251
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Paracha RZ, Ali A, Ahmad J, Hussain R, Niazi U, Muhammad SA. Structural evaluation of BTK and PKCδ mediated phosphorylation of MAL at positions Tyr86 and Tyr106. Comput Biol Chem 2014; 51:22-35. [PMID: 24840642 DOI: 10.1016/j.compbiolchem.2014.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/03/2014] [Accepted: 04/07/2014] [Indexed: 01/02/2023]
Abstract
A number of diseases including sepsis, rheumatoid arthritis, diabetes, cardiovascular diseases and hyperinflammatory immune disorders have been associated with Toll like receptor (TLR) 2 and TLR4. Endogenous adaptor protein known as MyD88 adapter-like protein (MAL) bind exclusively to the cytosolic portions of TLR2 and TLR4 to initiate downstream signalling. Brutons tyrosine kinase (BTK) and protein kinase C delta (PKCδ) have been implicated to phosphorylate MAL and activate it to initiate downstream signalling. BTK has been associated with phosphorylation at positions Tyr86 and Tyr106, necessary for the activation of MAL but definite residual target of PKCδ in MAL is still to be explored. To produce a better understanding of the functional domains involved in the formation of MAL-kinase complexes, computer-aided studies were used to characterize the protein-protein interactions (PPIs) of phosphorylated BTK and PKCδ with MAL. Docking and physicochemical studies indicated that BTK was involved in close contact with Tyr86 and Tyr106 of MAL whereas PKCδ may phosphorylate Tyr106 only. Moreover, the electrostatics charge distribution of binding interfaces of BTK and PKCδ were distinct but compatible with respective regions of MAL. Our results implicate that position of Tyr86 is specifically phosphorylated by BTK whereas Tyr106 can be phosphorylated by competitive action of both BTK and PKCδ. Additionally, the residues of MAL which are necessary for interaction with TLR2, TLR4, MyD88 and SOCS-1 also play their roles in maintaining interaction with kinases and can be targeted in future to reduce TLR2 and TLR4 induced pathological responses.
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Affiliation(s)
- Rehan Zafar Paracha
- Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Amjad Ali
- Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan.
| | - Jamil Ahmad
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan.
| | - Riaz Hussain
- Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad 44000, Pakistan
| | - Umar Niazi
- IBERS, Aberystwyth University, Edward Llwyd Building, Penglais Campus, Aberystwyth, Ceredigion, Wales SY23 3FG, UK
| | - Syed Aun Muhammad
- Department of Pharmacy, COMSATS Institute of Information Technology Abbottabad, 22060, Pakistan
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252
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Nayek A, Sen Gupta PS, Banerjee S, Mondal B, Bandyopadhyay AK. Salt-bridge energetics in halophilic proteins. PLoS One 2014; 9:e93862. [PMID: 24743799 PMCID: PMC3990605 DOI: 10.1371/journal.pone.0093862] [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: 01/02/2014] [Accepted: 03/07/2014] [Indexed: 11/19/2022] Open
Abstract
Halophilic proteins have greater abundance of acidic over basic and very low bulky hydrophobic residues. Classical electrostatic stabilization was suggested as the key determinant for halophilic adaptation of protein. However, contribution of specific electrostatic interactions (i.e. salt-bridges) to overall stability of halophilic proteins is yet to be understood. To understand this, we use Adaptive-Poison-Boltzmann-Solver Methods along with our home-built automation to workout net as well as associated component energy terms such as desolvation energy, bridge energy and background energy for 275 salt-bridges from 20 extremely halophilic proteins. We then perform extensive statistical analysis on general and energetic attributes on these salt-bridges. On average, 8 salt-bridges per 150 residues protein were observed which is almost twice than earlier report. Overall contributions of salt-bridges are −3.0 kcal mol−1. Majority (78%) of salt-bridges in our dataset are stable and conserved in nature. Although, average contributions of component energy terms are equal, their individual details vary greatly from one another indicating their sensitivity to local micro-environment. Notably, 35% of salt-bridges in our database are buried and stable. Greater desolvation penalty of these buried salt-bridges are counteracted by stable network salt-bridges apart from favorable equal contributions of bridge and background terms. Recruitment of extensive network salt-bridges (46%) with a net contribution of −5.0 kcal mol−1 per salt-bridge, seems to be a halophilic design wherein favorable average contribution of background term (−10 kcal mol−1) exceeds than that of bridge term (−7 kcal mol−1). Interiors of proteins from halophiles are seen to possess relatively higher abundance of charge and polar side chains than that of mesophiles which seems to be satisfied by cooperative network salt-bridges. Overall, our theoretical analyses provide insight into halophilic signature in its specific electrostatic interactions which we hope would help in protein engineering and bioinformatics studies.
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Affiliation(s)
- Arnab Nayek
- The Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
| | | | - Shyamashree Banerjee
- The Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
| | - Buddhadev Mondal
- Department of Zoology, Burdwan Raj College, The University of Burdwan, Burdwan, West Bengal, India
| | - Amal K. Bandyopadhyay
- The Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
- * E-mail:
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253
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Capelluto DGS, Zhao X, Lucas A, Lemkul JA, Xiao S, Fu X, Sun F, Bevan DR, Finkielstein CV. Biophysical and molecular-dynamics studies of phosphatidic acid binding by the Dvl-2 DEP domain. Biophys J 2014; 106:1101-11. [PMID: 24606934 PMCID: PMC4026774 DOI: 10.1016/j.bpj.2014.01.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/08/2014] [Accepted: 01/27/2014] [Indexed: 11/16/2022] Open
Abstract
The Wnt-dependent, β-catenin-independent pathway modulates cell movement and behavior. A downstream regulator of this signaling pathway is Dishevelled (Dvl), which, among other multiple interactions, binds to the Frizzled receptor and the plasma membrane via phosphatidic acid (PA) in a mechanism proposed to be pH-dependent. While the Dvl DEP domain is central to the β-catenin-independent Wnt signaling function, the mechanism underlying its physical interaction with the membrane remains elusive. In this report, we elucidate the structural and functional basis of PA association to the Dvl2 DEP domain. Nuclear magnetic resonance, molecular-dynamics simulations, and mutagenesis data indicated that the domain interacted with the phospholipid through the basic helix 3 and a contiguous loop with moderate affinity. The association suggested that PA binding promoted local conformational changes in helix 2 and β-strand 4, both of which are compromised to maintain a stable hydrophobic core in the DEP domain. We also show that the Dvl2 DEP domain bound PA in a pH-dependent manner in a mechanism that resembles deprotonation of PA. Collectively, our results structurally define the PA-binding properties of the Dvl2 DEP domain, which can be exploited for the investigation of binding mechanisms of other DEP domain-interacting proteins.
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Affiliation(s)
| | - Xiaolin Zhao
- Protein Signaling Domains Laboratory, Virginia Tech, Blacksburg, Virginia
| | - Andrew Lucas
- Protein Signaling Domains Laboratory, Virginia Tech, Blacksburg, Virginia; Integrated Cellular Responses Laboratory, Department of Biological Sciences, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia
| | - Justin A Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
| | - Shuyan Xiao
- Protein Signaling Domains Laboratory, Virginia Tech, Blacksburg, Virginia
| | - Xiangping Fu
- Integrated Cellular Responses Laboratory, Department of Biological Sciences, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia
| | - Furong Sun
- Protein Signaling Domains Laboratory, Virginia Tech, Blacksburg, Virginia
| | - David R Bevan
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
| | - Carla V Finkielstein
- Integrated Cellular Responses Laboratory, Department of Biological Sciences, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia
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254
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Architecture of a single membrane spanning cytochrome P450 suggests constraints that orient the catalytic domain relative to a bilayer. Proc Natl Acad Sci U S A 2014; 111:3865-70. [PMID: 24613931 DOI: 10.1073/pnas.1324245111] [Citation(s) in RCA: 202] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bitopic integral membrane proteins with a single transmembrane helix play diverse roles in catalysis, cell signaling, and morphogenesis. Complete monospanning protein structures are needed to show how interaction between the transmembrane helix and catalytic domain might influence association with the membrane and function. We report crystal structures of full-length Saccharomyces cerevisiae lanosterol 14α-demethylase, a membrane monospanning cytochrome P450 of the CYP51 family that catalyzes the first postcyclization step in ergosterol biosynthesis and is inhibited by triazole drugs. The structures reveal a well-ordered N-terminal amphipathic helix preceding a putative transmembrane helix that would constrain the catalytic domain orientation to lie partly in the lipid bilayer. The structures locate the substrate lanosterol, identify putative substrate and product channels, and reveal constrained interactions with triazole antifungal drugs that are important for drug design and understanding drug resistance.
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255
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Wakai N, Takemura K, Morita T, Kitao A. Mechanism of deep-sea fish α-actin pressure tolerance investigated by molecular dynamics simulations. PLoS One 2014; 9:e85852. [PMID: 24465747 PMCID: PMC3896411 DOI: 10.1371/journal.pone.0085852] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 12/03/2013] [Indexed: 12/01/2022] Open
Abstract
The pressure tolerance of monomeric α-actin proteins from the deep-sea fish Coryphaenoides armatus and C. yaquinae was compared to that of non-deep-sea fish C. acrolepis, carp, and rabbit/human/chicken actins using molecular dynamics simulations at 0.1 and 60 MPa. The amino acid sequences of actins are highly conserved across a variety of species. The actins from C. armatus and C. yaquinae have the specific substitutions Q137K/V54A and Q137K/L67P, respectively, relative to C. acrolepis, and are pressure tolerant to depths of at least 6000 m. At high pressure, we observed significant changes in the salt bridge patterns in deep-sea fish actins, and these changes are expected to stabilize ATP binding and subdomain arrangement. Salt bridges between ATP and K137, formed in deep-sea fish actins, are expected to stabilize ATP binding even at high pressure. At high pressure, deep-sea fish actins also formed a greater total number of salt bridges than non-deep-sea fish actins owing to the formation of inter-helix/strand and inter-subdomain salt bridges. Free energy analysis suggests that deep-sea fish actins are stabilized to a greater degree by the conformational energy decrease associated with pressure effect.
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Affiliation(s)
- Nobuhiko Wakai
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Takemura
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Takami Morita
- Research Center for Fisheries Oceanography and Marine Ecosystem, National Research Institute of Fisheries Sciences, Fisheries Research Agency, Kanagawa, Japan
| | - Akio Kitao
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
- * E-mail:
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256
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Trame CB, Chang Y, Axelrod HL, Eberhardt RY, Coggill P, Punta M, Rawlings ND. New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily. BMC Bioinformatics 2014; 15:1. [PMID: 24383880 PMCID: PMC3890501 DOI: 10.1186/1471-2105-15-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 12/17/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Acel_2062 protein from Acidothermus cellulolyticus is a protein of unknown function. Initial sequence analysis predicted that it was a metallopeptidase from the presence of a motif conserved amongst the Asp-zincins, which are peptidases that contain a single, catalytic zinc ion ligated by the histidines and aspartic acid within the motif (HEXXHXXGXXD). The Acel_2062 protein was chosen by the Joint Center for Structural Genomics for crystal structure determination to explore novel protein sequence space and structure-based function annotation. RESULTS The crystal structure confirmed that the Acel_2062 protein consisted of a single, zincin-like metallopeptidase-like domain. The Met-turn, a structural feature thought to be important for a Met-zincin because it stabilizes the active site, is absent, and its stabilizing role may have been conferred to the C-terminal Tyr113. In our crystallographic model there are two molecules in the asymmetric unit and from size-exclusion chromatography, the protein dimerizes in solution. A water molecule is present in the putative zinc-binding site in one monomer, which is replaced by one of two observed conformations of His95 in the other. CONCLUSIONS The Acel_2062 protein is structurally related to the zincins. It contains the minimum structural features of a member of this protein superfamily, and can be described as a "mini- zincin". There is a striking parallel with the structure of a mini-Glu-zincin, which represents the minimum structure of a Glu-zincin (a metallopeptidase in which the third zinc ligand is a glutamic acid). Rather than being an ancestral state, phylogenetic analysis suggests that the mini-zincins are derived from larger proteins.
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Affiliation(s)
| | | | | | | | | | | | - Neil D Rawlings
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.
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257
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Xu Z, Li S, Feng X, Zhan Y, Xu H. Function of aspartic acid residues in optimum pH control of l-arabinose isomerase from Lactobacillus fermentum. Appl Microbiol Biotechnol 2013; 98:3987-96. [DOI: 10.1007/s00253-013-5342-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/15/2013] [Accepted: 10/16/2013] [Indexed: 10/26/2022]
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258
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Xu Z, Li S, Li J, Li Y, Feng X, Wang R, Xu H, Zhou J. The structural basis of Erwinia rhapontici isomaltulose synthase. PLoS One 2013; 8:e74788. [PMID: 24069347 PMCID: PMC3777934 DOI: 10.1371/journal.pone.0074788] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 08/06/2013] [Indexed: 11/18/2022] Open
Abstract
Sucrose isomerase NX-5 from Erwiniarhapontici efficiently catalyzes the isomerization of sucrose to isomaltulose (main product) and trehalulose (by-product). To investigate the molecular mechanism controlling sucrose isomer formation, we determined the crystal structures of native NX-5 and its mutant complexes E295Q/sucrose and D241A/glucose at 1.70 Å, 1.70 Å and 2.00 Å, respectively. The overall structure and active site architecture of NX-5 resemble those of other reported sucrose isomerases. Strikingly, the substrate binding mode of NX-5 is also similar to that of trehalulose synthase from Pseudomonasmesoacidophila MX-45 (MutB). Detailed structural analysis revealed the catalytic RXDRX motif and the adjacent 10-residue loop of NX-5 and isomaltulose synthase PalI from Klebsiella sp. LX3 adopt a distinct orientation from those of trehalulose synthases. Mutations of the loop region of NX-5 resulted in significant changes of the product ratio between isomaltulose and trehalulose. The molecular dynamics simulation data supported the product specificity of NX-5 towards isomaltulose and the role of the loop330-339 in NX-5 catalysis. This work should prove useful for the engineering of sucrose isomerase for industrial carbohydrate biotransformations.
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Affiliation(s)
- Zheng Xu
- State Key Laboratory of Materials–Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing University of Technology, Nanjing, China
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Sha Li
- State Key Laboratory of Materials–Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing University of Technology, Nanjing, China
| | - Jie Li
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Yan Li
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Xiaohai Feng
- State Key Laboratory of Materials–Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing University of Technology, Nanjing, China
| | - Renxiao Wang
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Hong Xu
- State Key Laboratory of Materials–Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing University of Technology, Nanjing, China
- * E-mail: (HX); (JT)
| | - Jiahai Zhou
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (HX); (JT)
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259
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Molecular basis of differential selectivity of cyclobutyl-substituted imidazole inhibitors against CDKs: insights for rational drug design. PLoS One 2013; 8:e73836. [PMID: 24058495 PMCID: PMC3772847 DOI: 10.1371/journal.pone.0073836] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 07/25/2013] [Indexed: 11/19/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) belong to the CMGC subfamily of protein kinases and play crucial roles in eukaryotic cell division cycle. At least seven different CDKs have been reported to be implicated in the cell cycle regulation in vertebrates. These CDKs are highly homologous and contain a conserved catalytic core. This makes the design of inhibitors specific for a particular CDK difficult. There is, however, growing need for CDK5 specific inhibitors to treat various neurodegenerative diseases. Recently, cis-substituted cyclobutyl-4-aminoimidazole inhibitors have been identified as potent CDK5 inhibitors that gave up to 30-fold selectivity over CDK2. Available IC50 values also indicate a higher potency of this class of inhibitors over commercially available drugs, such as roscovitine. To understand the molecular basis of higher potency and selectivity of these inhibitors, here, we present molecular dynamics simulation results of CDK5/p25 and CDK2/CyclinE complexed with a series of cyclobutyl-substituted imidazole inhibitors and roscovitine. The atomic details of the stereospecificity and selectivity of these inhibitors are obtained from energetics and binding characteristics to the CDK binding pocket. The study not only complements the experimental findings, but also provides a wealth of detailed information that could help the structure-based drug designing processes.
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260
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Li C, Petukh M, Li L, Alexov E. Continuous development of schemes for parallel computing of the electrostatics in biological systems: implementation in DelPhi. J Comput Chem 2013; 34:1949-60. [PMID: 23733490 PMCID: PMC3707979 DOI: 10.1002/jcc.23340] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/03/2013] [Accepted: 05/02/2013] [Indexed: 11/07/2022]
Abstract
Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano-objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano-objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (Li, et al., J. Comput. Chem. 2012, 33, 1960) to include parallelization of the molecular surface and energy calculations components of the algorithm. The parallelization scheme utilizes different approaches such as space domain parallelization, algorithmic parallelization, multithreading, and task scheduling, depending on the quantity being calculated. This allows for efficient use of the computing resources of the corresponding computer cluster. The parallelization scheme is implemented in the popular software DelPhi and results in speedup of several folds. As a demonstration of the efficiency and capability of this methodology, the electrostatic potential, and electric field distributions are calculated for the bovine mitochondrial supercomplex illustrating their complex topology, which cannot be obtained by modeling the supercomplex components alone.
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Affiliation(s)
- Chuan Li
- Computational Biophysics and Bioinformatics, Physics Department, Clemson University, Clemson, SC 29642
| | - Marharyta Petukh
- Computational Biophysics and Bioinformatics, Physics Department, Clemson University, Clemson, SC 29642
| | - Lin Li
- Computational Biophysics and Bioinformatics, Physics Department, Clemson University, Clemson, SC 29642
| | - Emil Alexov
- Computational Biophysics and Bioinformatics, Physics Department, Clemson University, Clemson, SC 29642
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261
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Stefl S, Nishi H, Petukh M, Panchenko AR, Alexov E. Molecular mechanisms of disease-causing missense mutations. J Mol Biol 2013; 425:3919-36. [PMID: 23871686 DOI: 10.1016/j.jmb.2013.07.014] [Citation(s) in RCA: 187] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/04/2013] [Accepted: 07/10/2013] [Indexed: 12/23/2022]
Abstract
Genetic variations resulting in a change of amino acid sequence can have a dramatic effect on stability, hydrogen bond network, conformational dynamics, activity and many other physiologically important properties of proteins. The substitutions of only one residue in a protein sequence, so-called missense mutations, can be related to many pathological conditions and may influence susceptibility to disease and drug treatment. The plausible effects of missense mutations range from affecting the macromolecular stability to perturbing macromolecular interactions and cellular localization. Here we review the individual cases and genome-wide studies that illustrate the association between missense mutations and diseases. In addition, we emphasize that the molecular mechanisms of effects of mutations should be revealed in order to understand the disease origin. Finally, we report the current state-of-the-art methodologies that predict the effects of mutations on protein stability, the hydrogen bond network, pH dependence, conformational dynamics and protein function.
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Affiliation(s)
- Shannon Stefl
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
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262
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Guja KE, Venkataraman K, Yakubovskaya E, Shi H, Mejia E, Hambardjieva E, Karzai AW, Garcia-Diaz M. Structural basis for S-adenosylmethionine binding and methyltransferase activity by mitochondrial transcription factor B1. Nucleic Acids Res 2013; 41:7947-59. [PMID: 23804760 PMCID: PMC3763538 DOI: 10.1093/nar/gkt547] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic transcription factor B (TFB) proteins are homologous to KsgA/Dim1 ribosomal RNA (rRNA) methyltransferases. The mammalian TFB1, mitochondrial (TFB1M) factor is an essential protein necessary for mitochondrial gene expression. TFB1M mediates an rRNA modification in the small ribosomal subunit and thus plays a role analogous to KsgA/Dim1 proteins. This modification has been linked to mitochondrial dysfunctions leading to maternally inherited deafness, aminoglycoside sensitivity and diabetes. Here, we present the first structural characterization of the mammalian TFB1 factor. We have solved two X-ray crystallographic structures of TFB1M with (2.1 Å) and without (2.0 Å) its cofactor S-adenosyl-L-methionine. These structures reveal that TFB1M shares a conserved methyltransferase core with other KsgA/Dim1 methyltransferases and shed light on the structural basis of S-adenosyl-L-methionine binding and methyltransferase activity. Together with mutagenesis studies, these data suggest a model for substrate binding and provide insight into the mechanism of methyl transfer, clarifying the role of this factor in an essential process for mitochondrial function.
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Affiliation(s)
- Kip E Guja
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA, Medical Scientist Training Program, Stony Brook University Medical Center, Stony Brook, NY 11794, USA and Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
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263
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Abstract
This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to methods to extend the capabilities of the existing solvers to model large systems toward applications of calculations of the electrostatic potential and energies in molecular motors, mitochondria complex, photosynthetic machinery and systems involving large nano-objects.
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264
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Li L, Li C, Zhang Z, Alexov E. On the Dielectric "Constant" of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi. J Chem Theory Comput 2013; 9:2126-2136. [PMID: 23585741 PMCID: PMC3622359 DOI: 10.1021/ct400065j] [Citation(s) in RCA: 362] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Indexed: 01/26/2023]
Abstract
![]()
Implicit methods for modeling protein
electrostatics require dielectric
properties of the system to be known, in particular, the value of
the dielectric constant of protein. While numerous values of the internal
protein dielectric constant were reported in the literature, still
there is no consensus of what the optimal value is. Perhaps this is
due to the fact that the protein dielectric constant is not a “constant”
but is a complex function reflecting the properties of the protein’s
structure and sequence. Here, we report an implementation of a Gaussian-based
approach to deliver the dielectric constant distribution throughout
the protein and surrounding water phase by utilizing the 3D structure
of the corresponding macromolecule. In contrast to previous reports,
we construct a smooth dielectric function throughout the space of
the system to be modeled rather than just constructing a “Gaussian
surface” or smoothing molecule–water boundary. Analysis
on a large set of proteins shows that (a) the average dielectric constant
inside the protein is relatively low, about 6–7, and reaches
a value of about 20–30 at the protein’s surface, and
(b) high average local dielectric constant values are associated with
charged residues while low dielectric constant values are automatically
assigned to the regions occupied by hydrophobic residues. In terms
of energetics, a benchmarking test was carried out against the experimental
pKa’s of 89 residues in staphylococcal
nuclease (SNase) and showed that it results in a much better RMSD
(= 1.77 pK) than the corresponding calculations done
with a homogeneous high dielectric constant with an optimal value
of 10 (RMSD = 2.43 pK).
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Affiliation(s)
- Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, South Carolina 29634, United States
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265
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Enhancing human spermine synthase activity by engineered mutations. PLoS Comput Biol 2013; 9:e1002924. [PMID: 23468611 PMCID: PMC3585406 DOI: 10.1371/journal.pcbi.1002924] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 12/28/2012] [Indexed: 11/25/2022] Open
Abstract
Spermine synthase (SMS) is an enzyme which function is to convert spermidine into spermine. It was shown that gene defects resulting in amino acid changes of the wild type SMS cause Snyder-Robinson syndrome, which is a mild-to-moderate mental disability associated with osteoporosis, facial asymmetry, thin habitus, hypotonia, and a nonspecific movement disorder. These disease-causing missense mutations were demonstrated, both in silico and in vitro, to affect the wild type function of SMS by either destabilizing the SMS dimer/monomer or directly affecting the hydrogen bond network of the active site of SMS. In contrast to these studies, here we report an artificial engineering of a more efficient SMS variant by transferring sequence information from another organism. It is confirmed experimentally that the variant, bearing four amino acid substitutions, is catalytically more active than the wild type. The increased functionality is attributed to enhanced monomer stability, lowering the pKa of proton donor catalytic residue, optimized spatial distribution of the electrostatic potential around the SMS with respect to substrates, and increase of the frequency of mechanical vibration of the clefts presumed to be the gates toward the active sites. The study demonstrates that wild type SMS is not particularly evolutionarily optimized with respect to the reaction spermidine → spermine. Having in mind that currently there are no variations (non-synonymous single nucleotide polymorphism, nsSNP) detected in healthy individuals, it can be speculated that the human SMS function is precisely tuned toward its wild type and any deviation is unwanted and disease-causing. Proteins are constantly subjected to evolutionary pressure to assure the organism's survival and reproduction. At the same time, the proteins' amino acid sequence undergoes mutations, some of which may cause diseases while others may be reflecting natural differences within the population (non-synonymous single nucleotide polymorphism, nsSNP). In this study we examine the human spermine synthase (HsSMS), for which currently there are no nsSNPs, while rare disease mutations are known to cause Snyder-Robinson syndrome. What is so special with this protein? Maybe the HsSMS is so well optimized for its function that any change of the wild type sequence should be degrading its performance. To check such a possibility, we engineered a mutant of HsSMS with enhanced stability, electrostatic and mechanical properties. The mutant was confirmed experimentally to be a better enzyme than the wild type. Thus, the HsSMS is not evolutionally optimized with respect to its enzymatic reaction, its amino acid sequence differs only in sick individuals and so far its sequence was found to be identical in all healthy individuals. Therefore, it can be speculated that the HsSMS function is precisely tuned toward the wild type characteristics such so any deviation is unwanted and is disease-causing.
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Petukh M, Kimmet T, Alexov E. BION web server: predicting non-specifically bound surface ions. ACTA ACUST UNITED AC 2013; 29:805-6. [PMID: 23380591 DOI: 10.1093/bioinformatics/btt032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION Ions are essential component of the cell and frequently are found bound to various macromolecules, in particular to proteins. A binding of an ion to a protein greatly affects protein's biophysical characteristics and needs to be taken into account in any modeling approach. However, ion's bounded positions cannot be easily revealed experimentally, especially if they are loosely bound to macromolecular surface. RESULTS Here, we report a web server, the BION web server, which addresses the demand for tools of predicting surface bound ions, for which specific interactions are not crucial; thus, they are difficult to predict. The BION is easy to use web server that requires only coordinate file to be inputted, and the user is provided with various, but easy to navigate, options. The coordinate file with predicted bound ions is displayed on the output and is available for download.
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Affiliation(s)
- Marharyta Petukh
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
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Calmodulin-induced structural changes in endothelial nitric oxide synthase. FEBS Lett 2012; 587:297-301. [PMID: 23266515 DOI: 10.1016/j.febslet.2012.12.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 12/10/2012] [Accepted: 12/11/2012] [Indexed: 11/21/2022]
Abstract
We have derived structures of intact calmodulin (CaM)-free and CaM-bound endothelial nitric oxide synthase (eNOS) by reconstruction from cryo-electron micrographs. The CaM-free reconstruction is well fitted by the oxygenase domain dimer, but the reductase domains are not visible, suggesting they are mobile and thus delocalized. Additional protein is visible in the CaM-bound reconstruction, concentrated in volumes near two basic patches on each oxygenase domain. One of these corresponds with a presumptive docking site for the reductase domain FMN-binding module. The other is proposed to correspond with a docking site for CaM. A model is suggested in which CaM binding and docking position the reductase domains near the oxygenase domains and promote docking of the FMN-binding modules required for electron transfer.
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Smith N, Campbell B, Li L, Li C, Alexov E. Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling. BMC STRUCTURAL BIOLOGY 2012; 12:31. [PMID: 23217202 PMCID: PMC3532097 DOI: 10.1186/1472-6807-12-31] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 11/28/2012] [Indexed: 11/10/2022]
Abstract
Background With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system. Results Here we report the Protein Nano-Object Integrator (ProNOI) which allows for generating atomic-style geometrical objects with user desired shape and dimensions. Unlimited number of objects can be created and combined with biological macromolecules in Protein Data Bank (PDB) format file. Once the objects are generated, the users can use sliders to manipulate their shape, dimension and absolute position. In addition, the software offers the option to charge the objects with either specified surface or volumetric charge density and to model them with user-desired dielectric constants. According to the user preference, the biological macromolecule atoms can be assigned charges and radii according to four different force fields: Amber, Charmm, OPLS and PARSE. The biological macromolecules and the atomic-style objects are exported as a position, charge and radius (PQR) file, or if a default dielectric constant distribution is not selected, it is exported as a position, charge, radius and epsilon (PQRE) file. As illustration of the capabilities of the ProNOI, we created a composite object in a shape of a robot, aptly named the Clemson Robot, whose parts are charged with various volumetric charge densities and holds the barnase-barstar protein complex in its hand. Conclusions The Protein Nano-Object Integrator (ProNOI) is a convenient tool for generating atomic-style nano shapes in conjunction with biological macromolecule(s). Charges and radii on the macromolecule atoms and the atoms in the shapes are assigned according to the user’s preferences allowing various scenarios of modeling. The default output file is in PQR (PQRE) format which is readable by almost any software available in biophysical field. It can be downloaded from: http://compbio.clemson.edu/downloadDir/ProNO_integrator.tar.gz
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Affiliation(s)
- Nicholas Smith
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
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