. Standard serpins possess a single target bond and inhibit selected endopeptidases of particular specificity and class. In contrast, miropin uniquely blocked many serine and cysteine endopeptidases of disparate architecture and substrate specificity owing to several potential target bonds within the reactive-center loop and to plasticity in accommodating extra β-strands of variable length. Phylogenetic studies revealed a patchy distribution of bacterial serpins incompatible with a vertical descent model. This finding suggests that miropin was acquired from the host through horizontal gene transfer, perhaps facilitated by the long and intimate association of T. forsythia with the human gingiva.
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Affiliation(s)
- Theodoros Goulas
- From the Proteolysis Lab, Structural Biology Unit, María de Maeztu Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Spain
| | - Miroslaw Ksiazek
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology and
- the Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - Irene Garcia-Ferrer
- From the Proteolysis Lab, Structural Biology Unit, María de Maeztu Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Spain
| | - Alicja M Sochaj-Gregorczyk
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology and
- the Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland, and
| | - Irena Waligorska
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology and
| | - Marcin Wasylewski
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology and
| | - Jan Potempa
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology and
- the Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - F Xavier Gomis-Rüth
- From the Proteolysis Lab, Structural Biology Unit, María de Maeztu Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Spain,
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58
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Histone-binding of DPF2 mediates its repressive role in myeloid differentiation. Proc Natl Acad Sci U S A 2017; 114:6016-6021. [PMID: 28533407 DOI: 10.1073/pnas.1700328114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Double plant homeodomain finger 2 (DPF2) is a highly evolutionarily conserved member of the d4 protein family that is ubiquitously expressed in human tissues and was recently shown to inhibit the myeloid differentiation of hematopoietic stem/progenitor and acute myelogenous leukemia cells. Here, we present the crystal structure of the tandem plant homeodomain finger domain of human DPF2 at 1.6-Å resolution. We show that DPF2 interacts with the acetylated tails of both histones 3 and 4 via bipartite binding pockets on the DPF2 surface. Blocking these interactions through targeted mutagenesis of DPF2 abolishes its recruitment to target chromatin regions as well as its ability to prevent myeloid differentiation in vivo. Our findings suggest that the histone binding of DPF2 plays an important regulatory role in the transcriptional program that drives myeloid differentiation.
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59
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Liao TJ, Jang H, Tsai CJ, Fushman D, Nussinov R. The dynamic mechanism of RASSF5 and MST kinase activation by Ras. Phys Chem Chem Phys 2017; 19:6470-6480. [PMID: 28197608 PMCID: PMC5381522 DOI: 10.1039/c6cp08596b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
As a tumor suppressor, RASSF5 (NORE1A) activates MST1/2 thereby modulating the Hippo pathway. Structurally, activation involves RASSF5 and MST1/2 swapping their SARAH domains to form a SARAH heterodimer. This exposes the MST1/2 kinase domain which homodimerizes, leading to trans-autophosphorylation. The SARAH-SARAH interaction shifts RASSF5 away from its autoinhibited state and relieves MST1/2 autoinhibition. Separate crystal structures are available for the RA (Ras association) domain and SARAH dimer, where SARAH is a long straight α-helix. Using all-atom molecular dynamics simulations, we modeled the RASSF5 RA with a covalently connected SARAH to elucidate the dynamic mechanism of how SARAH mediates between autoinhibition and Ras triggered-activation. Our results show that in inactive RASSF5 the RA domain retains SARAH, yielding a self-associated conformation in which SARAH is in a kinked α-helical motif that increases the binding interface. When RASSF5 binds K-Ras4B-GTP, the equilibrium shifts toward SARAH's interacting with MST. Since the RA/SARAH affinity is relatively low, whereas that of the SARAH heterodimer is in the nM range, we suggest that RASSF5 exerts its tumor suppressor action through competition with other Ras effectors for Ras effector binding site, as well as coincidentally its recruitment to the membrane to help MST activation. Thus, SARAH plays a key role in RASSF5's tumor suppression action by linking the two major pathways in tumor cell proliferation: Ras and the MAPK (tumor cell proliferation-promoting) pathway, and the Hippo (tumor cell proliferation-suppressing) pathway.
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Affiliation(s)
- Tsung-Jen Liao
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA. and Biophysics Program, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
| | - David Fushman
- Biophysics Program, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA and Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA. and Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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60
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Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1. Proc Natl Acad Sci U S A 2017; 114:1560-1565. [PMID: 28143926 DOI: 10.1073/pnas.1615310114] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The basic helix-loop-helix PAS domain (bHLH-PAS) transcription factor CLOCK:BMAL1 (brain and muscle Arnt-like protein 1) sits at the core of the mammalian circadian transcription/translation feedback loop. Precise control of CLOCK:BMAL1 activity by coactivators and repressors establishes the ∼24-h periodicity of gene expression. Formation of a repressive complex, defined by the core clock proteins cryptochrome 1 (CRY1):CLOCK:BMAL1, plays an important role controlling the switch from repression to activation each day. Here we show that CRY1 binds directly to the PAS domain core of CLOCK:BMAL1, driven primarily by interaction with the CLOCK PAS-B domain. Integrative modeling and solution X-ray scattering studies unambiguously position a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous to the antenna chromophore-binding pocket of photolyase. CRY1 docks onto the transcription factor alongside the PAS domains, extending above the DNA-binding bHLH domain. Single point mutations at the interface on either CRY1 or CLOCK disrupt formation of the ternary complex, highlighting the importance of this interface for direct regulation of CLOCK:BMAL1 activity by CRY1.
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61
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Comparative Study of Elastic Network Model and Protein Contact Network for Protein Complexes: The Hemoglobin Case. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2483264. [PMID: 28243596 PMCID: PMC5294226 DOI: 10.1155/2017/2483264] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 11/17/2016] [Accepted: 12/20/2016] [Indexed: 01/12/2023]
Abstract
The overall topology and interfacial interactions play key roles in understanding structural and functional principles of protein complexes. Elastic Network Model (ENM) and Protein Contact Network (PCN) are two widely used methods for high throughput investigation of structures and interactions within protein complexes. In this work, the comparative analysis of ENM and PCN relative to hemoglobin (Hb) was taken as case study. We examine four types of structural and dynamical paradigms, namely, conformational change between different states of Hbs, modular analysis, allosteric mechanisms studies, and interface characterization of an Hb. The comparative study shows that ENM has an advantage in studying dynamical properties and protein-protein interfaces, while PCN is better for describing protein structures quantitatively both from local and from global levels. We suggest that the integration of ENM and PCN would give a potential but powerful tool in structural systems biology.
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62
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Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model. Molecules 2017; 22:molecules22010145. [PMID: 28275219 PMCID: PMC6155889 DOI: 10.3390/molecules22010145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 01/10/2023] Open
Abstract
DNA is a fundamental component of living systems where it plays a crucial role at both functional and structural level. The programmable properties of DNA make it an interesting building block for the construction of nanostructures. However, molecular mechanisms for the arrangement of these well-defined DNA assemblies are not fully understood. In this paper, the intrinsic dynamics of a DNA octahedron has been investigated by using two types of Elastic Network Models (ENMs). The application of ENMs to DNA nanocages include the analysis of the intrinsic flexibilities of DNA double-helices and hinge sites through the calculation of the square fluctuations, as well as the intrinsic collective dynamics in terms of cross-collective map calculation coupled with global motions analysis. The dynamics profiles derived from ENMs have then been evaluated and compared with previous classical molecular dynamics simulation trajectories. The results presented here revealed that ENMs can provide useful insights into the intrinsic dynamics of large DNA nanocages and represent a useful tool in the field of structural DNA nanotechnology.
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63
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Hamzeh-Mivehroud M, Sokouti B, Dastmalchi S. Molecular Docking at a Glance. Oncology 2017. [DOI: 10.4018/978-1-5225-0549-5.ch030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The current chapter introduces different aspects of molecular docking technique in order to give an overview to the readers about the topics which will be dealt with throughout this volume. Like many other fields of science, molecular docking studies has experienced a lagging period of slow and steady increase in terms of acquiring attention of scientific community as well as its frequency of application, followed by a pronounced era of exponential expansion in theory, methodology, areas of application and performance due to developments in related technologies such as computational resources and theoretical as well as experimental biophysical methods. In the following sections the evolution of molecular docking will be reviewed and its different components including methods, search algorithms, scoring functions, validation of the methods, and area of applications plus few case studies will be touched briefly.
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Affiliation(s)
| | | | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Iran & School of Pharmacy, Tabriz University of Medical Sciences, Iran
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64
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Clement N, Rasheed M, Bajaj C. Uncertainty Quantified Computational Analysis of the Energetics of Virus Capsid Assembly. PROCEEDINGS. IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE 2016; 2016:1706-1713. [PMID: 28936368 PMCID: PMC5604467 DOI: 10.1109/bibm.2016.7822775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Most of the existing research in assembly pathway prediction/analysis of viral capsids makes the simplifying assumption that the configuration of the intermediate states can be extracted directly from the final configuration of the entire capsid. This assumption does not take into account the conformational changes of the constituent proteins as well as minor changes to the binding interfaces that continue throughout the assembly process until stabilization. This paper presents a statistical-ensemble based approach which samples the configurational space for each monomer with the relative local orientation between monomers, to capture the uncertainties in binding and conformations. Furthermore, instead of using larger capsomers (trimers, pentamers) as building blocks, we allow all possible subassemblies to bind in all possible combinations. We represent the resulting assembly graph in two different ways: First, we use the Wilcoxon signed rank measure to compare the distributions of binding free energy computed on the sampled conformations to predict likely pathways. Second, we represent chemical equilibrium aspects of the transitions as a Bayesian Factor graph where both associations and dissociations are modeled based on concentrations and the binding free energies. We applied these protocols on the feline panleukopenia virus and the Nudaurelia capensis virus. Results from these experiments showed significant departure from those one would obtain if only the static configurations of the proteins were considered. Hence, we establish the importance of an uncertainty-aware protocol for pathway analysis, and provide a statistical framework as an important first step towards assembly pathway prediction with high statistical confidence.
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Affiliation(s)
- N Clement
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712
| | - M Rasheed
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712
| | - C Bajaj
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712
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65
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Liu YS, Deng H, Liu M, Gong L. VIV: Using visible internal volume to compute junction-aware shape descriptor of 3D articulated models. Neurocomputing 2016. [DOI: 10.1016/j.neucom.2015.06.115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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66
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Mabanglo MF, Xiang DF, Bigley AN, Raushel FM. Structure of a Novel Phosphotriesterase from Sphingobium sp. TCM1: A Familiar Binuclear Metal Center Embedded in a Seven-Bladed β-Propeller Protein Fold. Biochemistry 2016; 55:3963-74. [DOI: 10.1021/acs.biochem.6b00364] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mark F. Mabanglo
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
| | - Dao Feng Xiang
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
| | - Andrew N. Bigley
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
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Sarti E, Gladich I, Zamuner S, Correia BE, Laio A. Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses. Proteins 2016; 84:1312-20. [DOI: 10.1002/prot.25079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/27/2016] [Accepted: 05/19/2016] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | - Bruno E. Correia
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale De Lausanne; Lausanne Switzerland
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68
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Wei G, Xi W, Nussinov R, Ma B. Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. Chem Rev 2016; 116:6516-51. [PMID: 26807783 PMCID: PMC6407618 DOI: 10.1021/acs.chemrev.5b00562] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
All soluble proteins populate conformational ensembles that together constitute the native state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the distributions of the states on the energy landscape are determined by statistical thermodynamics; however, they are optimized to perform their biological functions. In this review we briefly describe advances in free energy landscape studies of protein conformational ensembles. Experimental (nuclear magnetic resonance, small-angle X-ray scattering, single-molecule spectroscopy, and cryo-electron microscopy) and computational (replica-exchange molecular dynamics, metadynamics, and Markov state models) approaches have made great progress in recent years. These address the challenging characterization of the highly flexible and heterogeneous protein ensembles. We focus on structural aspects of protein conformational distributions, from collective motions of single- and multi-domain proteins, intrinsically disordered proteins, to multiprotein complexes. Importantly, we highlight recent studies that illustrate functional adjustment of protein conformational ensembles in the crowded cellular environment. We center on the role of the ensemble in recognition of small- and macro-molecules (protein and RNA/DNA) and emphasize emerging concepts of protein dynamics in enzyme catalysis. Overall, protein ensembles link fundamental physicochemical principles and protein behavior and the cellular network and its regulation.
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Affiliation(s)
- Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Wenhui Xi
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
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69
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Opron K, Xia K, Burton Z, Wei GW. Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis. J Comput Chem 2016; 37:1283-95. [PMID: 26927815 PMCID: PMC5844491 DOI: 10.1002/jcc.24320] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 12/02/2015] [Accepted: 01/17/2016] [Indexed: 12/29/2022]
Abstract
Protein-nucleic acid complexes are important for many cellular processes including the most essential functions such as transcription and translation. For many protein-nucleic acid complexes, flexibility of both macromolecules has been shown to be critical for specificity and/or function. The flexibility-rigidity index (FRI) has been proposed as an accurate and efficient approach for protein flexibility analysis. In this article, we introduce FRI for the flexibility analysis of protein-nucleic acid complexes. We demonstrate that a multiscale strategy, which incorporates multiple kernels to capture various length scales in biomolecular collective motions, is able to significantly improve the state of art in the flexibility analysis of protein-nucleic acid complexes. We take the advantage of the high accuracy and O(N) computational complexity of our multiscale FRI method to investigate the flexibility of ribosomal subunits, which are difficult to analyze by alternative approaches. An anisotropic FRI approach, which involves localized Hessian matrices, is utilized to study the translocation dynamics in an RNA polymerase.
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Affiliation(s)
- Kristopher Opron
- Department of Biochemistry and Molecular Biology, Michigan State University, MI 48824, USA
| | - Kelin Xia
- Department of Mathematics Michigan State University, MI 48824, USA
| | - Zach Burton
- Department of Biochemistry and Molecular Biology, Michigan State University, MI 48824, USA
| | - Guo-Wei Wei
- Mathematical Biosciences Institute The Ohio State University, Columbus, Ohio 43210, USA
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70
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Xie Y, Li M, Chang W. Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana. PLoS One 2016; 11:e0156067. [PMID: 27223615 PMCID: PMC4880283 DOI: 10.1371/journal.pone.0156067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/09/2016] [Indexed: 11/20/2022] Open
Abstract
The genome of the Synechococcus elongatus strain PCC 7942 encodes a putative sugar kinase (SePSK), which shares 44.9% sequence identity with the xylulose kinase-1 (AtXK-1) from Arabidopsis thaliana. Sequence alignment suggests that both kinases belong to the ribulokinase-like carbohydrate kinases, a sub-family of FGGY family carbohydrate kinases. However, their exact physiological function and real substrates remain unknown. Here we solved the structures of SePSK and AtXK-1 in both their apo forms and in complex with nucleotide substrates. The two kinases exhibit nearly identical overall architecture, with both kinases possessing ATP hydrolysis activity in the absence of substrates. In addition, our enzymatic assays suggested that SePSK has the capability to phosphorylate D-ribulose. In order to understand the catalytic mechanism of SePSK, we solved the structure of SePSK in complex with D-ribulose and found two potential substrate binding pockets in SePSK. Using mutation and activity analysis, we further verified the key residues important for its catalytic activity. Moreover, our structural comparison with other family members suggests that there are major conformational changes in SePSK upon substrate binding, facilitating the catalytic process. Together, these results provide important information for a more detailed understanding of the cofactor and substrate binding mode as well as the catalytic mechanism of SePSK, and possible similarities with its plant homologue AtXK-1.
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Affiliation(s)
- Yuan Xie
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (WC); (ML)
| | - Wenrui Chang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (WC); (ML)
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71
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Opron K, Xia K, Wei GW. Communication: Capturing protein multiscale thermal fluctuations. J Chem Phys 2016; 142:211101. [PMID: 26049417 DOI: 10.1063/1.4922045] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Existing elastic network models are typically parametrized at a given cutoff distance and often fail to properly predict the thermal fluctuation of many macromolecules that involve multiple characteristic length scales. We introduce a multiscale flexibility-rigidity index (mFRI) method to resolve this problem. The proposed mFRI utilizes two or three correlation kernels parametrized at different length scales to capture protein interactions at corresponding scales. It is about 20% more accurate than the Gaussian network model (GNM) in the B-factor prediction of a set of 364 proteins. Additionally, the present method is able to deliver accurate predictions for some large macromolecules on which GNM fails to produce accurate predictions. Finally, for a protein of N residues, mFRI is of linear scaling (O(N)) in computational complexity, in contrast to the order of O(N(3)) for GNM.
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Affiliation(s)
- Kristopher Opron
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Kelin Xia
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, USA
| | - Guo-Wei Wei
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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72
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Li H, Chang YY, Yang LW, Bahar I. iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. Nucleic Acids Res 2015; 44:D415-22. [PMID: 26582920 PMCID: PMC4702874 DOI: 10.1093/nar/gkv1236] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/02/2015] [Indexed: 12/24/2022] Open
Abstract
Gaussian network model (GNM) is a simple yet powerful model for investigating the dynamics of proteins and their complexes. GNM analysis became a broadly used method for assessing the conformational dynamics of biomolecular structures with the development of a user-friendly interface and database, iGNM, in 2005. We present here an updated version, iGNM 2.0 http://gnmdb.csb.pitt.edu/, which covers more than 95% of the structures currently available in the Protein Data Bank (PDB). Advanced search and visualization capabilities, both 2D and 3D, permit users to retrieve information on inter-residue and inter-domain cross-correlations, cooperative modes of motion, the location of hinge sites and energy localization spots. The ability of iGNM 2.0 to provide structural dynamics data on the large majority of PDB structures and, in particular, on their biological assemblies makes it a useful resource for establishing the bridge between structure, dynamics and function.
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Affiliation(s)
- Hongchun Li
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA 15213, USA
| | - Yuan-Yu Chang
- Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 300, Taiwan
| | - Lee-Wei Yang
- Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 300, Taiwan
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA 15213, USA
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73
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Knott GJ, Lee M, Passon DM, Fox AH, Bond CS. Caenorhabditis elegans NONO-1: Insights into DBHS protein structure, architecture, and function. Protein Sci 2015; 24:2033-43. [PMID: 26435036 DOI: 10.1002/pro.2816] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 09/24/2015] [Indexed: 12/14/2022]
Abstract
Members of the Drosophila behavior/human splicing (DBHS) protein family have been characterized in the vertebrates Homo sapiens and Mus musculus, and the invertebrates Drosophila melanogaster and Chironomus tentans. Collectively, both vertebrate and invertebrate DBHS proteins function throughout gene regulation, largely but not always, within the nucleus. In this study, we report a structural and bioinformatic analysis of the DBHS protein family to guide future studies into DBHS protein function. To explore the structural plasticity of the family, we describe the 2.4 Å crystal structure of Caenorhabditis elegans non-POU domain-containing octamer-binding protein 1 (NONO-1). The structure is dimeric, with a domain arrangement consistent with mammalian DBHS proteins. Comparison with the DBHS structures available from H. sapiens reveals that there is inherent domain flexibility within the homologous DBHS region. Mapping amino acid similarity within the family to the NONO-1 dimer highlights the dimer interface, coiled-coil oligomerization motif, and putative RNA binding surfaces. Surprisingly, the interior surface of RNA recognition motif 2 (RRM2) that faces a large internal void is highly variable, but the external β2-β3 loops of RRM2 show remarkable preservation. Overall, the DBHS region is under strong purifying selection, whereas the sequences N- and C-terminal to the DBHS region are less constrained. The findings described in this study provide a molecular basis for further investigation into the mechanistic function of the DBHS protein family in biology.
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Affiliation(s)
- Gavin J Knott
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Mihwa Lee
- Department of Biochemistry and Genetics, La Trobe University, Melbourne, Victoria, Australia
| | - Daniel M Passon
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, 6009, Australia.,European Molecular Biology Laboratories, Hamburg, 22761, Germany
| | - Archa H Fox
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, 6009, Australia
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74
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Soner S, Ozbek P, Garzon JI, Ben-Tal N, Haliloglu T. DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics. PLoS Comput Biol 2015; 11:e1004461. [PMID: 26506003 PMCID: PMC4623975 DOI: 10.1371/journal.pcbi.1004461] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/08/2015] [Indexed: 12/31/2022] Open
Abstract
Protein-protein interfaces have been evolutionarily-designed to enable transduction between the interacting proteins. Thus, we hypothesize that analysis of the dynamics of the complex can reveal details about the nature of the interaction, and in particular whether it is obligatory, i.e., persists throughout the entire lifetime of the proteins, or not. Indeed, normal mode analysis, using the Gaussian network model, shows that for the most part obligatory and non-obligatory complexes differ in their decomposition into dynamic domains, i.e., the mobile elements of the protein complex. The dynamic domains of obligatory complexes often mix segments from the interacting chains, and the hinges between them do not overlap with the interface between the chains. In contrast, in non-obligatory complexes the interface often hinges between dynamic domains, held together through few anchor residues on one side of the interface that interact with their counterpart grooves in the other end. In automatic analysis, 117 of 139 obligatory (84.2%) and 203 of 246 non-obligatory (82.5%) complexes are correctly classified by our method: DynaFace. We further use DynaFace to predict obligatory and non-obligatory interactions among a set of 300 putative protein complexes. DynaFace is available at: http://safir.prc.boun.edu.tr/dynaface.
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Affiliation(s)
- Seren Soner
- Department of Computer Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey
| | - Pemra Ozbek
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Jose Ignacio Garzon
- Departments of Biochemistry and Molecular Biophysics and Systems Biology and Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Turkan Haliloglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey
- * E-mail:
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75
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Aubailly S, Piazza F. Cutoff lensing: predicting catalytic sites in enzymes. Sci Rep 2015; 5:14874. [PMID: 26445900 PMCID: PMC4597221 DOI: 10.1038/srep14874] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/10/2015] [Indexed: 01/12/2023] Open
Abstract
Predicting function-related amino acids in proteins with unknown function or unknown allosteric binding sites in drug-targeted proteins is a task of paramount importance in molecular biomedicine. In this paper we introduce a simple, light and computationally inexpensive structure-based method to identify catalytic sites in enzymes. Our method, termed cutoff lensing, is a general procedure consisting in letting the cutoff used to build an elastic network model increase to large values. A validation of our method against a large database of annotated enzymes shows that optimal values of the cutoff exist such that three different structure-based indicators allow one to recover a maximum of the known catalytic sites. Interestingly, we find that the larger the structures the greater the predictive power afforded by our method. Possible ways to combine the three indicators into a single figure of merit and into a specific sequential analysis are suggested and discussed with reference to the classic case of HIV-protease. Our method could be used as a complement to other sequence- and/or structure-based methods to narrow the results of large-scale screenings.
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Affiliation(s)
- Simon Aubailly
- Université d'Orléans, Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, 45071, Orléans, France
| | - Francesco Piazza
- Université d'Orléans, Centre de Biophysique Moléculaire, CNRS-UPR4301, Rue C. Sadron, 45071, Orléans, France
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76
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Acheson JF, Moseson H, Fox BG. Structure of T4moF, the Toluene 4-Monooxygenase Ferredoxin Oxidoreductase. Biochemistry 2015; 54:5980-8. [PMID: 26309236 DOI: 10.1021/acs.biochem.5b00692] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The 1.6 Å crystal structure of toluene 4-monooxygenase reductase T4moF is reported. The structure includes ferredoxin, flavin, and NADH binding domains. The position of the ferredoxin domain relative to the other two domains represents a new configuration for the iron-sulfur flavoprotein family. Close contacts between the C8 methyl group of FAD and [2Fe-2S] ligand Cys36-O represent a plausible pathway for electron transfer between the redox cofactors. Energy-minimized docking of NADH and calculation of hingelike motions between domains suggest how simple coordinated shifts of residues at the C-terminus of the enzyme could expose the N5 position of FAD for productive interaction with the nicotinamide ring. The domain configuration revealed by the T4moF structure provides an excellent steric and electrostatic match to the obligate electron acceptor, Rieske-type [2Fe-2S] ferredoxin T4moC. Protein-protein docking and energy minimization of the T4moFC complex indicate that T4moF [2Fe-2S] ligand Cys41 and T4moC [2Fe-2S] ligand His67, along with other electrostatic interactions between the protein partners, form the functional electron transfer interface.
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Affiliation(s)
- Justin F Acheson
- Department of Biochemistry, College of Agriculture and Life Sciences, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Hannah Moseson
- Department of Biochemistry, College of Agriculture and Life Sciences, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Brian G Fox
- Department of Biochemistry, College of Agriculture and Life Sciences, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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77
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Sumbul F, Acuner-Ozbabacan SE, Haliloglu T. Allosteric Dynamic Control of Binding. Biophys J 2015; 109:1190-201. [PMID: 26338442 DOI: 10.1016/j.bpj.2015.08.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 08/12/2015] [Accepted: 08/13/2015] [Indexed: 12/31/2022] Open
Abstract
Proteins have a highly dynamic nature and there is a complex interrelation between their structural dynamics and binding behavior. By assuming various conformational ensembles, they perform both local and global fluctuations to interact with other proteins in a dynamic infrastructure adapted to functional motion. Here, we show that there is a significant association between allosteric mutations, which lead to high-binding-affinity changes, and the hinge positions of global modes, as revealed by a large-scale statistical analysis of data in the Structural Kinetic and Energetic Database of Mutant Protein Interactions (SKEMPI). We further examined the mechanism of allosteric dynamics by conducting studies on human growth hormone (hGH) and pyrin domain (PYD), and the results show how mutations at the hinge regions could allosterically affect the binding-site dynamics or induce alternative binding modes by modifying the ensemble of accessible conformations. The long-range dissemination of perturbations in local chemistry or physical interactions through an impact on global dynamics can restore the allosteric dynamics. Our findings suggest a mechanism for the coupling of structural dynamics to the modulation of protein interactions, which remains a critical phenomenon in understanding the effect of mutations that lead to functional changes in proteins.
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Affiliation(s)
- Fidan Sumbul
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey
| | | | - Turkan Haliloglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey.
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78
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Forlani G, Makarova KS, Ruszkowski M, Bertazzini M, Nocek B. Evolution of plant δ(1)-pyrroline-5-carboxylate reductases from phylogenetic and structural perspectives. FRONTIERS IN PLANT SCIENCE 2015; 6:567. [PMID: 26284089 PMCID: PMC4522605 DOI: 10.3389/fpls.2015.00567] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/09/2015] [Indexed: 05/23/2023]
Abstract
Proline plays a crucial role in cell growth and stress responses, and its accumulation is essential for the tolerance of adverse environmental conditions in plants. Two routes are used to biosynthesize proline in plants. The main route uses glutamate as a precursor, while in the other route proline is derived from ornithine. The terminal step of both pathways, the conversion of δ(1)-pyrroline-5-carboxylate (P5C) to L-proline, is catalyzed by P5C reductase (P5CR) using NADH or NADPH as a cofactor. Since P5CRs are important housekeeping enzymes, they are conserved across all domains of life and appear to be relatively unaffected throughout evolution. However, global analysis of these enzymes unveiled significant functional diversity in the preference for cofactors (NADPH vs. NADH), variation in metal dependence and the differences in the oligomeric state. In our study we investigated evolutionary patterns through phylogenetic and structural analysis of P5CR representatives from all kingdoms of life, with emphasis on the plant species. We also attempted to correlate local sequence/structure variation among the functionally and structurally characterized members of the family.
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Affiliation(s)
- Giuseppe Forlani
- Department of Life Science and Biotechnology, University of FerraraFerrara, Italy
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, BethesdaMD, USA
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, ArgonneIL, USA
| | - Michele Bertazzini
- Department of Life Science and Biotechnology, University of FerraraFerrara, Italy
| | - Boguslaw Nocek
- The Bioscience Division, Argonne National Laboratory, ArgonneIL, USA
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79
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Stapleford KA, Coffey LL, Lay S, Bordería AV, Duong V, Isakov O, Rozen-Gagnon K, Arias-Goeta C, Blanc H, Beaucourt S, Haliloğlu T, Schmitt C, Bonne I, Ben-Tal N, Shomron N, Failloux AB, Buchy P, Vignuzzi M. Emergence and transmission of arbovirus evolutionary intermediates with epidemic potential. Cell Host Microbe 2015; 15:706-16. [PMID: 24922573 DOI: 10.1016/j.chom.2014.05.008] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/19/2014] [Accepted: 04/22/2014] [Indexed: 01/14/2023]
Abstract
The high replication and mutation rates of RNA viruses can result in the emergence of new epidemic variants. Thus, the ability to follow host-specific evolutionary trajectories of viruses is essential to predict and prevent epidemics. By studying the spatial and temporal evolution of chikungunya virus during natural transmission between mosquitoes and mammals, we have identified viral evolutionary intermediates prior to emergence. Analysis of virus populations at anatomical barriers revealed that the mosquito midgut and salivary gland pose population bottlenecks. By focusing on virus subpopulations in the saliva of multiple mosquito strains, we recapitulated the emergence of a recent epidemic strain of chikungunya and identified E1 glycoprotein mutations with potential to emerge in the future. These mutations confer fitness advantages in mosquito and mammalian hosts by altering virion stability and fusogenic activity. Thus, virus evolutionary trajectories can be predicted and studied in the short term before new variants displace currently circulating strains.
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Affiliation(s)
- Kenneth A Stapleford
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Lark L Coffey
- Center for Vectorborne Diseases, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, 5327 VM3A, Davis, CA 95616, USA
| | - Sreyrath Lay
- Virology Unit, Institut Pasteur in Cambodia 5, Monivong Boulevard, PO Box 983, Phnom Penh, Cambodia
| | - Antonio V Bordería
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Veasna Duong
- Virology Unit, Institut Pasteur in Cambodia 5, Monivong Boulevard, PO Box 983, Phnom Penh, Cambodia
| | - Ofer Isakov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Kathryn Rozen-Gagnon
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Camilo Arias-Goeta
- Arboviruses and Insect Vectors Lab, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Hervé Blanc
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Stéphanie Beaucourt
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Türkan Haliloğlu
- Department of Chemical Engineering and Polymer Research Center, Boğaziçi University, Bebek 34342, Istanbul, Turkey
| | - Christine Schmitt
- Ultrastructural Microscopy Platform, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Isabelle Bonne
- Ultrastructural Microscopy Platform, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anna-Bella Failloux
- Arboviruses and Insect Vectors Lab, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Philippe Buchy
- Virology Unit, Institut Pasteur in Cambodia 5, Monivong Boulevard, PO Box 983, Phnom Penh, Cambodia
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.
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80
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Vakser IA. Protein-protein docking: from interaction to interactome. Biophys J 2015; 107:1785-1793. [PMID: 25418159 DOI: 10.1016/j.bpj.2014.08.033] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 08/17/2014] [Accepted: 08/27/2014] [Indexed: 12/29/2022] Open
Abstract
The protein-protein docking problem is one of the focal points of activity in computational biophysics and structural biology. The three-dimensional structure of a protein-protein complex, generally, is more difficult to determine experimentally than the structure of an individual protein. Adequate computational techniques to model protein interactions are important because of the growing number of known protein structures, particularly in the context of structural genomics. Docking offers tools for fundamental studies of protein interactions and provides a structural basis for drug design. Protein-protein docking is the prediction of the structure of the complex, given the structures of the individual proteins. In the heart of the docking methodology is the notion of steric and physicochemical complementarity at the protein-protein interface. Originally, mostly high-resolution, experimentally determined (primarily by x-ray crystallography) protein structures were considered for docking. However, more recently, the focus has been shifting toward lower-resolution modeled structures. Docking approaches have to deal with the conformational changes between unbound and bound structures, as well as the inaccuracies of the interacting modeled structures, often in a high-throughput mode needed for modeling of large networks of protein interactions. The growing number of docking developers is engaged in the community-wide assessments of predictive methodologies. The development of more powerful and adequate docking approaches is facilitated by rapidly expanding information and data resources, growing computational capabilities, and a deeper understanding of the fundamental principles of protein interactions.
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Affiliation(s)
- Ilya A Vakser
- Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas.
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81
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Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors. Molecules 2015; 20:11569-603. [PMID: 26111183 PMCID: PMC6272567 DOI: 10.3390/molecules200611569] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 06/02/2015] [Accepted: 06/15/2015] [Indexed: 02/06/2023] Open
Abstract
Blocking protein-protein interactions (PPI) using small molecules or peptides modulates biochemical pathways and has therapeutic significance. PPI inhibition for designing drug-like molecules is a new area that has been explored extensively during the last decade. Considering the number of available PPI inhibitor databases and the limited number of 3D structures available for proteins, docking and scoring methods play a major role in designing PPI inhibitors as well as stabilizers. Docking methods are used in the design of PPI inhibitors at several stages of finding a lead compound, including modeling the protein complex, screening for hot spots on the protein-protein interaction interface and screening small molecules or peptides that bind to the PPI interface. There are three major challenges to the use of docking on the relatively flat surfaces of PPI. In this review we will provide some examples of the use of docking in PPI inhibitor design as well as its limitations. The combination of experimental and docking methods with improved scoring function has thus far resulted in few success stories of PPI inhibitors for therapeutic purposes. Docking algorithms used for PPI are in the early stages, however, and as more data are available docking will become a highly promising area in the design of PPI inhibitors or stabilizers.
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82
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Cordeiro TN, García J, Bernadó P, Millet O, Pons M. A Three-protein Charge Zipper Stabilizes a Complex Modulating Bacterial Gene Silencing. J Biol Chem 2015; 290:21200-12. [PMID: 26085102 DOI: 10.1074/jbc.m114.630400] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Indexed: 12/31/2022] Open
Abstract
The Hha/YmoA nucleoid-associated proteins help selectively silence horizontally acquired genetic material, including pathogenicity and antibiotic resistance genes and their maintenance in the absence of selective pressure. Members of the Hha family contribute to gene silencing by binding to the N-terminal dimerization domain of H-NS and modifying its selectivity. Hha-like proteins and the H-NS N-terminal domain are unusually rich in charged residues, and their interaction is mostly electrostatic-driven but, nonetheless, highly selective. The NMR-based structural model of the complex between Hha/YmoA and the H-NS N-terminal dimerization domain reveals that the origin of the selectivity is the formation of a three-protein charge zipper with interdigitated complementary charged residues from Hha and the two units of the H-NS dimer. The free form of YmoA shows collective microsecond-millisecond dynamics that can by measured by NMR relaxation dispersion experiments and shows a linear dependence with the salt concentration. The number of residues sensing the collective dynamics and the population of the minor form increased in the presence of H-NS. Additionally, a single residue mutation in YmoA (D43N) abolished H-NS binding and the dynamics of the apo-form, suggesting the dynamics and binding are functionally related.
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Affiliation(s)
- Tiago N Cordeiro
- From the Biomolecular NMR Laboratory, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain, Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université Montpellier 1 and 2, 34092 Montpellier, France
| | - Jesús García
- Institute for Research in Biomedicine (IRB-Barcelona), 08028 Barcelona, Spain, and
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université Montpellier 1 and 2, 34092 Montpellier, France
| | - Oscar Millet
- the Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC-bioGUNE), 48160 Elexalde, Derio, Spain
| | - Miquel Pons
- From the Biomolecular NMR Laboratory, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain,
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83
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Bergantino F, Guariniello S, Raucci R, Colonna G, De Luca A, Normanno N, Costantini S. Structure–fluctuation–function relationships of seven pro-angiogenic isoforms of VEGFA, important mediators of tumorigenesis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:410-25. [DOI: 10.1016/j.bbapap.2015.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/06/2015] [Accepted: 01/14/2015] [Indexed: 10/24/2022]
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84
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Sim J, Sim J, Park E, Lee J. Method for identification of rigid domains and hinge residues in proteins based on exhaustive enumeration. Proteins 2015; 83:1054-67. [DOI: 10.1002/prot.24799] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 02/28/2015] [Accepted: 03/10/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Jaehyun Sim
- Department of Oral Microbiology and Immunology; School of Dentistry, Seoul National University; Seoul 110-749 Korea
| | - Jun Sim
- Department of Bioinformatics and Life Science; Soongsil University; Seoul 156-743 Korea
| | - Eunsung Park
- Administrative Service Division, Apsun Dental Hospital; Seoul 135-590 Korea
| | - Julian Lee
- Department of Oral Microbiology and Immunology; School of Dentistry, Seoul National University; Seoul 110-749 Korea
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85
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Boyer B, Ezelin J, Poulain P, Saladin A, Zacharias M, Robert CH, Prévost C. An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA. PLoS One 2015; 10:e0116414. [PMID: 25785454 PMCID: PMC4364692 DOI: 10.1371/journal.pone.0116414] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 12/09/2014] [Indexed: 11/19/2022] Open
Abstract
Oligomeric macromolecules in the cell self-organize into a wide variety of geometrical motifs such as helices, rings or linear filaments. The recombinase proteins involved in homologous recombination present many such assembly motifs. Here, we examine in particular the polymorphic characteristics of RecA, the most studied member of the recombinase family, using an integrative approach that relates local modes of monomer/monomer association to the global architecture of their screw-type organization. In our approach, local modes of association are sampled via docking or Monte Carlo simulations. This enables shedding new light on fiber morphologies that may be adopted by the RecA protein. Two distinct RecA helical morphologies, the so-called "extended" and "compressed" forms, are known to play a role in homologous recombination. We investigate the variability within each form in terms of helical parameters and steric accessibility. We also address possible helical discontinuities in RecA filaments due to multiple monomer-monomer association modes. By relating local interface organization to global filament morphology, the strategies developed here to study RecA self-assembly are particularly well suited to other DNA-binding proteins and to filamentous protein assemblies in general.
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Affiliation(s)
- Benjamin Boyer
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
- MTI, INSERM UMR-M 973, Université Paris Diderot-Paris 7, Bât Lamarck, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Johann Ezelin
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Pierre Poulain
- DSIMB team, Inserm UMR-S 665 and Univ. Paris Diderot, Sorbonne Paris Cité, INTS, 6 rue Alexandre Cabanel, 75015 Paris, France
- Ets Poulain, Pointe-Noire, Republic of Congo
| | - Adrien Saladin
- MTI, INSERM UMR-M 973, Université Paris Diderot-Paris 7, Bât Lamarck, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Martin Zacharias
- Technische Universität München, Physik-Department, James-Franck-Str. 1, 85748 Garching, Germany
| | - Charles H. Robert
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Chantal Prévost
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
- * E-mail:
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86
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Mahboobi SH, Javanpour AA, Mofrad MRK. The interaction of RNA helicase DDX3 with HIV-1 Rev-CRM1-RanGTP complex during the HIV replication cycle. PLoS One 2015; 10:e0112969. [PMID: 25723178 PMCID: PMC4344243 DOI: 10.1371/journal.pone.0112969] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 10/17/2014] [Indexed: 01/17/2023] Open
Abstract
Molecular traffic between the nucleus and the cytoplasm is regulated by the nuclear pore complex (NPC), which acts as a highly selective channel perforating the nuclear envelope in eukaryotic cells. The human immunodeficiency virus (HIV) exploits the nucleocytoplasmic pathway to export its RNA transcripts across the NPC to the cytoplasm. Despite extensive study on the HIV life cycle and the many drugs developed to target this cycle, no current drugs have been successful in targeting the critical process of viral nuclear export, even though HIV's reliance on a single host protein, CRM1, to export its unspliced and partially spliced RNA transcripts makes it a tempting target. Due to recent findings implicating a DEAD-box helicase, DDX3, in HIV replication and a member of the export complex, it has become an appealing target for anti-HIV drug inhibition. In the present research, we have applied a hybrid computational protocol to analyze protein-protein interactions in the HIV mRNA export cycle. This method is based on molecular docking followed by molecular dynamics simulation and accompanied by approximate free energy calculation (MM/GBSA), computational alanine scanning, clustering, and evolutionary analysis. We highlight here some of the most likely binding modes and interfacial residues between DDX3 and CRM1 both in the absence and presence of RanGTP. This work shows that although DDX3 can bind to free CRM1, addition of RanGTP leads to more concentrated distribution of binding modes and stronger binding between CRM1 and RanGTP.
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Affiliation(s)
- Seyed Hanif Mahboobi
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, California, United States of America
| | - Alex A. Javanpour
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, California, United States of America
| | - Mohammad R. K. Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America
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87
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Ahalawat N, Murarka RK. Conformational changes and allosteric communications in human serum albumin due to ligand binding. J Biomol Struct Dyn 2015; 33:2192-204. [DOI: 10.1080/07391102.2014.996609] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Navjeet Ahalawat
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Bhauri, Bhopal, Madhya Pradesh 462066, India
| | - Rajesh K. Murarka
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Bhauri, Bhopal, Madhya Pradesh 462066, India
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88
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Mahajan S, Sanejouand YH. On the relationship between low-frequency normal modes and the large-scale conformational changes of proteins. Arch Biochem Biophys 2015; 567:59-65. [PMID: 25562404 DOI: 10.1016/j.abb.2014.12.020] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/16/2014] [Accepted: 12/20/2014] [Indexed: 11/15/2022]
Abstract
Normal mode analysis is a computational technique that allows to study the dynamics of biological macromolecules. It was first applied to small protein cases, more than thirty years ago. The interest in this technique then raised when it was realized that it can provide insights about the large-scale conformational changes a protein can experience, for instance upon ligand binding. As it was also realized that studying highly simplified protein models can provide similar insights, meaning that this kind of analysis can be both quick and simple to handle, several applications were proposed, in the context of various structural biology techniques. This review focuses on these applications, as well as on how the functional relevance of the lowest-frequency modes of proteins was established.
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89
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Gofman Y, Schärfe C, Marks DS, Haliloglu T, Ben-Tal N. Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel. PLoS Comput Biol 2014; 10:e1003976. [PMID: 25474149 PMCID: PMC4256070 DOI: 10.1371/journal.pcbi.1003976] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 10/09/2014] [Indexed: 11/18/2022] Open
Abstract
Cyclic nucleotide-gated (CNG) ion channels are nonselective cation channels, essential for visual and olfactory sensory transduction. Although the channels include voltage-sensor domains (VSDs), their conductance is thought to be independent of the membrane potential, and their gating regulated by cytosolic cyclic nucleotide-binding domains. Mutations in these channels result in severe, degenerative retinal diseases, which remain untreatable. The lack of structural information on CNG channels has prevented mechanistic understanding of disease-causing mutations, precluded structure-based drug design, and hampered in silico investigation of the gating mechanism. To address this, we built a 3D model of the cone tetrameric CNG channel, based on homology to two distinct templates with known structures: the transmembrane (TM) domain of a bacterial channel, and the cyclic nucleotide-binding domain of the mouse HCN2 channel. Since the TM-domain template had low sequence-similarity to the TM domains of the CNG channels, and to reconcile conflicts between the two templates, we developed a novel, hybrid approach, combining homology modeling with evolutionary coupling constraints. Next, we used elastic network analysis of the model structure to investigate global motions of the channel and to elucidate its gating mechanism. We found the following: (i) In the main mode of motion, the TM and cytosolic domains counter-rotated around the membrane normal. We related this motion to gating, a proposition that is supported by previous experimental data, and by comparison to the known gating mechanism of the bacterial KirBac channel. (ii) The VSDs could facilitate gating (supplementing the pore gate), explaining their presence in such 'voltage-insensitive' channels. (iii) Our elastic network model analysis of the CNGA3 channel supports a modular model of allosteric gating, according to which protein domains are quasi-independent: they can move independently, but are coupled to each other allosterically.
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Affiliation(s)
- Yana Gofman
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Charlotta Schärfe
- Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, Tübingen University, Tübingen, Germany
- Department of Systems Biology, Harvard University, Boston, Massachusetts, United States of America
| | - Debora S. Marks
- Department of Systems Biology, Harvard University, Boston, Massachusetts, United States of America
| | - Turkan Haliloglu
- Polymer Research Centre and Chemical Engineering Department, Bogazici University, Bebek-Istanbul, Turkey
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
- * E-mail:
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90
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Unexpected structure for the N-terminal domain of hepatitis C virus envelope glycoprotein E1. Nat Commun 2014; 5:4874. [PMID: 25224686 PMCID: PMC4175578 DOI: 10.1038/ncomms5874] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 07/31/2014] [Indexed: 12/21/2022] Open
Abstract
Hepatitis C virus (HCV) infection remains a major health problem worldwide. HCV entry into host cells and membrane fusion are achieved by two envelope glycoproteins, E1 and E2. We report here the 3.5-Å resolution crystal structure of the N-terminal domain of the HCV E1 ectodomain, which reveals a complex network of covalently linked intertwined homodimers that do not harbour the expected truncated class II fusion protein fold. Hepatitis C virus (HCV) gains entry into host cells via envelope glycoproteins E1 and E2. Here, El Omari et al. present the crystal structure of the N terminus of the E1 ectodomain of HCV and show that it adopts a different fold than predicted.
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91
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Morgan HP, Zhong W, McNae IW, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD. Structures of pyruvate kinases display evolutionarily divergent allosteric strategies. ROYAL SOCIETY OPEN SCIENCE 2014; 1:140120. [PMID: 26064527 PMCID: PMC4448766 DOI: 10.1098/rsos.140120] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 08/11/2014] [Indexed: 05/13/2023]
Abstract
The transition between the inactive T-state (apoenzyme) and active R-state (effector bound enzyme) of Trypanosoma cruzi pyruvate kinase (PYK) is accompanied by a symmetrical 8° rigid body rocking motion of the A- and C-domain cores in each of the four subunits, coupled with the formation of additional salt bridges across two of the four subunit interfaces. These salt bridges provide increased tetramer stability correlated with an enhanced specificity constant (k cat/S 0.5). A detailed kinetic and structural comparison between the potential drug target PYKs from the pathogenic protists T. cruzi, T. brucei and Leishmania mexicana shows that their allosteric mechanism is conserved. By contrast, a structural comparison of trypanosomatid PYKs with the evolutionarily divergent PYKs of humans and of bacteria shows that they have adopted different allosteric strategies. The underlying principle in each case is to maximize (k cat/S 0.5) by stabilizing and rigidifying the tetramer in an active R-state conformation. However, bacterial and mammalian PYKs have evolved alternative ways of locking the tetramers together. In contrast to the divergent allosteric mechanisms, the PYK active sites are highly conserved across species. Selective disruption of the varied allosteric mechanisms may therefore provide a useful approach for the design of species-specific inhibitors.
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92
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Kim SJ, Fernandez-Martinez J, Sampathkumar P, Martel A, Matsui T, Tsuruta H, Weiss TM, Shi Y, Markina-Inarrairaegui A, Bonanno JB, Sauder JM, Burley SK, Chait BT, Almo SC, Rout MP, Sali A. Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex. Mol Cell Proteomics 2014; 13:2911-26. [PMID: 25139911 DOI: 10.1074/mcp.m114.040915] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The nuclear pore complex (NPC) is the sole passageway for the transport of macromolecules across the nuclear envelope. Nup133, a major component in the essential Y-shaped Nup84 complex, is a large scaffold protein of the NPC's outer ring structure. Here, we describe an integrative modeling approach that produces atomic models for multiple states of Saccharomyces cerevisiae (Sc) Nup133, based on the crystal structures of the sequence segments and their homologs, including the related Vanderwaltozyma polyspora (Vp) Nup133 residues 55 to 502 (VpNup133(55-502)) determined in this study, small angle X-ray scattering profiles for 18 constructs of ScNup133 and one construct of VpNup133, and 23 negative-stain electron microscopy class averages of ScNup133(2-1157). Using our integrative approach, we then computed a multi-state structural model of the full-length ScNup133 and validated it with mutational studies and 45 chemical cross-links determined via mass spectrometry. Finally, the model of ScNup133 allowed us to annotate a potential ArfGAP1 lipid packing sensor (ALPS) motif in Sc and VpNup133 and discuss its potential significance in the context of the whole NPC; we suggest that ALPS motifs are scattered throughout the NPC's scaffold in all eukaryotes and play a major role in the assembly and membrane anchoring of the NPC in the nuclear envelope. Our results are consistent with a common evolutionary origin of Nup133 with membrane coating complexes (the protocoatomer hypothesis); the presence of the ALPS motifs in coatomer-like nucleoporins suggests an ancestral mechanism for membrane recognition present in early membrane coating complexes.
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Affiliation(s)
- Seung Joong Kim
- From the ‡Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California San Francisco, San Francisco, California 94158
| | - Javier Fernandez-Martinez
- ¶Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065
| | - Parthasarathy Sampathkumar
- ‖Department of Biochemistry, Ullmann Building, Room 409, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Anne Martel
- **Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 69, Menlo Park, California 94025
| | - Tsutomu Matsui
- **Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 69, Menlo Park, California 94025
| | - Hiro Tsuruta
- **Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 69, Menlo Park, California 94025
| | - Thomas M Weiss
- **Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 69, Menlo Park, California 94025
| | - Yi Shi
- ‡‡Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065
| | - Ane Markina-Inarrairaegui
- §§Laboratorio de Genetica Molecular de Aspergillus, Departamento de Biología Celular y Molecular, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Jeffery B Bonanno
- ‖Department of Biochemistry, Ullmann Building, Room 409, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - J Michael Sauder
- ¶¶Discovery Chemistry Research and Technologies (DCR&T), Eli Lilly and Company, Lilly Biotechnology Center, 10300 Campus Point Drive, Suite 200, San Diego, California 92121
| | - Stephen K Burley
- ‖‖Center for Integrative Proteomics Research, Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, 174 Frelinghuysen Road, Piscataway, New Jersey 08854
| | - Brian T Chait
- ‡‡Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065
| | - Steven C Almo
- ‖Department of Biochemistry, Ullmann Building, Room 409, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461;
| | - Michael P Rout
- ¶Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065;
| | - Andrej Sali
- From the ‡Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California San Francisco, San Francisco, California 94158;
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93
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Crystal structure of PhnF, a GntR-family transcriptional regulator of phosphate transport in Mycobacterium smegmatis. J Bacteriol 2014; 196:3472-81. [PMID: 25049090 DOI: 10.1128/jb.01965-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Bacterial uptake of phosphate is usually accomplished via high-affinity transporters that are commonly regulated by two-component systems, which are activated when the concentration of phosphate is low. Mycobacterium smegmatis possesses two such transporters, the widely distributed PstSCAB system and PhnDCE, a transporter that in other bacteria mediates the uptake of alternative phosphorus sources. We previously reported that the transcriptional regulator PhnF controls the production of the Phn system, acting as a repressor under high-phosphate conditions. Here we show that the phnDCE genes are common among environmental mycobacteria, where they are often associated with phnF-like genes. In contrast, pathogenic mycobacteria were not found to encode Phn-like systems but instead were found to possess multiple copies of the pst genes. A detailed biochemical analysis of PhnF binding to its identified binding sites in the phnD-phnF intergenic region of M. smegmatis has allowed us to propose a quantitative model for repressor binding, which shows that a PhnF dimer binds independently to each site. We present the crystal structure of M. smegmatis PhnF at 1.8-Å resolution, showing a homodimer with a helix-turn-helix N-terminal domain and a C-terminal domain with a UbiC transcription regulator-associated fold. The C-terminal domain crystallized with a bound sulfate ion instead of the so far unidentified physiological ligand, allowing the identification of residues involved in effector binding. Comparison of the positioning of the DNA binding domains in PhnF with that in homologous proteins suggests that its DNA binding activity is regulated via a conformational change in the linker region, triggering a movement of the N-terminal domains.
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94
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Shamsuddin R, Doktorova M, Jaswal S, Lee-St John A, McMenimen K. Computational prediction of hinge axes in proteins. BMC Bioinformatics 2014; 15 Suppl 8:S2. [PMID: 25080829 PMCID: PMC4120148 DOI: 10.1186/1471-2105-15-s8-s2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A protein's function is determined by the wide range of motions exhibited by its 3D structure. However, current experimental techniques are not able to reliably provide the level of detail required for elucidating the exact mechanisms of protein motion essential for effective drug screening and design. Computational tools are instrumental in the study of the underlying structure-function relationship. We focus on a special type of proteins called "hinge proteins" which exhibit a motion that can be interpreted as a rotation of one domain relative to another. RESULTS This work proposes a computational approach that uses the geometric structure of a single conformation to predict the feasible motions of the protein and is founded in recent work from rigidity theory, an area of mathematics that studies flexibility properties of general structures. Given a single conformational state, our analysis predicts a relative axis of motion between two specified domains. We analyze a dataset of 19 structures known to exhibit this hinge-like behavior. For 15, the predicted axis is consistent with a motion to a second, known conformation. We present a detailed case study for three proteins whose dynamics have been well-studied in the literature: calmodulin, the LAO binding protein and the Bence-Jones protein. CONCLUSIONS Our results show that incorporating rigidity-theoretic analyses can lead to effective computational methods for understanding hinge motions in macromolecules. This initial investigation is the first step towards a new tool for probing the structure-dynamics relationship in proteins.
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Patra D, Mishra P, Surolia A, Vijayan M. Structure, interactions and evolutionary implications of a domain-swapped lectin dimer from Mycobacterium smegmatis. Glycobiology 2014; 24:956-65. [DOI: 10.1093/glycob/cwu059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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96
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Bhowmick T, Ghosh S, Dixit K, Ganesan V, Ramagopal UA, Dey D, Sarma SP, Ramakumar S, Nagaraja V. Targeting Mycobacterium tuberculosis nucleoid-associated protein HU with structure-based inhibitors. Nat Commun 2014; 5:4124. [PMID: 24916461 DOI: 10.1038/ncomms5124] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 05/15/2014] [Indexed: 01/03/2023] Open
Abstract
The nucleoid-associated protein HU plays an important role in maintenance of chromosomal architecture and in global regulation of DNA transactions in bacteria. Although HU is essential for growth in Mycobacterium tuberculosis (Mtb), there have been no reported attempts to perturb HU function with small molecules. Here we report the crystal structure of the N-terminal domain of HU from Mtb. We identify a core region within the HU-DNA interface that can be targeted using stilbene derivatives. These small molecules specifically inhibit HU-DNA binding, disrupt nucleoid architecture and reduce Mtb growth. The stilbene inhibitors induce gene expression changes in Mtb that resemble those induced by HU deficiency. Our results indicate that HU is a potential target for the development of therapies against tuberculosis.
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Affiliation(s)
- Tuhin Bhowmick
- 1] Department of Physics, Indian Institute of Science, Bangalore 560012, India [2]
| | - Soumitra Ghosh
- 1] Department of Microbiology and Cell biology, Indian Institute of Science, Bangalore 560012, India [2]
| | - Karuna Dixit
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Varsha Ganesan
- Department of Microbiology and Cell biology, Indian Institute of Science, Bangalore 560012, India
| | - Udupi A Ramagopal
- 1] Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Ullmann Building, Room 409, Bronx, New York 10461, USA [2] Biological Sciences Division, Poornaprajna Institute of Scientific Research, Bangalore 562110, India
| | - Debayan Dey
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Siddhartha P Sarma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Valakunja Nagaraja
- 1] Department of Microbiology and Cell biology, Indian Institute of Science, Bangalore 560012, India [2] Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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97
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Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies. Proc Natl Acad Sci U S A 2014; 111:6714-9. [PMID: 24753590 DOI: 10.1073/pnas.1322908111] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To evade host immune mechanisms, many bacteria secrete immunomodulatory enzymes. Streptococcus pyogenes, one of the most common human pathogens, secretes a large endoglycosidase, EndoS, which removes carbohydrates in a highly specific manner from IgG antibodies. This modification renders antibodies incapable of eliciting host effector functions through either complement or Fc γ receptors, providing the bacteria with a survival advantage. On account of this antibody-specific modifying activity, EndoS is being developed as a promising injectable therapeutic for autoimmune diseases that rely on autoantibodies. Additionally, EndoS is a key enzyme used in the chemoenzymatic synthesis of homogenously glycosylated antibodies with tailored Fc γ receptor-mediated effector functions. Despite the tremendous utility of this enzyme, the molecular basis of EndoS specificity for, and processing of, IgG antibodies has remained poorly understood. Here, we report the X-ray crystal structure of EndoS and provide a model of its encounter complex with its substrate, the IgG1 Fc domain. We show that EndoS is composed of five distinct protein domains, including glycosidase, leucine-rich repeat, hybrid Ig, carbohydrate binding module, and three-helix bundle domains, arranged in a distinctive V-shaped conformation. Our data suggest that the substrate enters the concave interior of the enzyme structure, is held in place by the carbohydrate binding module, and that concerted conformational changes in both enzyme and substrate are required for subsequent antibody deglycosylation. The EndoS structure presented here provides a framework from which novel endoglycosidases could be engineered for additional clinical and biotechnological applications.
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98
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Bastolla U. Computing protein dynamics from protein structure with elastic network models. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2014. [DOI: 10.1002/wcms.1186] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ugo Bastolla
- Centro de Biologa Molecular Severo Ochoa (CSIC‐UAM)Universidad Autónoma de MadridMadridSpain
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99
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Lee H, Seo S, Kim M, Choi JB, Kim SM, Jeon TJ, Kim MK. Opening and closing of a toroidal group II chaperonin revealed by a symmetry constrained elastic network model. Protein Sci 2014; 23:703-13. [PMID: 24639244 DOI: 10.1002/pro.2454] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 03/01/2014] [Accepted: 03/09/2014] [Indexed: 11/08/2022]
Abstract
Recently, the atomic structures of both the closed and open forms of Group 2 chaperonin protein Mm-cpn were revealed through crystallography and cryo-electron microscopy. This toroidal-like chaperonin is composed of two eightfold rings that face back-to-back. To gain a computational advantage, we used a symmetry constrained elastic network model (SCENM), which requires only a repeated subunit structure and its symmetric connectivity to neighboring subunits to simulate the entire system. In the case of chaperonin, only six subunits (i.e., three from each ring) were used out of the eight subunits comprising each ring. A smooth and symmetric pathway between the open and closed conformations was generated by elastic network interpolation (ENI). To support this result, we also performed a symmetry-constrained normal mode analysis (NMA), which revealed the intrinsic vibration features of the given structures. The NMA and ENI results for the representative single subunit were duplicated according to the symmetry pattern to reconstruct the entire assembly. To test the feasibility of the symmetry model, its results were also compared with those obtained from the full model. This study allowed the folding mechanism of chaperonin Mm-cpn to be elucidated by SCENM in a timely manner.
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Affiliation(s)
- Hoomin Lee
- School of Mechanical Engineering, Sungkyunkwan University, 2066 Seoburo, Jangan-gu, Suwon, 440-746, Republic of Korea
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THz time scale structural rearrangements and binding modes in lysozyme-ligand interactions. J Biol Phys 2014; 40:121-37. [PMID: 24682643 DOI: 10.1007/s10867-014-9341-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 01/16/2014] [Indexed: 12/11/2022] Open
Abstract
Predicting the conformational changes in proteins that are relevant for substrate binding is an ongoing challenge in the aim of elucidating the functional states of proteins. The motions that are induced by protein-ligand interactions are governed by the protein global modes. Our measurements indicate that the detected changes in the global backbone motion of the enzyme upon binding reflect a shift from the large-scale collective dominant mode in the unbound state towards a functional twisting deformation that assists in closing the binding cleft. Correlated motion in lysozyme has been implicated in enzyme function in previous studies, but detailed characterization of the internal fluctuations that enable the protein to explore the ensemble of conformations that ultimately foster large-scale conformational change is yet unknown. For this reason, we use THz spectroscopy to investigate the picosecond time scale binding modes and collective structural rearrangements that take place in hen egg white lysozyme (HEWL) when bound by the inhibitor (NAG)3. These protein thermal motions correspond to fluctuations that have a role in both selecting and sampling from the available protein intrinsic conformations that communicate function. Hence, investigation of these fast, collective modes may provide knowledge about the mechanism leading to the preferred binding process in HEWL-(NAG)3. Specifically, in this work we find that the picosecond time scale hydrogen-bonding rearrangements taking place in the protein hydration shell with binding modify the packing density within the hydrophobic core on a local level. These localized, intramolecular contact variations within the protein core appear to facilitate the large cooperative movements within the interfacial region separating the α- and β- domain that mediate binding. The THz time-scale fluctuations identified in the protein-ligand system may also reveal a molecular mechanism for substrate recognition.
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