1
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Yang C, Sun X, Wu G. New insights into GATOR2-dependent interactions and its conformational changes in amino acid sensing. Biosci Rep 2024; 44:BSR20240038. [PMID: 38372438 PMCID: PMC10938194 DOI: 10.1042/bsr20240038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024] Open
Abstract
Eukaryotic cells coordinate growth under different environmental conditions via mechanistic target of rapamycin complex 1 (mTORC1). In the amino-acid-sensing signalling pathway, the GATOR2 complex, containing five evolutionarily conserved subunits (WDR59, Mios, WDR24, Seh1L and Sec13), is required to regulate mTORC1 activity by interacting with upstream CASTOR1 (arginine sensor) and Sestrin2 (leucine sensor and downstream GATOR1 complex). GATOR2 complex utilizes β-propellers to engage with CASTOR1, Sestrin2 and GATOR1, removal of these β-propellers results in substantial loss of mTORC1 capacity. However, structural information regarding the interface between amino acid sensors and GATOR2 remains elusive. With the recent progress of the AI-based tool AlphaFold2 (AF2) for protein structure prediction, structural models were predicted for Sentrin2-WDR24-Seh1L and CASTOR1-Mios β-propeller. Furthermore, the effectiveness of relevant residues within the interface was examined using biochemical experiments combined with molecular dynamics (MD) simulations. Notably, fluorescence resonance energy transfer (FRET) analysis detected the structural transition of GATOR2 in response to amino acid signals, and the deletion of Mios β-propeller severely impeded that change at distinct arginine levels. These findings provide structural perspectives on the association between GATOR2 and amino acid sensors and can facilitate future research on structure determination and function.
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Affiliation(s)
- Can Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, the Joint International Research Laboratory of Metabolic and Developmental Sciences MOE, Shanghai Jiao Tong University, Shanghai, China
| | - Xuan Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, the Joint International Research Laboratory of Metabolic and Developmental Sciences MOE, Shanghai Jiao Tong University, Shanghai, China
| | - Geng Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, the Joint International Research Laboratory of Metabolic and Developmental Sciences MOE, Shanghai Jiao Tong University, Shanghai, China
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2
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Bhowmik D, Bhuyan A, Gunalan S, Kothandan G, Kumar D. In silico and immunoinformatics based multiepitope subunit vaccine design for protection against visceral leishmaniasis. J Biomol Struct Dyn 2023:1-22. [PMID: 37655736 DOI: 10.1080/07391102.2023.2252901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023]
Abstract
Visceral leishmaniasis (VL) is a vector-borne neglected tropical protozoan disease with high fatality and no certified vaccine. Conventional vaccine preparation is challenging and tedious. Here in this work, we created a global multiepitope subunit vaccination against VL utilizing innovative immunoinformatics technique based on the extensively conserved epitopic regions of the PrimPol protein of Leishmania donovani consisting of four subunits which were analyzed and studied, out of which DNA primase large subunit and DNA polymerase α subunit B were evaluated as antigens by Vaxijen 2.0. The multiepitope vaccine design includes a single adjuvant β-defensins, eight CTL epitopes, eight HTL epitopes, seven linear BCL epitopes and one discontinuous BCL epitope to induce innate, cellular and humoral immune responses against VL. The Expasy ProtParam tool characterized the physiochemical parameters of the vaccine. At the same time, SOLpro evaluated our vaccine constructs to be soluble upon expression. We also modeled the stable tertiary structure of our vaccine construct through Robetta modeling for molecular docking studies with toll-like receptor proteins through HADDOCK 2.4. Simulations based on molecular dynamics revealed an intact vaccine and TLR8 complex, supporting our vaccine design's immunogenicity. Also, the immune simulation of our vaccine by the C-ImmSim server demonstrated the potency of the multiepitope vaccine construct to induce proper immune response for host defense. Codon optimization and in silico cloning of our vaccine further assured high expression. The outcomes of our study on multiepitope vaccine design significantly produced a potential candidate against VL and can potentially eradicate the disease in the future after clinical investigations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Deep Bhowmik
- Deparment of Microbiology, Assam University, Silchar, Assam, India
| | - Achyut Bhuyan
- Deparment of Microbiology, Assam University, Silchar, Assam, India
| | - Seshan Gunalan
- Biopolymer Modelling Laboratory, Centre of Advanced Study in Crystallography and Biophysics, Guindy Campus, University of Madras, Chennai, India
| | - Gugan Kothandan
- Biopolymer Modelling Laboratory, Centre of Advanced Study in Crystallography and Biophysics, Guindy Campus, University of Madras, Chennai, India
| | - Diwakar Kumar
- Deparment of Microbiology, Assam University, Silchar, Assam, India
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3
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Delgado A, Vera-Villalobos J, Paz JL, Lossada C, Hurtado-León ML, Marrero-Ponce Y, Toro-Mendoza J, Alvarado YJ, González-Paz L. Macromolecular crowding impact on anti-CRISPR AcrIIC3/NmeCas9 complex: Insights from scaled particle theory, molecular dynamics, and elastic networks models. Int J Biol Macromol 2023:125113. [PMID: 37257544 DOI: 10.1016/j.ijbiomac.2023.125113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023]
Abstract
The coupling of Cas9 and its inhibitor AcrIIC3, both from the bacterium Neisseria meningitidis (Nme), form a homodimer of the (NmeCas9/AcrIIC3)2 type. This coupling was studied to assess the impact of their interaction with the crowders in the following environments: (1) homogeneous crowded, (2) heterogeneous, and (3) microheterogeneous cytoplasmic. For this, statistical thermodynamic models based on the scaled particle theory (SPT) were used, considering the attractive and repulsive protein-crowders contributions and the stability of the formation of spherocylindrical homodimers and the effects of changes in the size of spherical dimers were estimated. Studies based on models of dynamics, elastic networks, and statistical potentials to the formation of complexes NmeCas9/AcrIIC3 using PEG as the crowding agent support the predictions from SPT. Macromolecular crowding stabilizes the formation of the dimers, being more significant when the attractive protein-crowder interactions are weaker and the crowders are smaller. The coupling is favored towards the formation of spherical and compact dimers due to crowding addition (excluded-volume effects) and the thermodynamic stability of the dimers is markedly dependent on the size of the crowders. These results support the experimental mechanistic proposal of inhibition of NmeCas9 mediated by AcrIIC3.
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Affiliation(s)
- Ariana Delgado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Biomedicina Molecular (CBM), Laboratorio de Química Biofísica Teórica y Experimental (LQBTE), 4001 Maracaibo, Zulia, Venezuela; Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Química, Laboratorio de Química Teórica y Computacional (LQTC), 4001 Maracaibo, Venezuela
| | - Joan Vera-Villalobos
- Facultad de Ciencias Naturales y Matemáticas, Departamento de Química y Ciencias Ambientales, Laboratorio de Análisis Químico Instrumental (LAQUINS), Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Carla Lossada
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Biomedicina Molecular (CBM), Laboratorio de Biocomputación (LB), 4001 Maracaibo, Zulia, Venezuela
| | - María Laura Hurtado-León
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), 4001 Maracaibo, Venezuela
| | - Yovani Marrero-Ponce
- Universidad San Francisco de Quito (USFQ), Grupo de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias de la Salud (COCSA), Escuela de Medicina, Edificio de Especialidades Médicas, Quito 170157, Pichincha, Ecuador; Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Baja California 22860, Mexico; Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles y vía Interoceánica, Quito 170157, Pichincha, Ecuador
| | - Jhoan Toro-Mendoza
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Biomedicina Molecular (CBM), Laboratorio de Química Biofísica Teórica y Experimental (LQBTE), 4001 Maracaibo, Zulia, Venezuela
| | - Ysaías J Alvarado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Biomedicina Molecular (CBM), Laboratorio de Química Biofísica Teórica y Experimental (LQBTE), 4001 Maracaibo, Zulia, Venezuela.
| | - Lenin González-Paz
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Biomedicina Molecular (CBM), Laboratorio de Biocomputación (LB), 4001 Maracaibo, Zulia, Venezuela.
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Noor A, Qayyum S, Ali Z, Muhammad N. Syntheses and Structural Characterization of Divalent Metal Complexes (Co, Ni, Pd and Zn) of Sterically Hindered Thiourea Ligand and A Theoretical Insight of their Interaction with SARS-CoV-2 Enzyme. J Mol Struct 2022; 1274:134442. [PMID: 36337589 PMCID: PMC9621400 DOI: 10.1016/j.molstruc.2022.134442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 11/08/2022]
Abstract
Reacting two equivalents of sterically hindered 1,3-bis(2,6-diethylphenyl)thiourea ligand (L) with CoCl2, NiBr2, PdX2 (X = Cl; Br) and ZnI2 in acetonitrile afforded the corresponding bulky thiourea ligand stabilized four coordinated monomeric [L2CoCl2] (1), [L2NiBr2] (2), [L2PdX2] (3a: X = Cl; 3b: X = Br) and [L2ZnI2] (4.2CH3CN) complexes. Compound 1, 2 and 4.2CH3CN are tetrahedral whereas Pd complexes (3a and 3b) are square planar. In solution, palladium complexes are dominated by cis-isomers. Structural characterization shows inter- and intramolecular hydrogen bonding. Hirshfeld surface and fingerprint plots indicated significant intermolecular interactions in the crystal network. Molecular docking analysis revealed relatively higher SARS-CoV-2 enzyme interacting abilities of the synthesized complexes compared to the free ligand. All compounds have been characterized by elemental analyses, NMR spectroscopy and single-crystal X-ray diffraction.
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Affiliation(s)
- Awal Noor
- Department of Basic Sciences, Preparatory Year Deanship, King Faisal University, 31982 Al-Hassa, Saudi Arabia,Corresponding Author:
| | - Sadaf Qayyum
- Department of Basic Sciences, Preparatory Year Deanship, King Faisal University, 31982 Al-Hassa, Saudi Arabia
| | - Zafar Ali
- Department of Chemistry, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Niaz Muhammad
- Department of Chemistry, Abdul Wali Khan University, Mardan, KPK, Pakistan
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5
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Mondal A, Paul D, Dastidar SG, Saha T, Goswami AM. In silico analyses of Wnt1 nsSNPs reveal structurally destabilizing variants, altered interactions with Frizzled receptors and its deregulation in tumorigenesis. Sci Rep 2022; 12:14934. [PMID: 36056132 PMCID: PMC9440047 DOI: 10.1038/s41598-022-19299-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022] Open
Abstract
Wnt1 is the first mammalian Wnt gene, which is discovered as proto-oncogene and in human the gene is located on the chromosome 12q13. Mutations in Wnt1 are reported to be associated with various cancers and other human diseases. The structural and functional consequences of most of the non-synonymous SNPs (nsSNPs), present in the human Wnt1 gene, are not known. In the present work, extensive bioinformatics analyses are used to screen 292 nsSNPs of Wnt1 for predicting pathogenic and harmless polymorphisms. We have identified 10 highly deleterious nsSNPs among which 7 are located within the highly conserved areas. These 10 nsSNPs are also predicted to affect the post-translational modifications of Wnt1. Further, structure based stability analyses of these 10 highly deleterious nsSNPs revealed 8 variants as highly destabilizing. These 8 highly destabilizing variants were shown to have high BC score and high RMSIP score from normal mode analyses. Based on the deformation energies, obtained from the normal mode analyses, variants like G169A, G169S, G331R and G331S were found to be unstable. Molecular Dynamics (MD) simulations revealed structural stability and fluctuation of WT Wnt1 and its prioritized variants. RMSD remained fluctuating mostly between 4 and 5 Å and occasionally between 3.5 and 5.5 Å ranges. RMSF in the CTD region (residues 330–360) of the binding pocket were lower compared to that of WT. Studying the impacts of nsSNPs on the binding interface of Wnt1 and seven Frizzled receptors have predicted substitutions which can stabilize or destabilize the binding interface. We have found that Wnt1 and FZD8-CRD is the best docked complex in our study. MD simulation based analyses of wild type Wnt1-FZD8-CRD complex and the 8 prioritized variants revealed that RMSF was higher in the unstructured regions and RMSD remained fluctuating in the region of 5 Å ± 1 Å. We have also observed differential Wnt1 gene expression pattern in normal, tumor and metastatic conditions across different tissues. Wnt1 gene expression was significantly higher in metastatic tissues of lungs, colon and skin; and was significantly lower in metastatic tissues of breast, esophagus and kidney. We have also found that Wnt1 deregulation is associated with survival outcome in patients with gastric and breast cancer. Furthermore, these computationally screened highly deleterious nsSNPs of Wnt1 can be analyzed in population based genetic studies and may help understand the Wnt1 associated diseases.
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Affiliation(s)
- Amalesh Mondal
- Department of Physiology, Katwa College, Purba Bardhaman, Katwa, West Bengal, 713130, India.,Department of Molecular Biology and Biotechnology, University of Kalyani, Nadia, Kalyani, India
| | - Debarati Paul
- Division of Bioinformatics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Shubhra Ghosh Dastidar
- Division of Bioinformatics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Tanima Saha
- Department of Molecular Biology and Biotechnology, University of Kalyani, Nadia, Kalyani, India.
| | - Achintya Mohan Goswami
- Department of Physiology, Krishnagar Govt. College, Nadia, Krishnagar, West Bengal, 741101, India.
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6
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Mononuclear Tricoordinate Copper(I) and Silver(I) Halide Complexes of a Sterically Bulky Thiourea Ligand and a Computational Insight of Their Interaction with Human Insulin. Molecules 2022; 27:molecules27134231. [PMID: 35807475 PMCID: PMC9268019 DOI: 10.3390/molecules27134231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 12/04/2022] Open
Abstract
Reaction of two equivalents of the bulky 1,3-bis(2,6-diethylphenyl)thiourea ligand (L) with MX (being M = Cu+, Ag+; and X = Cl−, Br−, I−) in acetonitrile afforded neutral complexes of the type [MXL2] [CuClL2].2CH3CN (1a); [CuBrL2].2CH3CN (1b); [CuIL2] (1c): [AgClL2] (2a); [AgBrL2] (2b) and [AgIL2] (2c). The two aromatic groups in free ligand were found to be trans with respect to the thiourea unit, which was a reason to link the ligand molecules via intermolecular hydrogen bonding. Intramolecular hydrogen bonding was observed in all metal complexes. The copper complexes 1a and 1b are acetonitrile solvated and show not only intra- but also intermolecular hydrogen bonding between the coordinated thiourea and the solvated acetonitrile molecules. Silver complexes reported here are the first examples of structurally characterized tricoordinated thiourea-stabilized monomeric silver(I) halides. Molecular docking studies were carried out to analyze the binding modes of the metal complexes inside the active site of the human insulin (HI) protein. Analysis of the docked conformations revealed that the electrostatic and aromatic interactions of the protein N-terminal residues (i.e., Phe and His) may assist in anchoring and stabilizing the metal complexes inside the active site. According to the results of docking studies, the silver complexes exhibited the strongest inhibitory capability against the HI protein, which possesses a deactivating group, directly bonded to silver. All compounds were fully characterized by elemental analysis, NMR spectroscopy, and molecular structures of the ligand, and five out of six metal complexes were also confirmed by single-crystal X-ray diffraction.
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7
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Zimmermann MT. Molecular Modeling is an Enabling Approach to Complement and Enhance Channelopathy Research. Compr Physiol 2022; 12:3141-3166. [PMID: 35578963 DOI: 10.1002/cphy.c190047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Hundreds of human membrane proteins form channels that transport necessary ions and compounds, including drugs and metabolites, yet details of their normal function or how function is altered by genetic variants to cause diseases are often unknown. Without this knowledge, researchers are less equipped to develop approaches to diagnose and treat channelopathies. High-resolution computational approaches such as molecular modeling enable researchers to investigate channelopathy protein function, facilitate detailed hypothesis generation, and produce data that is difficult to gather experimentally. Molecular modeling can be tailored to each physiologic context that a protein may act within, some of which may currently be difficult or impossible to assay experimentally. Because many genomic variants are observed in channelopathy proteins from high-throughput sequencing studies, methods with mechanistic value are needed to interpret their effects. The eminent field of structural bioinformatics integrates techniques from multiple disciplines including molecular modeling, computational chemistry, biophysics, and biochemistry, to develop mechanistic hypotheses and enhance the information available for understanding function. Molecular modeling and simulation access 3D and time-dependent information, not currently predictable from sequence. Thus, molecular modeling is valuable for increasing the resolution with which the natural function of protein channels can be investigated, and for interpreting how genomic variants alter them to produce physiologic changes that manifest as channelopathies. © 2022 American Physiological Society. Compr Physiol 12:3141-3166, 2022.
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Affiliation(s)
- Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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8
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A Comparative Evaluation of the Structural and Dynamic Properties of Insect Odorant Binding Proteins. Biomolecules 2022; 12:biom12020282. [PMID: 35204784 PMCID: PMC8961588 DOI: 10.3390/biom12020282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 02/01/2023] Open
Abstract
Insects devote a major part of their metabolic resources to the production of odorant binding proteins (OBPs). Although initially, these proteins were implicated in the solubilisation, binding and transport of semiochemicals to olfactory receptors, it is now recognised that they may play diverse, as yet uncharacterised, roles in insect physiology. The structures of these OBPs, the majority of which are known as “classical” OBPs, have shed some light on their potential functional roles. However, the dynamic properties of these proteins have received little attention despite their functional importance. Structural dynamics are encoded in the native protein fold and enable the adaptation of proteins to substrate binding. This paper provides a comparative review of the structural and dynamic properties of OBPs, making use of sequence/structure analysis, statistical and theoretical physics-based methods. It provides a new layer of information and additional methodological tools useful in unravelling the relationship between structure, dynamics and function of insect OBPs. The dynamic properties of OBPs, studied by means of elastic network models, reflect the similarities/dissimilarities observed in their respective structures and provides insights regarding protein motions that may have important implications for ligand recognition and binding. Furthermore, it was shown that the OBPs studied in this paper share conserved structural ‘core’ that may be of evolutionary and functional importance.
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9
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González-Paz L, Hurtado-León ML, Lossada C, Fernández-Materán FV, Vera-Villalobos J, Loroño M, Paz JL, Jeffreys L, Alvarado YJ. Structural deformability induced in proteins of potential interest associated with COVID-19 by binding of homologues present in ivermectin: Comparative study based in elastic networks models. J Mol Liq 2021; 340:117284. [PMID: 34421159 PMCID: PMC8367659 DOI: 10.1016/j.molliq.2021.117284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 12/24/2022]
Abstract
The COVID-19 pandemic has accelerated the study of the potential of multi-target drugs (MTDs). The mixture of homologues called ivermectin (avermectin-B1a + avermectin-B1b) has been shown to be a MTD with potential antiviral activity against SARS-CoV-2 in vitro. However, there are few reports on the effect of each homologue on the flexibility and stiffness of proteins associated with COVID-19, described as ivermectin targets. We observed that each homologue was stably bound to the proteins studied and was able to induce detectable changes with Elastic Network Models (ENM). The perturbations induced by each homologue were characteristic of each compound and, in turn, were represented by a disruption of native intramolecular networks (interactions between residues). The homologues were able to slightly modify the conformation and stability of the connection points between the Cα atoms of the residues that make up the structural network of proteins (nodes), compared to free proteins. Each homologue was able to modified differently the distribution of quasi-rigid regions of the proteins, which could theoretically alter their biological activities. These results could provide a biophysical-computational view of the potential MTD mechanism that has been reported for ivermectin.
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Affiliation(s)
- Lenin González-Paz
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología. Laboratorio de Genética y Biología Molecular (LGBM), 4001 Maracaibo, Republica Bolivariana de Venezuela.,Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Estudios Botánicos y Agroforestales (CEBA), Laboratorio de Protección Vegetal (LPV), 4001 Maracaibo, Republica Bolivariana de Venezuela
| | - María Laura Hurtado-León
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología. Laboratorio de Genética y Biología Molecular (LGBM), 4001 Maracaibo, Republica Bolivariana de Venezuela
| | - Carla Lossada
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Republica Bolivariana de Venezuela
| | - Francelys V Fernández-Materán
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Republica Bolivariana de Venezuela
| | - Joan Vera-Villalobos
- Facultad de Ciencias Naturales y Matemáticas, Departamento de Química y Ciencias Ambientales, Laboratorio de Análisis Químico Instrumental (LAQUINS), Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Marcos Loroño
- Departamento Académico de Química Analítica e Instrumental, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - J L Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Laura Jeffreys
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Ysaias J Alvarado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Republica Bolivariana de Venezuela
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10
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Padhi AK, Dandapat J, Saudagar P, Uversky VN, Tripathi T. Interface-based design of the favipiravir-binding site in SARS-CoV-2 RNA-dependent RNA polymerase reveals mutations conferring resistance to chain termination. FEBS Lett 2021; 595:2366-2382. [PMID: 34409597 PMCID: PMC8426738 DOI: 10.1002/1873-3468.14182] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/18/2021] [Accepted: 08/16/2021] [Indexed: 01/18/2023]
Abstract
Favipiravir is a broad‐spectrum inhibitor of viral RNA‐dependent RNA polymerase (RdRp) currently being used to manage COVID‐19. Accumulation of mutations in severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) RdRp may facilitate antigenic drift, generating favipiravir resistance. Focussing on the chain‐termination mechanism utilized by favipiravir, we used high‐throughput interface‐based protein design to generate > 100 000 designs of the favipiravir‐binding site of RdRp and identify mutational hotspots. We identified several single‐point mutants and designs having a sequence identity of 97%–98% with wild‐type RdRp, suggesting that SARS‐CoV‐2 can develop favipiravir resistance with few mutations. Out of 134 mutations documented in the CoV‐GLUE database, 63 specific mutations were already predicted as resistant in our calculations, thus attaining ˜ 47% correlation with the sequencing data. These findings improve our understanding of the potential signatures of adaptation in SARS‐CoV‐2 against favipiravir.
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Affiliation(s)
- Aditya K Padhi
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
| | - Jagneshwar Dandapat
- Centre of Excellence in Integrated Omics and Computational Biology, Utkal University, Bhubaneswar, India.,Post Graduate Department of Biotechnology, Utkal University, Bhubaneswar, India
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology-Warangal, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
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11
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Padhi AK, Tripathi T. Targeted design of drug binding sites in the main protease of SARS-CoV-2 reveals potential signatures of adaptation. Biochem Biophys Res Commun 2021; 555:147-153. [PMID: 33813274 PMCID: PMC7997393 DOI: 10.1016/j.bbrc.2021.03.118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 03/20/2021] [Indexed: 12/15/2022]
Abstract
Several existing drugs are currently being tested worldwide to treat COVID-19 patients. Recent data indicate that SARS-CoV-2 is rapidly evolving into more transmissible variants. It is therefore highly possible that SARS-CoV-2 can accumulate adaptive mutations modulating drug susceptibility and hampering viral antigenicity. Thus, it is vital to predict potential non-synonymous mutation sites and predict the evolution of protein structural modifications leading to drug tolerance. As two FDA-approved anti-hepatitis C virus (HCV) drugs, boceprevir, and telaprevir, have been shown to effectively inhibit SARS-CoV-2 by targeting the main protease (Mpro), here we used a high-throughput interface-based protein design strategy to identify mutational hotspots and potential signatures of adaptation in these drug binding sites of Mpro. Several mutants exhibited reduced binding affinity to these drugs, out of which hotspot residues having a strong tendency to undergo positive selection were identified. The data further indicated that these anti-HCV drugs have larger footprints in the mutational landscape of Mpro and hence encompass the highest potential for positive selection and adaptation. These findings are crucial in understanding the potential structural modifications in the drug binding sites of Mpro and thus its signatures of adaptation. Furthermore, the data could provide systemic strategies for robust antiviral design and discovery against COVID-19 in the future.
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Affiliation(s)
- Aditya K. Padhi
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Kanagawa, 230-0045, Japan,Corresponding author
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India,Corresponding author
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12
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Could Dermaseptin Analogue be a Competitive Inhibitor for ACE2 Towards Binding with Viral Spike Protein Causing COVID19?: Computational Investigation. Int J Pept Res Ther 2021; 27:1043-1056. [PMID: 33488318 PMCID: PMC7811342 DOI: 10.1007/s10989-020-10149-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2020] [Indexed: 12/12/2022]
Abstract
Initial phase of COVID-19 infection is associated with the binding of viral spike protein S1 receptor binding domain (RBD) with the host cell surface receptor, ACE2. Peptide inhibitors typically interact with spike proteins in order to block its interaction with ACE2, and this knowledge would promote the use of such peptides as therapeutic scaffolds. The present study examined the competitive inhibitor activity of a broad spectrum antimicrobial peptide, Dermaseptin-S4 (S4) and its analogues. Three structural S4 analogues viz., S4 (K4), S4 (K20) and S4 (K4K20) were modelled by substituting charged lysine for non-polar residues in S4 and subsequently, docked with S1. Further, the comparative analysis of inter-residue contacts and non-covalent intermolecular interactions among S1–S4 (K4), S1–S4 (K4K20) and S1–ACE2 complexes were carried out to explore their mode of binding with S1. Interestingly, S1–S4 (K4) established more inter-molecular interactions compared to S4 (K4K20) and S1–ACE2. In order to substantiate this study, the normal mode analysis (NMA) was conducted to show how the structural stability of the flexible loop region in S1 is affected by atomic displacements in unbound S1 and docked complexes. Markedly, the strong interactions consistently maintained by S1–S4 (K4) complex revealed their conformational transition over the harmonic motion period. Moreover, S1–S4 (K4) peptide complex showed a higher energy deformation profile compared to S1–S4 (K4K20), where the higher energy deformation suggests the rigidity of the docked complex and thus it’s harder deformability, which is also substantiated by molecular dynamics simulation. In conclusion, S1–S4 (K4) complex has definitely exhibited a functionally significant dynamics compared to S1–ACE2 complex; this peptide inhibitor, S4 (K4) will need to be considered as the best therapeutic scaffold to block SARS-CoV-2 infection.
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13
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Banerjee A, Mitra P. Ebola Virus VP35 Protein: Modeling of the Tetrameric Structure and an Analysis of Its Interaction with Human PKR. J Proteome Res 2020; 19:4533-4542. [PMID: 32871072 PMCID: PMC7640970 DOI: 10.1021/acs.jproteome.0c00473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Indexed: 01/12/2023]
Abstract
The Viral Protein 35 (VP35), a crucial protein of the Zaire Ebolavirus (EBOV), interacts with a plethora of human proteins to cripple the human immune system. Despite its importance, the entire structure of the tetrameric assembly of EBOV VP35 and the means by which it antagonizes the autophosphorylation of the kinase domain of human protein kinase R (PKRK) is still elusive. We consult existing structural information to model a tetrameric assembly of the VP35 protein where 93% of the protein is modeled using crystal structure templates. We analyze our modeled tetrameric structure to identify interchain bonding networks and use molecular dynamics simulations and normal-mode analysis to unravel the flexibility and deformability of the different regions of the VP35 protein. We establish that the C-terminal of VP35 (VP35C) directly interacts with PKRK to prevent it from autophosphorylation. Further, we identify three plausible VP35C-PKRK complexes with better affinity than the PKRK dimer formed during autophosphorylation and use protein design to establish a new stretch in VP35C that interacts with PKRK. The proposed tetrameric assembly will aid in better understanding of the VP35 protein, and the reported VP35C-PKRK complexes along with their interacting sites will help in the shortlisting of small molecule inhibitors.
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Affiliation(s)
- Anupam Banerjee
- Advanced
Technology Development Centre, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Pralay Mitra
- Department
of Computer Science and Engineering, Indian
Institute of Technology Kharagpur, West Bengal 721302, India
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14
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Grant BJ, Skjaerven L, Yao XQ. The Bio3D packages for structural bioinformatics. Protein Sci 2020; 30:20-30. [PMID: 32734663 DOI: 10.1002/pro.3923] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 12/21/2022]
Abstract
Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis named ensemble difference distance matrix analysis (eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise determinants underlying specific functional processes. An eDDM workflow is detailed along with an example application to a large protein family. As a new member of the Bio3D family, the Bio3D-eddm package supports both experimental and theoretical simulation-generated structures, is integrated with other methods for dissecting sequence-structure-function relationships, and can be used in a highly automated and reproducible manner. Bio3D is distributed as an integrated set of platform independent open source R packages available from: http://thegrantlab.org/bio3d/.
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Affiliation(s)
- Barry J Grant
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, California, USA
| | - Lars Skjaerven
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, California, USA
| | - Xin-Qiu Yao
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
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15
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Basak N, Krishnan V, Pandey V, Punjabi M, Hada A, Marathe A, Jolly M, Palaka BK, Ampasala DR, Sachdev A. Expression profiling and in silico homology modeling of Inositol penta kisphosphate 2-kinase, a potential candidate gene for low phytate trait in soybean. 3 Biotech 2020; 10:268. [PMID: 32523862 DOI: 10.1007/s13205-020-02260-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/14/2020] [Indexed: 11/27/2022] Open
Abstract
Low phytate soybeans are desirable both from a nutritional and economic standpoint. Inositol 1, 3, 4, 5, 6-pentakisphosphate 2-kinase (IPK1), optimizes the metabolic flux of phytate generation in soybean and thus shows much promise as a likely candidate for pathway regulation. In the present study, the differential spatial and temporal expression profiling of GmIpk1 and its two homologs Glyma06g03310 and Glyma04g03310 were carried out in Glycine max L. var Pusa 9712 revealing the early stages of seed development to be the potential target for gene manipulation. NCBI databank was screened using BLASTp to retrieve 32 plant IPK1 sequences showing high homology to GmIPK1 and its homologs. Bio-computational tools were employed to predict the protein's properties, conserved domains, and secondary structures. Using state-of-the-art in silico physicochemical approach, the three-dimensional (3D) GmIPK1 protein model (PMD ID-PM0079931), was developed based on Arabidopsis thaliana (PDB ID: 4AQK). Superimposition of 4AQK and best model of GmIPK1 revealed that the GmIPK1 aligned well and shows a sequence identity score of 54.32% with 4AQK and a low RMSD of 0.163 nm and almost similar structural features. The modeled structure was further refined considering the stereochemical geometry, energy and packing environment between the model and the template along with validation of its intrinsic dynamics. Molecular dynamics simulation studies of GmIPK1 were carried out to obtain structural insights and to understand the interactive behavior of this enzyme with ligands ADP and IP6. The results of this study provide some fundamental knowledge on the distinct mechanistic step performed by the key residues to elucidate the structure-function relationship of GmIPK1, as an initiative towards engineering "low phytate soybean".
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Affiliation(s)
- Nabaneeta Basak
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- Crop Physiology and Biochemistry Division, ICAR-National Rice Research Institute, Cuttack, Odisha 753006 India
| | - Veda Krishnan
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Vanita Pandey
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- Quality and Basic Sciences Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India
| | - Mansi Punjabi
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Alkesh Hada
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Ashish Marathe
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- Biotechnology Lab, ICAR-National Institute of Biotic Stress Management, Raipur, Chattisgarh 493225 India
| | - Monica Jolly
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | - Dinakara R Ampasala
- Centre for Bioinformatics, Pondicherry University, Puducherry, 605 014 India
| | - Archana Sachdev
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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16
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Stanisci A, Tøndervik A, Gaardløs M, Lervik A, Skjåk-Bræk G, Sletta H, Aachmann FL. Identification of a Pivotal Residue for Determining the Block Structure-Forming Properties of Alginate C-5 Epimerases. ACS OMEGA 2020; 5:4352-4361. [PMID: 32149266 PMCID: PMC7057702 DOI: 10.1021/acsomega.9b04490] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 02/11/2020] [Indexed: 05/13/2023]
Abstract
Alginate is a linear copolymer composed of 1→4 linked β-d-mannuronic acid (M) and its epimer α-l-guluronic acid (G). The polysaccharide is first produced as homopolymeric mannuronan and subsequently, at the polymer level, C-5 epimerases convert M residues to G residues. The bacterium Azotobacter vinelandii encodes a family of seven secreted and calcium ion-dependent mannuronan C-5 epimerases (AlgE1-AlgE7). These epimerases consist of two types of structural modules: the A-modules, which contain the catalytic site, and the R-modules, which influence activity through substrate and calcium binding. In this study, we rationally designed new hybrid mannuronan C-5 epimerases constituting the A-module from AlgE6 and the R-module from AlgE4. This led to a better understanding of the molecular mechanism determining differences in MG- and GG-block-forming properties of the enzymes. A long loop with either tyrosine or phenylalanine extruding from the β-helix of the enzyme proved essential in defining the final alginate block structure, probably by affecting substrate binding. Normal mode analysis of the A-module from AlgE6 supports the results.
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Affiliation(s)
- Annalucia Stanisci
- Department
of Biotechnology and Food Science, NTNU
Norwegian University of Science and Technology, Norwegian Biopolymer
Laboratory (NOBIPOL), Sem Sælands vei 6/8, NO 7491 Trondheim, Norway
| | - Anne Tøndervik
- Department
of Biotechnology and Nanomedicine, SINTEF
Industry, Richard Birkelands
veg 3 B, NO 7491 Trondheim, Norway
| | - Margrethe Gaardløs
- Department
of Biotechnology and Food Science, NTNU
Norwegian University of Science and Technology, Norwegian Biopolymer
Laboratory (NOBIPOL), Sem Sælands vei 6/8, NO 7491 Trondheim, Norway
| | - Anders Lervik
- Department
of Chemistry, NTNU Norwegian University
of Science and Technology, Høgskoleringen 5, NO 7491 Trondheim, Norway
| | - Gudmund Skjåk-Bræk
- Department
of Biotechnology and Food Science, NTNU
Norwegian University of Science and Technology, Norwegian Biopolymer
Laboratory (NOBIPOL), Sem Sælands vei 6/8, NO 7491 Trondheim, Norway
| | - Håvard Sletta
- Department
of Biotechnology and Nanomedicine, SINTEF
Industry, Richard Birkelands
veg 3 B, NO 7491 Trondheim, Norway
| | - Finn L. Aachmann
- Department
of Biotechnology and Food Science, NTNU
Norwegian University of Science and Technology, Norwegian Biopolymer
Laboratory (NOBIPOL), Sem Sælands vei 6/8, NO 7491 Trondheim, Norway
- E-mail: . Phone: +4773593317. Fax: +4773591283
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17
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Yang JF, Wang F, Chen YZ, Hao GF, Yang GF. LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor. Brief Bioinform 2019; 21:2206-2218. [DOI: 10.1093/bib/bbz141] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/12/2019] [Accepted: 10/14/2019] [Indexed: 12/14/2022] Open
Abstract
Abstract
Protein dynamics is central to all biological processes, including signal transduction, cellular regulation and biological catalysis. Among them, in-depth exploration of ligand-driven protein dynamics contributes to an optimal understanding of protein function, which is particularly relevant to drug discovery. Hence, a wide range of computational tools have been designed to investigate the important dynamic information in proteins. However, performing and analyzing protein dynamics is still challenging due to the complicated operation steps, giving rise to great difficulty, especially for nonexperts. Moreover, there is a lack of web protocol to provide online facility to investigate and visualize ligand-driven protein dynamics. To this end, in this study, we integrated several bioinformatic tools to develop a protocol, named Ligand and Receptor Molecular Dynamics (LARMD, http://chemyang.ccnu.edu.cn/ccb/server/LARMD/ and http://agroda.gzu.edu.cn:9999/ccb/server/LARMD/), for profiling ligand-driven protein dynamics. To be specific, estrogen receptor (ER) was used as a case to reveal ERβ-selective mechanism, which plays a vital role in the treatment of inflammatory diseases and many types of cancers in clinical practice. Two different residues (Ile373/Met421 and Met336/Leu384) in the pocket of ERβ/ERα were the significant determinants for selectivity, especially Met336 of ERβ. The helix H8, helix H11 and H7-H8 loop influenced the migration of selective agonist (WAY-244). These computational results were consistent with the experimental results. Therefore, LARMD provides a user-friendly online protocol to study the dynamic property of protein and to design new ligand or site-directed mutagenesis.
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Affiliation(s)
- Jing-Fang Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P.R.China
- International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University,Wuhan, 430079, China
| | - Fan Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P.R.China
- International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University,Wuhan, 430079, China
| | - Yu-Zong Chen
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543
| | - Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P.R.China
- International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University,Wuhan, 430079, China
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P.R.China
- International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University,Wuhan, 430079, China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjing 300072, P.R.China
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18
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Kuriata A, Gierut AM, Oleniecki T, Ciemny MP, Kolinski A, Kurcinski M, Kmiecik S. CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures. Nucleic Acids Res 2019; 46:W338-W343. [PMID: 29762700 PMCID: PMC6031000 DOI: 10.1093/nar/gky356] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/27/2018] [Indexed: 11/13/2022] Open
Abstract
Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface. CABS-flex 2.0 is freely available at http://biocomp.chem.uw.edu.pl/CABSflex2.
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Affiliation(s)
- Aleksander Kuriata
- University of Warsaw, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Aleksandra Maria Gierut
- University of Warsaw, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland.,Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Krakow, Poland
| | - Tymoteusz Oleniecki
- University of Warsaw, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
| | - Maciej Pawel Ciemny
- University of Warsaw, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland.,Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Andrzej Kolinski
- University of Warsaw, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Mateusz Kurcinski
- University of Warsaw, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Sebastian Kmiecik
- University of Warsaw, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
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19
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Li H, Chang YY, Lee JY, Bahar I, Yang LW. DynOmics: dynamics of structural proteome and beyond. Nucleic Acids Res 2019; 45:W374-W380. [PMID: 28472330 PMCID: PMC5793847 DOI: 10.1093/nar/gkx385] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/25/2017] [Indexed: 01/07/2023] Open
Abstract
DynOmics (dynomics.pitt.edu) is a portal developed to leverage rapidly growing structural proteomics data by efficiently and accurately evaluating the dynamics of structurally resolved systems, from individual molecules to large complexes and assemblies, in the context of their physiological environment. At the core of the portal is a newly developed server, ENM 1.0, which permits users to efficiently generate information on the collective dynamics of any structure in PDB format, user-uploaded or database-retrieved. ENM 1.0 integrates two widely used elastic network models (ENMs)—the Gaussian Network Model (GNM) and the Anisotropic Network Model (ANM), extended to take account of molecular environment. It enables users to assess potentially functional sites, signal transduction or allosteric communication mechanisms, and protein–protein and protein–DNA interaction poses, in addition to delivering ensembles of accessible conformers reconstructed at atomic details based on the global modes of motions predicted by the ANM. The ‘environment’ is defined in a flexible manner, from lipid bilayer and crystal contacts, to substrate or ligands bound to a protein, or surrounding subunits in a multimeric structure or assembly. User-friendly interactive features permit users to easily visualize how the environment alter the intrinsic dynamics of the query systems. ENM 1.0 can be accessed at http://enm.pitt.edu/ or http://dyn.life.nthu.edu.tw/oENM/.
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Affiliation(s)
- Hongchun Li
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh PA, 15213, USA
| | - Yuan-Yu Chang
- Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Taiwan
| | - Ji Young Lee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh PA, 15213, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh PA, 15213, USA
| | - Lee-Wei Yang
- Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Taiwan
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20
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Chasapis CT. Building Bridges Between Structural and Network-Based Systems Biology. Mol Biotechnol 2019; 61:221-229. [DOI: 10.1007/s12033-018-0146-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models. Int J Mol Sci 2018; 19:ijms19113496. [PMID: 30404229 PMCID: PMC6274762 DOI: 10.3390/ijms19113496] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 12/13/2022] Open
Abstract
Fluctuations of protein three-dimensional structures and large-scale conformational transitions are crucial for the biological function of proteins and their complexes. Experimental studies of such phenomena remain very challenging and therefore molecular modeling can be a good alternative or a valuable supporting tool for the investigation of large molecular systems and long-time events. In this minireview, we present two alternative approaches to the coarse-grained (CG) modeling of dynamic properties of protein systems. We discuss two CG representations of polypeptide chains used for Monte Carlo dynamics simulations of protein local dynamics and conformational transitions, and highly simplified structure-based elastic network models of protein flexibility. In contrast to classical all-atom molecular dynamics, the modeling strategies discussed here allow the quite accurate modeling of much larger systems and longer-time dynamic phenomena. We briefly describe the main features of these models and outline some of their applications, including modeling of near-native structure fluctuations, sampling of large regions of the protein conformational space, or possible support for the structure prediction of large proteins and their complexes.
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22
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Intrinsic dynamics study identifies two amino acids of TIMP-1 critical for its LRP-1-mediated endocytosis in neurons. Sci Rep 2017; 7:5375. [PMID: 28710453 PMCID: PMC5511134 DOI: 10.1038/s41598-017-05039-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 05/24/2017] [Indexed: 01/28/2023] Open
Abstract
The tissue inhibitor of metalloproteinases-1 (TIMP-1) exerts inhibitory activity against matrix metalloproteinases and cytokine-like effects. We previously showed that TIMP-1 reduces neurite outgrowth in mouse cortical neurons and that this cytokine-like effect depends on TIMP-1 endocytosis mediated by the low-density lipoprotein receptor-related protein-1 (LRP-1). To gain insight into the interaction between TIMP-1 and LRP-1, we considered conformational changes that occur when a ligand binds to its receptor. TIMP-1 conformational changes have been studied using biomolecular simulations, and our results provide evidence for a hinge region that is critical for the protein movement between the N- and C-terminal TIMP-1 domains. In silico mutants have been proposed on residues F12 and K47, which are located in the hinge region. Biological analyses of these mutants show that F12A or K47A mutation does not alter MMP inhibitory activity but impairs the effect of TIMP-1 on neurite outgrowth. Interestingly, these mutants bind to LRP-1 but are not endocytosed. We conclude that the intrinsic dynamics of TIMP-1 are not involved in its binding to LRP-1 but rather in the initiation of endocytosis and associated biological effects.
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23
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Madani A, Garakani K, Mofrad MRK. Molecular mechanics of Staphylococcus aureus adhesin, CNA, and the inhibition of bacterial adhesion by stretching collagen. PLoS One 2017; 12:e0179601. [PMID: 28665944 PMCID: PMC5493303 DOI: 10.1371/journal.pone.0179601] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/31/2017] [Indexed: 02/05/2023] Open
Abstract
Bacterial adhesion to collagen, the most abundant protein in humans, is a critical step in the initiation and persistence of numerous bacterial infections. In this study, we explore the collagen binding mechanism of the multi-modular cell wall anchored collagen adhesin (CNA) in Staphylococcus aureus and examine how applied mechanical forces can modulate adhesion ability. The common structural-functional elements and domain organization of CNA are present across over 50 genera of bacteria. Through the use of molecular dynamics models and normal mode analysis, we shed light on the CNA's structural and conformational dynamics and its interactions with collagen that lead to collagen binding. Our results suggest that the linker region, CNA165-173, acts as a hinge exhibiting bending, extensional, and torsional modes of structural flexibility and its residues are key in the interaction of the CNA-collagen complex. Steered molecular dynamics simulations were conducted with umbrella sampling. During the course of these simulations, the 'locking' latch from the CNA N2 domain was dissociated from its groove in the CNA N1 domain, implying the importance of the latch for effective ligand binding. Finally, we observed that the binding efficiency of the CNA N1-N2 domains to collagen decreases greatly with increasing tensile force application to the collagen peptides. Thus, CNA and similar adhesins might preferentially bind to sites in which collagen fibers are cleaved, such as in wounded, injured, or inflamed tissues, or in which the collagenous tissue is less mature. As alternative techniques for control of bacterial infection are in-demand due to the rise of bacterial antibiotic resistance, results from our computational studies with respect to the mechanoregulation of the collagen binding site may inspire new therapeutics and engineering solutions by mechanically preventing colonization and/or further pathogenesis.
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Affiliation(s)
- Ali Madani
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, California, United States of America
| | - Kiavash Garakani
- 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
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America
- * E-mail:
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24
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Stetz G, Verkhivker GM. Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks. J Chem Inf Model 2016; 56:1490-517. [DOI: 10.1021/acs.jcim.5b00755] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Gabrielle Stetz
- Graduate
Program in Computational and Data Sciences, Department of Computational
Sciences, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Gennady M. Verkhivker
- Graduate
Program in Computational and Data Sciences, Department of Computational
Sciences, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
- Chapman University School of Pharmacy, Irvine, California 92618, United States
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25
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Tiwari SP, Reuter N. Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes. PLoS Comput Biol 2016; 12:e1004834. [PMID: 27015412 PMCID: PMC4807811 DOI: 10.1371/journal.pcbi.1004834] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/25/2016] [Indexed: 11/19/2022] Open
Abstract
The conservation of the intrinsic dynamics of proteins emerges as we attempt to understand the relationship between sequence, structure and functional conservation. We characterise the conservation of such dynamics in a case where the structure is conserved but function differs greatly. The triosephosphate isomerase barrel fold (TBF), renowned for its 8 β-strand-α-helix repeats that close to form a barrel, is one of the most diverse and abundant folds found in known protein structures. Proteins with this fold have diverse enzymatic functions spanning five of six Enzyme Commission classes, and we have picked five different superfamily candidates for our analysis using elastic network models. We find that the overall shape is a large determinant in the similarity of the intrinsic dynamics, regardless of function. In particular, the β-barrel core is highly rigid, while the α-helices that flank the β-strands have greater relative mobility, allowing for the many possibilities for placement of catalytic residues. We find that these elements correlate with each other via the loops that link them, as opposed to being directly correlated. We are also able to analyse the types of motions encoded by the normal mode vectors of the α-helices. We suggest that the global conservation of the intrinsic dynamics in the TBF contributes greatly to its success as an enzymatic scaffold both through evolution and enzyme design.
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Affiliation(s)
- Sandhya P. Tiwari
- Department of Molecular Biology, University of Bergen, Pb. 7803, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Pb. 7803, Bergen, Norway
| | - Nathalie Reuter
- Department of Molecular Biology, University of Bergen, Pb. 7803, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Pb. 7803, Bergen, Norway
- * E-mail:
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26
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Hati S, Bhattacharyya S. Incorporating modeling and simulations in undergraduate biophysical chemistry course to promote understanding of structure-dynamics-function relationships in proteins. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 44:140-159. [PMID: 26801683 DOI: 10.1002/bmb.20942] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 11/15/2015] [Indexed: 06/05/2023]
Abstract
A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and simulations. In particular, modern computational tools are employed to elucidate the relationship between structure, dynamics, and function in proteins. Computer-based laboratory protocols that we introduced in three modules allow students to visualize the secondary, super-secondary, and tertiary structures of proteins, analyze non-covalent interactions in protein-ligand complexes, develop three-dimensional structural models (homology model) for new protein sequences and evaluate their structural qualities, and study proteins' intrinsic dynamics to understand their functions. In the fourth module, students are assigned to an authentic research problem, where they apply their laboratory skills (acquired in modules 1-3) to answer conceptual biophysical questions. Through this process, students gain in-depth understanding of protein dynamics-the missing link between structure and function. Additionally, the requirement of term papers sharpens students' writing and communication skills. Finally, these projects result in new findings that are communicated in peer-reviewed journals.
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Affiliation(s)
- Sanchita Hati
- Department of Chemistry, University Wisconsin, Eau Claire, Wisconsin
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27
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Kelly CM, Muzard J, Brooks BR, Lee GU, Buchete NV. Structure and dynamics of the fibronectin-III domains of Aplysia californica cell adhesion molecules. Phys Chem Chem Phys 2016; 17:9634-43. [PMID: 25729787 DOI: 10.1039/c4cp05307a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Due to their homophilic and heterophilic binding properties, cell adhesion molecules (CAMs) such as integrin, cadherin and the immunoglobulin superfamily CAMs are of primary importance in cell-cell and cell-substrate interactions, signalling pathways and other crucial biological processes. We study the molecular structures and conformational dynamics of the two fibronectin type III (Fn-III) extracellular domains of the Aplysia californica CAM (apCAM) protein, by constructing and probing an atomically-detailed structural model based on apCAM's homology with other CAMs. The stability and dynamic properties of the Fn-III domains, individually and in tandem, are probed and analysed using all-atom explicit-solvent molecular dynamics (MD) simulations and normal mode analysis of their corresponding elastic network models. The refined structural model of the Fn-III tandem of apCAM reveals a specific pattern of amino acid interactions that controls the stability of the β-sheet rich structure and could affect apCAM's response to physical or chemical changes of its environment. It also exposes the important role of several specific charged residues in modulating the structural properties of the linker segment connecting the two Fn-III domains, as well as of the inter-domain interface.
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Affiliation(s)
- Catherine M Kelly
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland.
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28
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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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29
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Dorner ME, McMunn RD, Bartholow TG, Calhoon BE, Conlon MR, Dulli JM, Fehling SC, Fisher CR, Hodgson SW, Keenan SW, Kruger AN, Mabin JW, Mazula DL, Monte CA, Olthafer A, Sexton AE, Soderholm BR, Strom AM, Hati S. Comparison of intrinsic dynamics of cytochrome p450 proteins using normal mode analysis. Protein Sci 2015; 24:1495-507. [PMID: 26130403 DOI: 10.1002/pro.2737] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/18/2015] [Accepted: 06/14/2015] [Indexed: 12/24/2022]
Abstract
Cytochrome P450 enzymes are hemeproteins that catalyze the monooxygenation of a wide-range of structurally diverse substrates of endogenous and exogenous origin. These heme monooxygenases receive electrons from NADH/NADPH via electron transfer proteins. The cytochrome P450 enzymes, which constitute a diverse superfamily of more than 8,700 proteins, share a common tertiary fold but < 25% sequence identity. Based on their electron transfer protein partner, cytochrome P450 proteins are classified into six broad classes. Traditional methods of pro are based on the canonical paradigm that attributes proteins' function to their three-dimensional structure, which is determined by their primary structure that is the amino acid sequence. It is increasingly recognized that protein dynamics play an important role in molecular recognition and catalytic activity. As the mobility of a protein is an intrinsic property that is encrypted in its primary structure, we examined if different classes of cytochrome P450 enzymes display any unique patterns of intrinsic mobility. Normal mode analysis was performed to characterize the intrinsic dynamics of five classes of cytochrome P450 proteins. The present study revealed that cytochrome P450 enzymes share a strong dynamic similarity (root mean squared inner product > 55% and Bhattacharyya coefficient > 80%), despite the low sequence identity (< 25%) and sequence similarity (< 50%) across the cytochrome P450 superfamily. Noticeable differences in Cα atom fluctuations of structural elements responsible for substrate binding were noticed. These differences in residue fluctuations might be crucial for substrate selectivity in these enzymes.
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Affiliation(s)
- Mariah E Dorner
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Ryan D McMunn
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Thomas G Bartholow
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Brecken E Calhoon
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Michelle R Conlon
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Jessica M Dulli
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Samuel C Fehling
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Cody R Fisher
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Shane W Hodgson
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Shawn W Keenan
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Alyssa N Kruger
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Justin W Mabin
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Daniel L Mazula
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Christopher A Monte
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Augustus Olthafer
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Ashley E Sexton
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Beatrice R Soderholm
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Alexander M Strom
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
| | - Sanchita Hati
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54702
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30
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Frappier V, Chartier M, Najmanovich RJ. ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability. Nucleic Acids Res 2015; 43:W395-400. [PMID: 25883149 PMCID: PMC4489264 DOI: 10.1093/nar/gkv343] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 03/27/2015] [Accepted: 04/06/2015] [Indexed: 11/24/2022] Open
Abstract
ENCoM is a coarse-grained normal mode analysis method recently introduced that unlike previous such methods is unique in that it accounts for the nature of amino acids. The inclusion of this layer of information was shown to improve conformational space sampling and apply for the first time a coarse-grained normal mode analysis method to predict the effect of single point mutations on protein dynamics and thermostability resulting from vibrational entropy changes. Here we present a web server that allows non-technical users to have access to ENCoM calculations to predict the effect of mutations on thermostability and dynamics as well as to generate geometrically realistic conformational ensembles. The server is accessible at: http://bcb.med.usherbrooke.ca/encom.
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Affiliation(s)
- Vincent Frappier
- Department of Biochemistry, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Quebec, J1H 5N4, Canada
| | - Matthieu Chartier
- Department of Biochemistry, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Quebec, J1H 5N4, Canada
| | - Rafael J Najmanovich
- Department of Biochemistry, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Quebec, J1H 5N4, Canada
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31
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Eyal E, Lum G, Bahar I. The anisotropic network model web server at 2015 (ANM 2.0). Bioinformatics 2015; 31:1487-9. [PMID: 25568280 PMCID: PMC4410662 DOI: 10.1093/bioinformatics/btu847] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/11/2014] [Accepted: 12/21/2014] [Indexed: 11/12/2022] Open
Abstract
SUMMARY The anisotropic network model (ANM) is one of the simplest yet powerful tools for exploring protein dynamics. Its main utility is to predict and visualize the collective motions of large complexes and assemblies near their equilibrium structures. The ANM server, introduced by us in 2006 helped making this tool more accessible to non-sophisticated users. We now provide a new version (ANM 2.0), which allows inclusion of nucleic acids and ligands in the network model and thus enables the investigation of the collective motions of protein-DNA/RNA and -ligand systems. The new version offers the flexibility of defining the system nodes and the interaction types and cutoffs. It also includes extensive improvements in hardware, software and graphical interfaces. AVAILABILITY AND IMPLEMENTATION ANM 2.0 is available at http://anm.csb.pitt.edu CONTACT eran.eyal@sheba.health.gov.il, eyal.eran@gmail.com.
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Affiliation(s)
- Eran Eyal
- Cancer Research Institute, Sheba Medical Center, 2 Sheba Rd, Ramat Gan 52621, Israel and Department of Computational and System Biology, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, PA 15213, USA
| | - Gengkon Lum
- Cancer Research Institute, Sheba Medical Center, 2 Sheba Rd, Ramat Gan 52621, Israel and Department of Computational and System Biology, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, PA 15213, USA
| | - Ivet Bahar
- Cancer Research Institute, Sheba Medical Center, 2 Sheba Rd, Ramat Gan 52621, Israel and Department of Computational and System Biology, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, PA 15213, USA
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32
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Yates LA, Durrant BP, Fleurdépine S, Harlos K, Norbury CJ, Gilbert RJC. Structural plasticity of Cid1 provides a basis for its distributive RNA terminal uridylyl transferase activity. Nucleic Acids Res 2015; 43:2968-79. [PMID: 25712096 PMCID: PMC4357723 DOI: 10.1093/nar/gkv122] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Terminal uridylyl transferases (TUTs) are responsible for the post-transcriptional addition of uridyl residues to RNA 3′ ends, leading in some cases to altered stability. The Schizosaccharomyces pombe TUT Cid1 is a model enzyme that has been characterized structurally at moderate resolution and provides insights into the larger and more complex mammalian TUTs, ZCCHC6 and ZCCHC11. Here, we report a higher resolution (1.74 Å) crystal structure of Cid1 that provides detailed evidence for uracil selection via the dynamic flipping of a single histidine residue. We also describe a novel closed conformation of the enzyme that may represent an intermediate stage in a proposed product ejection mechanism. The structural insights gained, combined with normal mode analysis and biochemical studies, demonstrate that the plasticity of Cid1, particularly about a hinge region (N164–N165), is essential for catalytic activity, and provide an explanation for its distributive uridylyl transferase activity. We propose a model clarifying observed differences between the in vitro apparently processive activity and in vivo distributive monouridylylation activity of Cid1. We suggest that modulating the flexibility of such enzymes—for example by the binding of protein co-factors—may allow them alternatively to add single or multiple uridyl residues to the 3′ termini of RNA molecules.
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Affiliation(s)
- Luke A Yates
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Benjamin P Durrant
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Sophie Fleurdépine
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Chris J Norbury
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Robert J C Gilbert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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33
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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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Tiwari SP, Fuglebakk E, Hollup SM, Skjærven L, Cragnolini T, Grindhaug SH, Tekle KM, Reuter N. WEBnm@ v2.0: Web server and services for comparing protein flexibility. BMC Bioinformatics 2014; 15:427. [PMID: 25547242 PMCID: PMC4339738 DOI: 10.1186/s12859-014-0427-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 12/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics-function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. RESULTS We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma . CONCLUSION WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.
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Affiliation(s)
- Sandhya P Tiwari
- Department of Molecular Biology, University of Bergen, Bergen, Norway.
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Edvin Fuglebakk
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Siv M Hollup
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Lars Skjærven
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Tristan Cragnolini
- Department of Molecular Biology, University of Bergen, Bergen, Norway.
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
- Present address: University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Svenn H Grindhaug
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Kidane M Tekle
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Nathalie Reuter
- Department of Molecular Biology, University of Bergen, Bergen, Norway.
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
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35
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Han H, Kursula P. The olfactomedin domain from gliomedin is a β-propeller with unique structural properties. J Biol Chem 2014; 290:3612-21. [PMID: 25525261 DOI: 10.1074/jbc.m114.627547] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
All members of the olfactomedin (OLF) family have a conserved extracellular OLF domain, for which a structure has not been available. We present here the crystal structure of the OLF domain from gliomedin. Gliomedin is a protein expressed by Schwann cells in peripheral nerves, important for the formation of the nodes of Ranvier. Gliomedin interacts with neuronal cell adhesion molecules, such as neurofascin, but the structural details of the interaction are not known. The structure of the OLF domain presents a five-bladed β-propeller fold with unusual geometric properties. The symmetry of the structure is not 5-fold, but rather reveals a twisted arrangement. The conserved top face of the gliomedin OLF domain is likely to be important for binding to neuronal ligands. Our results provide a structural basis for the functions of gliomedin in Schwann cells, enable the understanding of the role of the gliomedin OLF domain in autoimmune neuropathies, and unravel the locations of human disease-causing mutations in other OLF family members, including myocilin.
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Affiliation(s)
- Huijong Han
- From the Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, 90014 Oulu, Finland, the German Electron Synchrotron (DESY), 22607 Hamburg, Germany, and
| | - Petri Kursula
- From the Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, 90014 Oulu, Finland, the German Electron Synchrotron (DESY), 22607 Hamburg, Germany, and the Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway
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36
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Skjærven L, Yao XQ, Scarabelli G, Grant BJ. Integrating protein structural dynamics and evolutionary analysis with Bio3D. BMC Bioinformatics 2014; 15:399. [PMID: 25491031 PMCID: PMC4279791 DOI: 10.1186/s12859-014-0399-6] [Citation(s) in RCA: 249] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 11/26/2014] [Indexed: 12/01/2022] Open
Abstract
Background Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how observed displacements and predicted motions from these traditionally separate analyses relate to each other, as well as to the evolution of sequence, structure and function within large protein families, remains a considerable challenge. This is in part due to the general lack of tools that integrate information of molecular structure, dynamics and evolution. Results Here, we describe the integration of new methodologies for evolutionary sequence, structure and simulation analysis into the Bio3D package. This major update includes unique high-throughput normal mode analysis for examining and contrasting the dynamics of related proteins with non-identical sequences and structures, as well as new methods for quantifying dynamical couplings and their residue-wise dissection from correlation network analysis. These new methodologies are integrated with major biomolecular databases as well as established methods for evolutionary sequence and comparative structural analysis. New functionality for directly comparing results derived from normal modes, molecular dynamics and principal component analysis of heterogeneous experimental structure distributions is also included. We demonstrate these integrated capabilities with example applications to dihydrofolate reductase and heterotrimeric G-protein families along with a discussion of the mechanistic insight provided in each case. Conclusions The integration of structural dynamics and evolutionary analysis in Bio3D enables researchers to go beyond a prediction of single protein dynamics to investigate dynamical features across large protein families. The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0399-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lars Skjærven
- Department of Biomedicine, University of Bergen, Bergen, Norway. .,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Xin-Qiu Yao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
| | - Guido Scarabelli
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
| | - Barry J Grant
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
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37
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Fuglebakk E, Tiwari SP, Reuter N. Comparing the intrinsic dynamics of multiple protein structures using elastic network models. Biochim Biophys Acta Gen Subj 2014; 1850:911-922. [PMID: 25267310 DOI: 10.1016/j.bbagen.2014.09.021] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/15/2014] [Accepted: 09/16/2014] [Indexed: 12/15/2022]
Abstract
BACKGROUND Elastic network models (ENMs) are based on the simple idea that a protein can be described as a set of particles connected by springs, which can then be used to describe its intrinsic flexibility using, for example, normal mode analysis. Since the introduction of the first ENM by Monique Tirion in 1996, several variants using coarser protein models have been proposed and their reliability for the description of protein intrinsic dynamics has been widely demonstrated. Lately an increasing number of studies have focused on the meaning of slow dynamics for protein function and its potential conservation through evolution. This leads naturally to comparisons of the intrinsic dynamics of multiple protein structures with varying levels of similarity. SCOPE OF REVIEW We describe computational strategies for calculating and comparing intrinsic dynamics of multiple proteins using elastic network models, as well as a selection of examples from the recent literature. MAJOR CONCLUSIONS The increasing interest for comparing dynamics across protein structures with various levels of similarity, has led to the establishment and validation of reliable computational strategies using ENMs. Comparing dynamics has been shown to be a viable way for gaining greater understanding for the mechanisms employed by proteins for their function. Choices of ENM parameters, structure alignment or similarity measures will likely influence the interpretation of the comparative analysis of protein motion. GENERAL SIGNIFICANCE Understanding the relation between protein function and dynamics is relevant to the fundamental understanding of protein structure-dynamics-function relationship. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Affiliation(s)
- Edvin Fuglebakk
- Department of Molecular Biology, University of Bergen, Pb. 7803, N-5020 Bergen, Norway; Computational Biology Unit, Department of Informatics, University of Bergen, Pb. 7803, N-5020 Bergen, Norway.
| | - Sandhya P Tiwari
- Department of Molecular Biology, University of Bergen, Pb. 7803, N-5020 Bergen, Norway; Computational Biology Unit, Department of Informatics, University of Bergen, Pb. 7803, N-5020 Bergen, Norway.
| | - Nathalie Reuter
- Department of Molecular Biology, University of Bergen, Pb. 7803, N-5020 Bergen, Norway; Computational Biology Unit, Department of Informatics, University of Bergen, Pb. 7803, N-5020 Bergen, Norway.
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38
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Birol M, Enchev RI, Padilla A, Stengel F, Aebersold R, Betzi S, Yang Y, Hoh F, Peter M, Dumas C, Echalier A. Structural and biochemical characterization of the Cop9 signalosome CSN5/CSN6 heterodimer. PLoS One 2014; 9:e105688. [PMID: 25144743 PMCID: PMC4140821 DOI: 10.1371/journal.pone.0105688] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 07/23/2014] [Indexed: 11/18/2022] Open
Abstract
The Cop9 signalosome complex (CSN) regulates the functional cycle of the major E3 ubiquitin ligase family, the cullin RING E3 ubiquitin ligases (CRLs). Activated CRLs are covalently modified by the ubiquitin-like protein Nedd8 (neural precursor cell expressed developmentally down-regulated protein 8). CSN serves an essential role in myriad cellular processes by reversing this modification through the isopeptidase activity of its CSN5 subunit. CSN5 alone is inactive due to an auto-inhibited conformation of its catalytic domain. Here we report the molecular basis of CSN5 catalytic domain activation and unravel a molecular hierarchy in CSN deneddylation activity. The association of CSN5 and CSN6 MPN (for Mpr1/Pad1 N-terminal) domains activates its isopeptidase activity. The CSN5/CSN6 module, however, is inefficient in CRL deneddylation, indicating a requirement of further elements in this reaction such as other CSN subunits. A hybrid molecular model of CSN5/CSN6 provides a structural framework to explain these functional observations. Docking this model into a published CSN electron density map and using distance constraints obtained from cross-linking coupled to mass-spectrometry, we find that the C-termini of the CSN subunits could form a helical bundle in the centre of the structure. They likely play a key scaffolding role in the spatial organization of CSN and precise positioning of the dimeric MPN catalytic core.
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Affiliation(s)
- Melissa Birol
- Centre de Biochimie Structurale, Unité Mixte de Recherche (UMR) 5048, Centre National de Recherche Scientifique (CNRS), Université Montpellier 1 (UM1), Université Montpellier 2 (UM2), Montpellier, France
- Institut national de la santé et de la recherche médicale (INSERM) U1054, Paris, France
| | | | - André Padilla
- Centre de Biochimie Structurale, Unité Mixte de Recherche (UMR) 5048, Centre National de Recherche Scientifique (CNRS), Université Montpellier 1 (UM1), Université Montpellier 2 (UM2), Montpellier, France
- Institut national de la santé et de la recherche médicale (INSERM) U1054, Paris, France
| | - Florian Stengel
- ETH Zurich, Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
| | - Ruedi Aebersold
- ETH Zurich, Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Stéphane Betzi
- Centre de Recherche en Cancérologie de Marseille, Centre de Biochimie Structurale, Unité Mixte de Recherche (UMR) 7258, Institut national de la santé et de la recherche médicale (INSERM) U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Yinshan Yang
- Centre de Biochimie Structurale, Unité Mixte de Recherche (UMR) 5048, Centre National de Recherche Scientifique (CNRS), Université Montpellier 1 (UM1), Université Montpellier 2 (UM2), Montpellier, France
- Institut national de la santé et de la recherche médicale (INSERM) U1054, Paris, France
| | - François Hoh
- Centre de Biochimie Structurale, Unité Mixte de Recherche (UMR) 5048, Centre National de Recherche Scientifique (CNRS), Université Montpellier 1 (UM1), Université Montpellier 2 (UM2), Montpellier, France
- Institut national de la santé et de la recherche médicale (INSERM) U1054, Paris, France
| | - Matthias Peter
- ETH Zurich, Department of Biology, Institute of Biochemistry, Zurich, Switzerland
| | - Christian Dumas
- Centre de Biochimie Structurale, Unité Mixte de Recherche (UMR) 5048, Centre National de Recherche Scientifique (CNRS), Université Montpellier 1 (UM1), Université Montpellier 2 (UM2), Montpellier, France
- Institut national de la santé et de la recherche médicale (INSERM) U1054, Paris, France
| | - Aude Echalier
- Centre de Biochimie Structurale, Unité Mixte de Recherche (UMR) 5048, Centre National de Recherche Scientifique (CNRS), Université Montpellier 1 (UM1), Université Montpellier 2 (UM2), Montpellier, France
- Institut national de la santé et de la recherche médicale (INSERM) U1054, Paris, France
- * E-mail:
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Computational screening of disease associated mutations on NPC1 gene and its structural consequence in Niemann-Pick type-C1. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11515-014-1314-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Bernardo CEP, Silva PJ. Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition. PeerJ 2014; 2:e470. [PMID: 25071993 PMCID: PMC4103094 DOI: 10.7717/peerj.470] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/16/2014] [Indexed: 11/23/2022] Open
Abstract
The binding of several rubromycin-based ligands to HIV1-reverse transcriptase was analyzed using molecular docking and molecular dynamics simulations. MM-PBSA analysis and examination of the trajectories allowed the identification of several promising compounds with predicted high affinity towards reverse transcriptase mutants which have proven resistant to current drugs. Important insights on the complex interplay of factors determining the ability of ligands to selectively target each mutant have been obtained.
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Affiliation(s)
- Carlos E P Bernardo
- REQUIMTE/Faculdade de Ciências da Saúde, Universidade Fernando Pessoa , Rua Carlos da Maia, Porto , Portugal
| | - Pedro J Silva
- REQUIMTE/Faculdade de Ciências da Saúde, Universidade Fernando Pessoa , Rua Carlos da Maia, Porto , Portugal
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41
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Jamroz M, Kolinski A, Kmiecik S. CABS-flex predictions of protein flexibility compared with NMR ensembles. ACTA ACUST UNITED AC 2014; 30:2150-4. [PMID: 24735558 PMCID: PMC4103595 DOI: 10.1093/bioinformatics/btu184] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Motivation: Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics (MD). In this work, we evaluate CABS-flex and MD predictions by comparison with protein structural variations within NMR ensembles. Results: Based on a benchmark set of 140 proteins, we show that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. On average, this correlation is stronger than that between MD and NMR ensembles. In conclusion, CABS-flex is useful and complementary to MD in predicting protein regions that undergo conformational changes as well as the extent of such changes. Availability and implementation: The CABS-flex is freely available to all users at http://biocomp.chem.uw.edu.pl/CABSflex. Contact: sekmi@chem.uw.edu.pl Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Michal Jamroz
- Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Andrzej Kolinski
- Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Sebastian Kmiecik
- Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
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42
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43
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Damásio ARL, Rubio MV, Oliveira LC, Segato F, Dias BA, Citadini AP, Paixão DA, Squina FM. Understanding the function of conserved variations in the catalytic loops of fungal glycoside hydrolase family 12. Biotechnol Bioeng 2014; 111:1494-505. [PMID: 24578305 DOI: 10.1002/bit.25209] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 01/24/2014] [Accepted: 01/27/2014] [Indexed: 11/11/2022]
Abstract
Enzymes that cleave the xyloglucan backbone at unbranched glucose residues have been identified in GH families 5, 7, 12, 16, 44, and 74. Fungi produce enzymes that populate 20 of 22 families that are considered critical for plant biomass deconstruction. We searched for GH12-encoding genes in 27 Eurotiomycetes genomes. After analyzing 50 GH12-related sequences, the conserved variations of the amino acid sequences were examined. Compared to the endoglucanases, the endo-xyloglucanase-associated YSG deletion at the negative subsites of the catalytic cleft with a SST insertion at the reducing end of the substrate-binding crevice is highly conserved. In addition, a highly conserved alanine residue was identified in all xyloglucan-specific enzymes, and this residue is substituted by arginine in more promiscuous glucanases. To understand the basis for the xyloglucan specificity displayed by certain GH12 enzymes, two fungal GH12 endoglucanases were chosen for mutagenesis and functional studies: an endo-xyloglucanase from Aspergillus clavatus (AclaXegA) and an endoglucanase from A. terreus (AtEglD). Comprehensive molecular docking studies and biochemical analyses were performed, revealing that mutations at the entrance of the catalytic cleft in AtEglD result in a wider binding cleft and the alteration of the substrate-cleavage pattern, implying that a trio of residues coordinates the interactions and binding to linear glycans. The loop insertion at the crevice-reducing end of AclaXegA is critical for catalytic efficiency to hydrolyze xyloglucan. The understanding of the structural elements governing endo-xyloglucanase activity on linear and branched glucans will facilitate future enzyme modifications with potential applications in industrial biotechnology.
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Affiliation(s)
- André R L Damásio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas-SP, Brazil
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44
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Blacklock K, Verkhivker GM. Allosteric regulation of the Hsp90 dynamics and stability by client recruiter cochaperones: protein structure network modeling. PLoS One 2014; 9:e86547. [PMID: 24466147 PMCID: PMC3896489 DOI: 10.1371/journal.pone.0086547] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 12/06/2013] [Indexed: 12/29/2022] Open
Abstract
The fundamental role of the Hsp90 chaperone in supporting functional activity of diverse protein clients is anchored by specific cochaperones. A family of immune sensing client proteins is delivered to the Hsp90 system with the aid of cochaperones Sgt1 and Rar1 that act cooperatively with Hsp90 to form allosterically regulated dynamic complexes. In this work, functional dynamics and protein structure network modeling are combined to dissect molecular mechanisms of Hsp90 regulation by the client recruiter cochaperones. Dynamic signatures of the Hsp90-cochaperone complexes are manifested in differential modulation of the conformational mobility in the Hsp90 lid motif. Consistent with the experiments, we have determined that targeted reorganization of the lid dynamics is a unifying characteristic of the client recruiter cochaperones. Protein network analysis of the essential conformational space of the Hsp90-cochaperone motions has identified structurally stable interaction communities, interfacial hubs and key mediating residues of allosteric communication pathways that act concertedly with the shifts in conformational equilibrium. The results have shown that client recruiter cochaperones can orchestrate global changes in the dynamics and stability of the interaction networks that could enhance the ATPase activity and assist in the client recruitment. The network analysis has recapitulated a broad range of structural and mutagenesis experiments, particularly clarifying the elusive role of Rar1 as a regulator of the Hsp90 interactions and a stability enhancer of the Hsp90-cochaperone complexes. Small-world organization of the interaction networks in the Hsp90 regulatory complexes gives rise to a strong correspondence between highly connected local interfacial hubs, global mediator residues of allosteric interactions and key functional hot spots of the Hsp90 activity. We have found that cochaperone-induced conformational changes in Hsp90 may be determined by specific interaction networks that can inhibit or promote progression of the ATPase cycle and thus control the recruitment of client proteins.
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Affiliation(s)
- Kristin Blacklock
- School of Computational Sciences and Crean School of Health and Life Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- School of Computational Sciences and Crean School of Health and Life Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Department of Pharmacology, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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45
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Mahnam K, Saffar B, Mobini-Dehkordi M, Fassihi A, Mohammadi A. Design of a novel metal binding peptide by molecular dynamics simulation to sequester Cu and Zn ions. Res Pharm Sci 2014; 9:69-82. [PMID: 25598801 PMCID: PMC4292183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Heavy metal toxicity has serious adverse effects on the environment. The metal sequestering characteristics of a novel metal binding peptide (Glu-Cys)11 Gly+linker+hexahistidine (EC11:His6) was investigated to determine if it can absorb Cu(2+) or Zn(2+) cations. Molecular dynamics simulations were carried out using a model of 6 Cu(2+) or Zn(2+) and other ions enclosed in a fully hydrated simulation box with the designed peptide. Totally, 240 nano second (ns) simulations were done in three phases. Results showed that the selected linker is able to separate two domains of this peptide and that the carboxyl oxygens of Glu residues of EC11 in the designed peptide can absorb these ions. Sequestration of Cu(2+) or Zn(2+) ions by the designed peptide does not change overall tertiary and secondary structures of peptide.
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Affiliation(s)
- K. Mahnam
- Biology Department, Faculty of Science, Shahrekord University, Shahrekord, I.R. Iran
| | - B. Saffar
- Genetics Department, Faculty of Science, Shahrekord University, Shahrekord, I.R. Iran
- Research Institute of Biotechnology, Shahrekord University, Shahrekord, I.R. Iran
| | - M. Mobini-Dehkordi
- Genetics Department, Faculty of Science, Shahrekord University, Shahrekord, I.R. Iran
- Research Institute of Biotechnology, Shahrekord University, Shahrekord, I.R. Iran
| | - A. Fassihi
- Department of Medicinal Chemistry, and Isfahan Bioinformatic Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - A. Mohammadi
- Genetics Department, Faculty of Science, Shahrekord University, Shahrekord, I.R. Iran
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46
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Blacklock K, Verkhivker GM. Experimentally Guided Structural Modeling and Dynamics Analysis of Hsp90–p53 Interactions: Allosteric Regulation of the Hsp90 Chaperone by a Client Protein. J Chem Inf Model 2013; 53:2962-78. [DOI: 10.1021/ci400434g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Kristin Blacklock
- School
of Computational Sciences and Crean School of Health and Life Sciences,
Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Gennady M. Verkhivker
- School
of Computational Sciences and Crean School of Health and Life Sciences,
Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
- Department
of Pharmacology, University of California San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
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47
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48
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Blacklock K, Verkhivker GM. Differential modulation of functional dynamics and allosteric interactions in the Hsp90-cochaperone complexes with p23 and Aha1: a computational study. PLoS One 2013; 8:e71936. [PMID: 23977182 PMCID: PMC3747073 DOI: 10.1371/journal.pone.0071936] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 07/10/2013] [Indexed: 12/27/2022] Open
Abstract
Allosteric interactions of the molecular chaperone Hsp90 with a large cohort of cochaperones and client proteins allow for molecular communication and event coupling in signal transduction networks. The integration of cochaperones into the Hsp90 system is driven by the regulatory mechanisms that modulate the progression of the ATPase cycle and control the recruitment of the Hsp90 clientele. In this work, we report the results of computational modeling of allosteric regulation in the Hsp90 complexes with the cochaperones p23 and Aha1. By integrating protein docking, biophysical simulations, modeling of allosteric communications, protein structure network analysis and the energy landscape theory we have investigated dynamics and stability of the Hsp90-p23 and Hsp90-Aha1 interactions in direct comparison with the extensive body of structural and functional experiments. The results have revealed that functional dynamics and allosteric interactions of Hsp90 can be selectively modulated by these cochaperones via specific targeting of the regulatory hinge regions that could restrict collective motions and stabilize specific chaperone conformations. The protein structure network parameters have quantified the effects of cochaperones on conformational stability of the Hsp90 complexes and identified dynamically stable communities of residues that can contribute to the strengthening of allosteric interactions. According to our results, p23-mediated changes in the Hsp90 interactions may provide "molecular brakes" that could slow down an efficient transmission of the inter-domain allosteric signals, consistent with the functional role of p23 in partially inhibiting the ATPase cycle. Unlike p23, Aha1-mediated acceleration of the Hsp90-ATPase cycle may be achieved via modulation of the equilibrium motions that facilitate allosteric changes favoring a closed dimerized form of Hsp90. The results of our study have shown that Aha1 and p23 can modulate the Hsp90-ATPase activity and direct the chaperone cycle by exerting the precise control over structural stability, global movements and allosteric communications in Hsp90.
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Affiliation(s)
- Kristin Blacklock
- School of Computational Sciences and Crean School of Health and Life Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- School of Computational Sciences and Crean School of Health and Life Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Department of Pharmacology, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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Crystal structures of the first condensation domain of CDA synthetase suggest conformational changes during the synthetic cycle of nonribosomal peptide synthetases. J Mol Biol 2013; 425:3137-50. [PMID: 23756159 DOI: 10.1016/j.jmb.2013.06.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/26/2013] [Accepted: 06/03/2013] [Indexed: 11/24/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large modular macromolecular machines that produce small peptide molecules with wide-ranging biological activities, such as antibiotics and green chemicals. The condensation (C) domain is responsible for amide bond formation, the central chemical step in nonribosomal peptide synthesis. Here we present two crystal structures of the first condensation domain of the calcium-dependent antibiotic (CDA) synthetase (CDA-C1) from Streptomyces coelicolor, determined at resolutions 1.8Å and 2.4Å. The conformations adopted by CDA-C1 are quite similar in these two structures yet distinct from those seen in other NRPS C domain structures. HPLC-based reaction assays show that this CDA-C1 construct is catalytically active, and small-angle X-ray scattering experiments suggest that the conformation observed in these crystal structures could faithfully represent the conformation in solution. We have performed targeted molecular dynamics simulations, normal mode analyses and energy-minimized linear interpolation to investigate the conformational changes required to transition between the observed structures. We discuss the implications of these conformational changes in the synthetic cycle and of the observation that the "latch" that covers the active site is consistently formed in all studied C domains.
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50
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Nogales-Cadenas R, Jonic S, Tama F, Arteni AA, Tabas-Madrid D, Vázquez M, Pascual-Montano A, Sorzano COS. 3DEM Loupe: Analysis of macromolecular dynamics using structures from electron microscopy. Nucleic Acids Res 2013; 41:W363-7. [PMID: 23671335 PMCID: PMC3692114 DOI: 10.1093/nar/gkt385] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Electron microscopy (EM) provides access to structural information of macromolecular complexes in the 3-20 Å resolution range. Normal mode analysis has been extensively used with atomic resolution structures and successfully applied to EM structures. The major application of normal modes is the identification of possible conformational changes in proteins. The analysis can throw light on the mechanism following ligand binding, protein-protein interactions, channel opening and other functional macromolecular movements. In this article, we present a new web server, 3DEM Loupe, which allows normal mode analysis of any uploaded EM volume using a user-friendly interface and an intuitive workflow. Results can be fully explored in 3D through animations and movies generated by the server. The application is freely available at http://3demloupe.cnb.csic.es.
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