1
|
Elamin T, Brandstetter H, Dall E. Legumain Activity Is Controlled by Extended Active Site Residues and Substrate Conformation. Int J Mol Sci 2022; 23:12548. [PMID: 36293424 PMCID: PMC9604545 DOI: 10.3390/ijms232012548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Legumain is a lysosomal cysteine protease with strict specificity for cleaving after asparagine residues. By sequence comparison, legumain belongs to MEROPS clan CD of the cysteine proteases, which indicates its structural and mechanistic relation to caspases. Contrasting caspases, legumain harbors a pH-dependent ligase activity in addition to the protease activity. Although we already have a significant body of knowledge on the catalytic activities of legumain, many mechanistic details are still elusive. In this study, we provide evidence that extended active site residues and substrate conformation are steering legumain activities. Biochemical experiments and bioinformatics analysis showed that the catalytic Cys189 and His148 residues are regulated by sterically close Glu190, Ser215 and Asn42 residues. While Glu190 serves as an activity brake, Ser215 and Asn42 have a favorable effect on legumain protease activity. Mutagenesis studies using caspase-9 as model enzyme additionally showed that a similar Glu190 activity brake is also implemented in the caspases. Furthermore, we show that the substrate's conformational flexibility determines whether it will be hydrolyzed or ligated by legumain. The functional understanding of the extended active site residues and of substrate prerequisites will allow us to engineer proteases with increased enzymatic activity and better ligase substrates, with relevance for biotechnological applications.
Collapse
Affiliation(s)
| | | | - Elfriede Dall
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| |
Collapse
|
2
|
Localization of Energetic Frustration in Proteins. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2376:387-398. [PMID: 34845622 DOI: 10.1007/978-1-0716-1716-8_22] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
We present a detailed heuristic method to quantify the degree of local energetic frustration manifested by protein molecules. Current applications are realized in computational experiments where a protein structure is visualized highlighting the energetic conflicts or the concordance of the local interactions in that structure. Minimally frustrated linkages highlight the stable folding core of the molecule. Sites of high local frustration, in contrast, often indicate functionally relevant regions such as binding, active, or allosteric sites.
Collapse
|
3
|
Yu H, Hernández López RI, Steadman D, Méndez‐Sánchez D, Higson S, Cázares‐Körner A, Sheppard TD, Ward JM, Hailes HC, Dalby PA. Engineering transketolase to accept both unnatural donor and acceptor substrates and produce α‐hydroxyketones. FEBS J 2019; 287:1758-1776. [DOI: 10.1111/febs.15108] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/26/2019] [Accepted: 10/23/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Haoran Yu
- Department of Biochemical Engineering University College London UK
| | | | | | | | - Sally Higson
- Department of Chemistry University College London UK
| | | | | | - John M. Ward
- Department of Biochemical Engineering University College London UK
| | | | - Paul A. Dalby
- Department of Biochemical Engineering University College London UK
| |
Collapse
|
4
|
Kovalchuk N, Wu W, Bazanova N, Reid N, Singh R, Shirley N, Eini O, Johnson AAT, Langridge P, Hrmova M, Lopato S. Wheat wounding-responsive HD-Zip IV transcription factor GL7 is predominantly expressed in grain and activates genes encoding defensins. PLANT MOLECULAR BIOLOGY 2019; 101:41-61. [PMID: 31183604 DOI: 10.1007/s11103-019-00889-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/31/2019] [Indexed: 06/09/2023]
Abstract
Several classes of transcription factors are involved in the activation of defensins. A new type of the transcription factor responsible for the regulation of wheat grain specific defensins was characterised in this work. HD-Zip class IV transcription factors constitute a family of multidomain proteins. A full-length cDNA of HD-Zip IV, designated TaGL7 was isolated from the developing grain of bread wheat, using a specific DNA sequence as bait in the Y1H screen. 3D models of TaGL7 HD complexed with DNA cis-elements rationalised differences that underlined accommodations of binding and non-binding DNA, while the START-like domain model predicted binding of lipidic molecules inside a concave hydrophobic cavity. The 3'-untranslated region of TaGL7 was used as a probe to isolate the genomic clone of TdGL7 from a BAC library prepared from durum wheat. The spatial and temporal activity of the TdGL7 promoter was tested in transgenic wheat, barley and rice. TdGL7 was expressed mostly in ovary at fertilisation and its promoter was active in a liquid endosperm during cellularisation and later in the endosperm transfer cells, aleurone, and starchy endosperm. The pattern of TdGL7 expression resembled that of genes that encode grain-specific lipid transfer proteins, particularly defensins. In addition, GL7 expression was upregulated by mechanical wounding, similarly to defensin genes. Co-bombardment of cultured wheat cells with TdGL7 driven by constitutive promoter and seven grain or root specific defensin promoters fused to GUS gene, revealed activation of four promoters. The data confirmed the previously proposed role of HD-Zip IV transcription factors in the regulation of genes that encode lipid transfer proteins involved in lipid transport and defence. The TdGL7 promoter could be used to engineer cereal grains with enhanced resistance to insects and fungal infections.
Collapse
Affiliation(s)
- Nataliya Kovalchuk
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Wei Wu
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
- Agronomy College, Sichuan Agricultural University, Ya'an, 625014, China
| | - Natalia Bazanova
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
- Commonwealth Scientific and Industrial Research Organisation, Glen Osmond, 5064, SA, Australia
| | - Nicolas Reid
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Rohan Singh
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Neil Shirley
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Omid Eini
- Department of Plant Protection, School of Agriculture, University of Zanjan, Zanjan, Iran
| | | | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Maria Hrmova
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia.
- School of Life Sciences, Huaiyin Normal University, Huai'an, China.
| | - Sergiy Lopato
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| |
Collapse
|
5
|
Wang L, Zhang Y, Zou S. The characterization of pc-polylines representing protein backbones. Proteins 2019; 88:307-318. [PMID: 31442337 DOI: 10.1002/prot.25803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/08/2019] [Accepted: 08/19/2019] [Indexed: 11/10/2022]
Abstract
The backbone of a protein is typically represented as either a C α -polyline, a three-dimensional (3D) polyline that passes through the C α atoms, or a tuple of ϕ,ψ pairs while its fold is usually assigned using the 3D topological arrangement of the secondary structure elements (SSEs). It is tricky to obtain the SSE composition for a protein from the C α -polyline representation while its 3D SSE arrangement is not apparent in the two-dimensional (2D) ϕ,ψ representation. In this article, we first represent the backbone of a protein as a pc-polyline that passes through the centers of its peptide planes. We then analyze the pc-polylines for six different sets of proteins with high quality crystal structures. The results show that SSE composition becomes recognizable in pc-polyline presentation and consequently the geometrical property of the pc-polyline of a protein could be used to assign its secondary structure. Furthermore, our analysis finds that for each of the six sets the total length of a pc-polyline increases linearly with the number of the peptide planes. Interestingly a comparison of the six regression lines shows that they have almost identical slopes but different intercepts. Most interestingly there exist decent linear correlations between the intercepts of the six lines and either the average helix contents or the average sheet contents and between the intercepts and the average backbone hydrogen bonding energetics. Finally, we discuss the implications of the identified correlations for structure classification and protein folding, and the potential applications of pc-polyline representation to structure prediction and protein design.
Collapse
Affiliation(s)
- Lincong Wang
- The College of Computer Science and Technology, Jilin University, Changchun, Jilin, China
| | - Yao Zhang
- The College of Computer Science and Technology, Jilin University, Changchun, Jilin, China
| | - Shuxue Zou
- The College of Computer Science and Technology, Jilin University, Changchun, Jilin, China
| |
Collapse
|
6
|
Binding of the protein ICln to α-integrin contributes to the activation of ICl swell current. Sci Rep 2019; 9:12195. [PMID: 31434921 PMCID: PMC6704128 DOI: 10.1038/s41598-019-48496-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/06/2019] [Indexed: 12/13/2022] Open
Abstract
IClswell is the chloride current induced by cell swelling, and plays a fundamental role in several biological processes, including the regulatory volume decrease (RVD). ICln is a highly conserved, ubiquitously expressed and multifunctional protein involved in the activation of IClswell. In platelets, ICln binds to the intracellular domain of the integrin αIIb chain, however, whether the ICln/integrin interaction plays a role in RVD is not known. Here we show that a direct molecular interaction between ICln and the integrin α-chain is not restricted to platelets and involves highly conserved amino acid motifs. Integrin α recruits ICln to the plasma membrane, thereby facilitating the activation of IClswell during hypotonicity. Perturbation of the ICln/integrin interaction prevents the transposition of ICln towards the cell surface and, in parallel, impedes the activation of IClswell. We suggest that the ICln/integrin interaction interface may represent a new molecular target enabling specific IClswell suppression in pathological conditions when this current is deregulated or plays a detrimental role.
Collapse
|
7
|
Abstract
Conflicting biological goals often meet in the specification of protein sequences for structure and function. Overall, strong energetic conflicts are minimized in folded native states according to the principle of minimal frustration, so that a sequence can spontaneously fold, but local violations of this principle open up the possibility to encode the complex energy landscapes that are required for active biological functions. We survey the local energetic frustration patterns of all protein enzymes with known structures and experimentally annotated catalytic residues. In agreement with previous hypotheses, the catalytic sites themselves are often highly frustrated regardless of the protein oligomeric state, overall topology, and enzymatic class. At the same time a secondary shell of more weakly frustrated interactions surrounds the catalytic site itself. We evaluate the conservation of these energetic signatures in various family members of major enzyme classes, showing that local frustration is evolutionarily more conserved than the primary structure itself.
Collapse
|
8
|
Joung I, Kim JY, Joo K, Lee J. Non-sequential protein structure alignment by conformational space annealing and local refinement. PLoS One 2019; 14:e0210177. [PMID: 30699145 PMCID: PMC6353097 DOI: 10.1371/journal.pone.0210177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 12/18/2018] [Indexed: 11/18/2022] Open
Abstract
Protein structure alignment is an important tool for studying evolutionary biology and protein modeling. A tool which intensively searches for the globally optimal non-sequential alignments is rarely found. We propose ALIGN-CSA which shows improvement in scores, such as DALI-score, SP-score, SO-score and TM-score over the benchmark set including 286 cases. We performed benchmarking of existing popular alignment scoring functions, where the dependence of the search algorithm was effectively eliminated by using ALIGN-CSA. For the benchmarking, we set the minimum block size to 4 to prevent much fragmented alignments where the biological relevance of small alignment blocks is hard to interpret. With this condition, globally optimal alignments were searched by ALIGN-CSA using the four scoring functions listed above, and TM-score is found to be the most effective in generating alignments with longer match lengths and smaller RMSD values. However, DALI-score is the most effective in generating alignments similar to the manually curated reference alignments, which implies that DALI-score is more biologically relevant score. Due to the high demand on computational resources of ALIGN-CSA, we also propose a relatively fast local refinement method, which can control the minimum block size and whether to allow the reverse alignment. ALIGN-CSA can be used to obtain much improved alignment at the cost of relatively more extensive computation. For faster alignment, we propose a refinement protocol that improves the score of a given alignment obtained by various external tools. All programs are available from http://lee.kias.re.kr.
Collapse
Affiliation(s)
- InSuk Joung
- Center for In Silico Protein Science, Korea Institute for Advanced Study, Seoul, Korea
| | - Jong Yun Kim
- Center for In Silico Protein Science, Korea Institute for Advanced Study, Seoul, Korea
| | - Keehyoung Joo
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea
- Center for Advanced Computation, Korea Institute for Advanced Study, Seoul, Korea
| | - Jooyoung Lee
- Center for In Silico Protein Science, Korea Institute for Advanced Study, Seoul, Korea
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea
- Center for Advanced Computation, Korea Institute for Advanced Study, Seoul, Korea
- * E-mail:
| |
Collapse
|
9
|
Naschberger A, Orry A, Lechner S, Bowler MW, Nurizzo D, Novokmet M, Keller MA, Oemer G, Seppi D, Haslbeck M, Pansi K, Dieplinger H, Rupp B. Structural Evidence for a Role of the Multi-functional Human Glycoprotein Afamin in Wnt Transport. Structure 2017; 25:1907-1915.e5. [PMID: 29153507 DOI: 10.1016/j.str.2017.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/14/2017] [Accepted: 10/23/2017] [Indexed: 11/19/2022]
Abstract
Afamin, a human plasma glycoprotein and putative transporter of hydrophobic molecules, has been shown to act as extracellular chaperone for poorly soluble, acylated Wnt proteins, forming a stable, soluble complex with functioning Wnt proteins. The 2.1-Å crystal structure of glycosylated human afamin reveals an almost exclusively hydrophobic binding cleft capable of harboring large hydrophobic moieties. Lipid analysis confirms the presence of lipids, and density in the primary binding pocket of afamin was modeled as palmitoleic acid, presenting the native O-acylation on serine 209 in human Wnt3a. The modeled complex between the experimental afamin structure and a Wnt3a homology model based on the XWnt8-Fz8-CRD fragment complex crystal structure is compelling, with favorable interactions comparable with the crystal structure complex. Afamin readily accommodates the conserved palmitoylated serine 209 of Wnt3a, providing a structural basis how afamin solubilizes hydrophobic and poorly soluble Wnt proteins.
Collapse
Affiliation(s)
- Andreas Naschberger
- Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria; Division of Biological Chemistry, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Andrew Orry
- MolSoft LLC, 11199 Sorrento Valley Road, San Diego, CA 92121, USA
| | - Stefan Lechner
- Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38043 Grenoble, France
| | - Didier Nurizzo
- Structural Biology Group, ESRF, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Mislav Novokmet
- Genos, Glycoscience Laboratory, Hondlova 2/11, 10000 Zagreb, Croatia
| | - Markus A Keller
- Division of Human Genetics, Medical University of Innsbruck, Peter-Mayr-Straße 1, 6020 Innsbruck, Austria
| | - Gregor Oemer
- Genos, Glycoscience Laboratory, Hondlova 2/11, 10000 Zagreb, Croatia
| | - Daniele Seppi
- Division of Biological Chemistry, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Martin Haslbeck
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Kathrin Pansi
- Division of Biological Chemistry, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Hans Dieplinger
- Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria
| | - Bernhard Rupp
- Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria; k.-k. Hofkristallamt, San Diego, CA 92084, USA.
| |
Collapse
|
10
|
Crystal Structure of a Group I Energy Coupling Factor Vitamin Transporter S Component in Complex with Its Cognate Substrate. Cell Chem Biol 2017; 23:827-836. [PMID: 27447050 PMCID: PMC5037267 DOI: 10.1016/j.chembiol.2016.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/18/2016] [Accepted: 06/02/2016] [Indexed: 12/27/2022]
Abstract
Energy coupling factor (ECF) transporters are responsible for the uptake of essential scarce nutrients in prokaryotes. This ATP-binding cassette transporter family comprises two subgroups that share a common architecture forming a tripartite membrane protein complex consisting of a translocation component and ATP hydrolyzing module and a substrate-capture (S) component. Here, we present the crystal structure of YkoE from Bacillus subtilis, the S component of the previously uncharacterized group I ECF transporter YkoEDC. Structural and biochemical analyses revealed the constituent residues of the thiamine-binding pocket as well as an unexpected mode of vitamin recognition. In addition, our experimental and bioinformatics data demonstrate major differences between YkoE and group II ECF transporters and indicate how group I vitamin transporter S components have diverged from other group I and group II ECF transporters. The crystal structure of a group I ECF transporter S component was determined The thiamine-bound structure was determined in lipidic environment The structure reveals major differences to group II S components CGMD simulations indicate the orientation of the protein in the membrane
Collapse
|
11
|
Jia Z, Ackroyd C, Han T, Agrawal V, Liu Y, Christensen K, Dominy B. Effects from metal ion in tumor endothelial marker 8 and anthrax protective antigen: BioLayer Interferometry experiment and molecular dynamics simulation study. J Comput Chem 2017; 38:1183-1190. [PMID: 28437008 DOI: 10.1002/jcc.24768] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 01/08/2017] [Accepted: 01/14/2017] [Indexed: 11/09/2022]
Abstract
One of the anthrax receptors, tumor endothelial marker 8 (TEM8), is reported to be a potential anticancer target due to its over-expression during tumor angiogenesis. To extend our BioLayer Interferometry study in PA-TEM8 binding, we present a computational approach to reveal the role of an integral metal ion on receptor structure and binding thermodynamics. We estimated the interaction energy between PA and TEM8 using computer simulation. Consistent with experimental study, computational results indicate the metal ion in TEM8 contributes significantly to the binding affinity, and PA-TEM8 binding is more favorable in the presence of Mg2+ than Ca2+ . Further, computational analysis suggests that the differences in PA-TEM8 binding affinity are comparable to the closely related integrin proteins. The conformation change, which linked to changes in activity of integrins, was not found in TEM8. In the present of Mg2+ , TEM8 remains in a conformation analogous to an integrin open (high-affinity) conformation. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Zhe Jia
- Clemson University Department of Chemistry, 309 Hunter Lab Clemson University, Clemson, South Carolina, 29634
| | - Christine Ackroyd
- Department of Chemistry and Biochemistry, C205 BNSN, Brigham Young University, Provo, Utah, 84602
| | - Tingting Han
- Clemson University Department of Chemistry, 309 Hunter Lab Clemson University, Clemson, South Carolina, 29634
| | - Vibhor Agrawal
- Clemson University Department of Chemistry, 309 Hunter Lab Clemson University, Clemson, South Carolina, 29634
| | - Yinling Liu
- Clemson University Department of Chemistry, 309 Hunter Lab Clemson University, Clemson, South Carolina, 29634
| | - Kenneth Christensen
- Department of Chemistry and Biochemistry, C205 BNSN, Brigham Young University, Provo, Utah, 84602
| | - Brian Dominy
- Clemson University Department of Chemistry, 309 Hunter Lab Clemson University, Clemson, South Carolina, 29634
| |
Collapse
|
12
|
Collier JH, Allison L, Lesk AM, Stuckey PJ, Garcia de la Banda M, Konagurthu AS. Statistical inference of protein structural alignments using information and compression. Bioinformatics 2017; 33:1005-1013. [PMID: 28065899 DOI: 10.1093/bioinformatics/btw757] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/22/2016] [Indexed: 11/14/2022] Open
Abstract
Motivation Structural molecular biology depends crucially on computational techniques that compare protein three-dimensional structures and generate structural alignments (the assignment of one-to-one correspondences between subsets of amino acids based on atomic coordinates). Despite its importance, the structural alignment problem has not been formulated, much less solved, in a consistent and reliable way. To overcome these difficulties, we present here a statistical framework for the precise inference of structural alignments, built on the Bayesian and information-theoretic principle of Minimum Message Length (MML). The quality of any alignment is measured by its explanatory power-the amount of lossless compression achieved to explain the protein coordinates using that alignment. Results We have implemented this approach in MMLigner , the first program able to infer statistically significant structural alignments. We also demonstrate the reliability of MMLigner 's alignment results when compared with the state of the art. Importantly, MMLigner can also discover different structural alignments of comparable quality, a challenging problem for oligomers and protein complexes. Availability and Implementation Source code, binaries and an interactive web version are available at http://lcb.infotech.monash.edu.au/mmligner . Contact arun.konagurthu@monash.edu. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- James H Collier
- Faculty of Information Technology, Monash University, Clayton, VIC 3800, Australia
| | - Lloyd Allison
- Faculty of Information Technology, Monash University, Clayton, VIC 3800, Australia
| | - Arthur M Lesk
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Peter J Stuckey
- Department of Computing and Information Systems, University of Melbourne, Parkville, VIC 3010, Australia
| | | | - Arun S Konagurthu
- Faculty of Information Technology, Monash University, Clayton, VIC 3800, Australia
| |
Collapse
|
13
|
Correlated Mutation in the Evolution of Catalysis in Uracil DNA Glycosylase Superfamily. Sci Rep 2017; 7:45978. [PMID: 28397787 PMCID: PMC5387724 DOI: 10.1038/srep45978] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/07/2017] [Indexed: 02/07/2023] Open
Abstract
Enzymes in Uracil DNA glycosylase (UDG) superfamily are essential for the removal of uracil. Family 4 UDGa is a robust uracil DNA glycosylase that only acts on double-stranded and single-stranded uracil-containing DNA. Based on mutational, kinetic and modeling analyses, a catalytic mechanism involving leaving group stabilization by H155 in motif 2 and water coordination by N89 in motif 3 is proposed. Mutual Information analysis identifies a complexed correlated mutation network including a strong correlation in the EG doublet in motif 1 of family 4 UDGa and in the QD doublet in motif 1 of family 1 UNG. Conversion of EG doublet in family 4 Thermus thermophilus UDGa to QD doublet increases the catalytic efficiency by over one hundred-fold and seventeen-fold over the E41Q and G42D single mutation, respectively, rectifying the strong correlation in the doublet. Molecular dynamics simulations suggest that the correlated mutations in the doublet in motif 1 position the catalytic H155 in motif 2 to stabilize the leaving uracilate anion. The integrated approach has important implications in studying enzyme evolution and protein structure and function.
Collapse
|
14
|
Al-Jassar C, Andreeva A, Barnabas DD, McLaughlin SH, Johnson CM, Yu M, van Breugel M. The Ciliopathy-Associated Cep104 Protein Interacts with Tubulin and Nek1 Kinase. Structure 2016; 25:146-156. [PMID: 28017521 PMCID: PMC5222566 DOI: 10.1016/j.str.2016.11.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 11/04/2016] [Accepted: 11/18/2016] [Indexed: 12/26/2022]
Abstract
Cilia are thin cell projections with essential roles in cell motility, fluid movement, sensing, and signaling. They are templated from centrioles that dock against the plasma membrane and subsequently extend their peripheral microtubule array. The molecular mechanisms underpinning cilia assembly are incompletely understood. Cep104 is a key factor involved in cilia formation and length regulation that rides on the ends of elongating and shrinking cilia. It is mutated in Joubert syndrome, a genetically heterogeneous ciliopathy. Here we provide structural and biochemical data that Cep104 contains a tubulin-binding TOG (tumor overexpressed gene) domain and a novel C2HC zinc finger array. Furthermore, we identify the kinase Nek1, another ciliopathy-associated protein, as a potential binding partner of this array. Finally, we show that Nek1 competes for binding to Cep104 with the distal centriole-capping protein CP110. Our data suggest a model for Cep104 activity during ciliogenesis and provide a novel link between Cep104 and Nek1.
Collapse
Affiliation(s)
- Caezar Al-Jassar
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Antonina Andreeva
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Deepak D Barnabas
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephen H McLaughlin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher M Johnson
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Minmin Yu
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Mark van Breugel
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| |
Collapse
|
15
|
Rasti B, Namazi M, Karimi-Jafari MH, Ghasemi JB. Proteochemometric Modeling of the Interaction Space of Carbonic Anhydrase and its Inhibitors: An Assessment of Structure-based and Sequence-based Descriptors. Mol Inform 2016; 36. [PMID: 27860295 DOI: 10.1002/minf.201600102] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 10/26/2016] [Indexed: 11/08/2022]
Abstract
Due to its physiological and clinical roles, carbonic anhydrase (CA) is one of the most interesting case studies. There are different classes of CAinhibitors including sulfonamides, polyamines, coumarins and dithiocarbamates (DTCs). However, many of them hardly act as a selective inhibitor against a specific isoform. Therefore, finding highly selective inhibitors for different isoforms of CA is still an ongoing project. Proteochemometrics modeling (PCM) is able to model the bioactivity of multiple compounds against different isoforms of a protein. Therefore, it would be extremely applicable when investigating the selectivity of different ligands towards different receptors. Given the facts, we applied PCM to investigate the interaction space and structural properties that lead to the selective inhibition of CA isoforms by some dithiocarbamates. Our models have provided interesting structural information that can be considered to design compounds capable of inhibiting different isoforms of CA in an improved selective manner. Validity and predictivity of the models were confirmed by both internal and external validation methods; while Y-scrambling approach was applied to assess the robustness of the models. To prove the reliability and the applicability of our findings, we showed how ligands-receptors selectivity can be affected by removing any of these critical findings from the modeling process.
Collapse
Affiliation(s)
- Behnam Rasti
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mohsen Namazi
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - M H Karimi-Jafari
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Jahan B Ghasemi
- Department of Analytical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| |
Collapse
|
16
|
Acevedo W, González-Nilo F, Agosin E. Docking and Molecular Dynamics of Steviol Glycoside-Human Bitter Receptor Interactions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:7585-7596. [PMID: 27640213 DOI: 10.1021/acs.jafc.6b02840] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Stevia is one of the sweeteners with the greatest consumer demand because of its natural origin and minimal calorie content. Steviol glycosides (SG) are the main active compounds present in the leaves of Stevia rebaudiana and are responsible for its sweetness. However, recent in vitro studies in HEK 293 cells revealed that SG specifically activate the hT2R4 and hT2R14 bitter taste receptors, triggering this mouth feel. The objective of this study was to characterize the interaction of SG with these two receptors at the molecular level. The results showed that SG have only one site for orthosteric binding to these receptors. The binding free energy (ΔGbinding) between the receptor and SG was negatively correlated with SG bitterness intensity, for both hT2R4 (r = -0.95) and hT2R14 (r = -0.89). We also determined, by steered molecular dynamics simulations, that the force required to extract stevioside from the receptors was greater than that required for rebaudioside A, in accordance with the ΔG values obtained by molecular docking. Finally, we identified the loop responsible for the activation by SG of both receptors. As a whole, these results contribute to a better understanding of the resulting off-flavor perception of these natural sweeteners in foods and beverages, allowing for better prediction, and control, of the resulting bitterness.
Collapse
Affiliation(s)
- Waldo Acevedo
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile , Avenida Vicuña Mackenna, 4860 Santiago, Chile
| | - Fernando González-Nilo
- Universidad Andrés Bello , Center for Bioinformatics and Integrative Biology, Faculty of Biological Sciences, Avenida República 239, Santiago, Chile
| | - Eduardo Agosin
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile , Avenida Vicuña Mackenna, 4860 Santiago, Chile
| |
Collapse
|
17
|
Costanzo LD, Ghosh S, Zardecki C, Burley SK. Using the Tools and Resources of the RCSB Protein Data Bank. ACTA ACUST UNITED AC 2016; 55:1.9.1-1.9.35. [DOI: 10.1002/cpbi.13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Luigi Di Costanzo
- RCSB Protein Data Bank, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey Piscataway New Jersey
| | - Sutapa Ghosh
- RCSB Protein Data Bank, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey Piscataway New Jersey
| | - Christine Zardecki
- RCSB Protein Data Bank, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey Piscataway New Jersey
| | - Stephen K. Burley
- RCSB Protein Data Bank, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey Piscataway New Jersey
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey Piscataway New Jersey
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego California
- San Diego Supercomputer Center, University of California San Diego California
| |
Collapse
|
18
|
Abstract
Structural domains are believed to be modules within proteins that can fold and function independently. Some proteins show tandem repetitions of apparent modular structure that do not fold independently, but rather co-operate in stabilizing structural forms that comprise several repeat-units. For many natural repeat-proteins, it has been shown that weak energetic links between repeats lead to the breakdown of co-operativity and the appearance of folding sub-domains within an apparently regular repeat array. The quasi-1D architecture of repeat-proteins is crucial in detailing how the local energetic balances can modulate the folding dynamics of these proteins, which can be related to the physiological behaviour of these ubiquitous biological systems.
Collapse
|
19
|
Parra RG, Espada R, Verstraete N, Ferreiro DU. Structural and Energetic Characterization of the Ankyrin Repeat Protein Family. PLoS Comput Biol 2015; 11:e1004659. [PMID: 26691182 PMCID: PMC4687027 DOI: 10.1371/journal.pcbi.1004659] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/10/2015] [Indexed: 11/21/2022] Open
Abstract
Ankyrin repeat containing proteins are one of the most abundant solenoid folds. Usually implicated in specific protein-protein interactions, these proteins are readily amenable for design, with promising biotechnological and biomedical applications. Studying repeat protein families presents technical challenges due to the high sequence divergence among the repeating units. We developed and applied a systematic method to consistently identify and annotate the structural repetitions over the members of the complete Ankyrin Repeat Protein Family, with increased sensitivity over previous studies. We statistically characterized the number of repeats, the folding of the repeat-arrays, their structural variations, insertions and deletions. An energetic analysis of the local frustration patterns reveal the basic features underlying fold stability and its relation to the functional binding regions. We found a strong linear correlation between the conservation of the energetic features in the repeat arrays and their sequence variations, and discuss new insights into the organization and function of these ubiquitous proteins. Some natural proteins are formed with repetitions of similar amino acid stretches. Ankyrin-repeat proteins constitute one of the most abundant families of this class of proteins that serve as model systems to analyze how variations in sequences exert effects in structures and biological functions. We present an in-depth analysis of the ankyrin repeat protein family, characterizing the variations in the repeating arrays both at the structural and energetic level. We introduce a consistent annotation for the repeat characteristics and describe how the structural differences are related to the sequences by their underlying energetic signatures.
Collapse
Affiliation(s)
- R. Gonzalo Parra
- Protein Physiology Lab, Dep de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, Buenos Aires, Argentina
| | - Rocío Espada
- Protein Physiology Lab, Dep de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, Buenos Aires, Argentina
| | - Nina Verstraete
- Protein Physiology Lab, Dep de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, Buenos Aires, Argentina
| | - Diego U. Ferreiro
- Protein Physiology Lab, Dep de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, Buenos Aires, Argentina
- * E-mail:
| |
Collapse
|
20
|
Schafferhans A, Rost B. Taking structure searches to the next dimension. Structure 2015; 22:938-9. [PMID: 25007224 DOI: 10.1016/j.str.2014.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Structure comparisons are now the first step when a new experimental high-resolution protein structure has been determined. In this issue of Structure, Wiederstein and colleagues describe their latest tool for comparing structures, which gives us the unprecedented power to discover crucial structural connections between whole complexes of proteins in the full structural database in real time.
Collapse
Affiliation(s)
- Andrea Schafferhans
- Department of Informatics, Bioinformatics-I12, TUM, Boltzmannstrasse 3, 85748 Garching/Munich, Germany.
| | - Burkhard Rost
- Department of Informatics, Bioinformatics-I12, TUM, Boltzmannstrasse 3, 85748 Garching/Munich, Germany
| |
Collapse
|
21
|
Reddy JG, Kumar D, Hosur RV. Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:79-87. [PMID: 25178811 DOI: 10.1002/mrc.4135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 07/29/2014] [Accepted: 08/04/2014] [Indexed: 06/03/2023]
Abstract
Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The primary requirement for all such investigations is sequence-specific resonance assignment. The demand now is to obtain this information as rapidly as possible and in all types of protein systems, stable/unstable, soluble/insoluble, small/big, structured/unstructured, and so on. In this context, we introduce here two reduced dimensionality experiments – (3,2)D-hNCOcanH and (3,2)D-hNcoCAnH – which enhance the previously described 2D NMR-based assignment methods quite significantly. Both the experiments can be recorded in just about 2-3 h each and hence would be of immense value for high-throughput structural proteomics and drug discovery research. The applicability of the method has been demonstrated using alpha-helical bovine apo calbindin-D9k P43M mutant (75 aa) protein. Automated assignment of this data using AUTOBA has been presented, which enhances the utility of these experiments. The backbone resonance assignments so derived are utilized to estimate secondary structures and the backbone fold using Web-based algorithms. Taken together, we believe that the method and the protocol proposed here can be used for routine high-throughput structural studies of proteins.
Collapse
Affiliation(s)
- Jithender G Reddy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, 1-Homi Bhabha Road, Colaba, Mumbai, 400005, India
| | | | | |
Collapse
|
22
|
Collier JH, Allison L, Lesk AM, Garcia de la Banda M, Konagurthu AS. A new statistical framework to assess structural alignment quality using information compression. Bioinformatics 2015; 30:i512-8. [PMID: 25161241 PMCID: PMC4147913 DOI: 10.1093/bioinformatics/btu460] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Motivation: Progress in protein biology depends on the reliability of results from a handful of computational techniques, structural alignments being one. Recent reviews have highlighted substantial inconsistencies and differences between alignment results generated by the ever-growing stock of structural alignment programs. The lack of consensus on how the quality of structural alignments must be assessed has been identified as the main cause for the observed differences. Current methods assess structural alignment quality by constructing a scoring function that attempts to balance conflicting criteria, mainly alignment coverage and fidelity of structures under superposition. This traditional approach to measuring alignment quality, the subject of considerable literature, has failed to solve the problem. Further development along the same lines is unlikely to rectify the current deficiencies in the field. Results: This paper proposes a new statistical framework to assess structural alignment quality and significance based on lossless information compression. This is a radical departure from the traditional approach of formulating scoring functions. It links the structural alignment problem to the general class of statistical inductive inference problems, solved using the information-theoretic criterion of minimum message length. Based on this, we developed an efficient and reliable measure of structural alignment quality, I-value. The performance of I-value is demonstrated in comparison with a number of popular scoring functions, on a large collection of competing alignments. Our analysis shows that I-value provides a rigorous and reliable quantification of structural alignment quality, addressing a major gap in the field. Availability: http://lcb.infotech.monash.edu.au/I-value Contact: arun.konagurthu@monash.edu Supplementary information:Online supplementary data are available at http://lcb.infotech.monash.edu.au/I-value/suppl.html
Collapse
Affiliation(s)
- James H Collier
- Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia and Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Lloyd Allison
- Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia and Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Arthur M Lesk
- Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia and Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Maria Garcia de la Banda
- Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia and Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Arun S Konagurthu
- Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia and Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
23
|
Cortés-Ciriano I, Ain QU, Subramanian V, Lenselink EB, Méndez-Lucio O, IJzerman AP, Wohlfahrt G, Prusis P, Malliavin TE, van Westen GJP, Bender A. Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00216d] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteochemometric (PCM) modelling is a computational method to model the bioactivity of multiple ligands against multiple related protein targets simultaneously.
Collapse
Affiliation(s)
- Isidro Cortés-Ciriano
- Unité de Bioinformatique Structurale
- Institut Pasteur and CNRS UMR 3825
- Structural Biology and Chemistry Department
- 75 724 Paris
- France
| | - Qurrat Ul Ain
- Unilever Centre for Molecular Informatics
- Department of Chemistry
- CB2 1EW Cambridge
- UK
| | | | - Eelke B. Lenselink
- Division of Medicinal Chemistry
- Leiden Academic Centre for Drug Research
- Leiden
- The Netherlands
| | - Oscar Méndez-Lucio
- Unilever Centre for Molecular Informatics
- Department of Chemistry
- CB2 1EW Cambridge
- UK
| | - Adriaan P. IJzerman
- Division of Medicinal Chemistry
- Leiden Academic Centre for Drug Research
- Leiden
- The Netherlands
| | - Gerd Wohlfahrt
- Computer-Aided Drug Design
- Orion Pharma
- FIN-02101 Espoo
- Finland
| | - Peteris Prusis
- Computer-Aided Drug Design
- Orion Pharma
- FIN-02101 Espoo
- Finland
| | - Thérèse E. Malliavin
- Unité de Bioinformatique Structurale
- Institut Pasteur and CNRS UMR 3825
- Structural Biology and Chemistry Department
- 75 724 Paris
- France
| | - Gerard J. P. van Westen
- European Molecular Biology Laboratory
- European Bioinformatics Institute
- Wellcome Trust Genome Campus
- Hinxton
- UK
| | - Andreas Bender
- Unilever Centre for Molecular Informatics
- Department of Chemistry
- CB2 1EW Cambridge
- UK
| |
Collapse
|
24
|
Konrat R. NMR contributions to structural dynamics studies of intrinsically disordered proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:74-85. [PMID: 24656082 PMCID: PMC3985426 DOI: 10.1016/j.jmr.2013.11.011] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/13/2013] [Accepted: 11/18/2013] [Indexed: 05/04/2023]
Abstract
Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This article will summarize key advances in basic physical-chemistry and NMR methodology, outline their limitations and envision future R&D directions.
Collapse
Affiliation(s)
- Robert Konrat
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria.
| |
Collapse
|
25
|
Manzetti S, Zhang J, van der Spoel D. Thiamin Function, Metabolism, Uptake, and Transport. Biochemistry 2014; 53:821-35. [DOI: 10.1021/bi401618y] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sergio Manzetti
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
for Cell and Molecular Biology, University of Uppsala, Box 596, 751
24 Uppsala, Sweden
- Fjordforsk A.S., Fresvik 6896, Norway
| | - Jin Zhang
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
for Cell and Molecular Biology, University of Uppsala, Box 596, 751
24 Uppsala, Sweden
- Department
of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - David van der Spoel
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
for Cell and Molecular Biology, University of Uppsala, Box 596, 751
24 Uppsala, Sweden
| |
Collapse
|
26
|
Kotamarthi HC, Sharma R, Koti Ainavarapu SR. Single-molecule studies on PolySUMO proteins reveal their mechanical flexibility. Biophys J 2013; 104:2273-81. [PMID: 23708367 DOI: 10.1016/j.bpj.2013.04.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 04/04/2013] [Accepted: 04/05/2013] [Indexed: 01/08/2023] Open
Abstract
Proteins with β-sandwich and β-grasp topologies are resistant to mechanical unfolding as shown by single-molecule force spectroscopy studies. Their high mechanical stability has generally been associated with the mechanical clamp geometry present at the termini. However, there is also evidence for the importance of interactions other than the mechanical clamp in providing mechanical stability, which needs to be tested thoroughly. Here, we report the mechanical unfolding properties of ubiquitin-like proteins (SUMO1 and SUMO2) and their comparison with those of ubiquitin. Although ubiquitin and SUMOs have similar size and structural topology, they differ in their sequences and structural contacts, making them ideal candidates to understand the variations in the mechanical stability of a given protein topology. We observe a two-state unfolding pathway for SUMO1 and SUMO2, similar to that of ubiquitin. Nevertheless, the unfolding forces of SUMO1 (∼130 pN) and SUMO2 (∼120 pN) are lower than that of ubiquitin (∼190 pN) at a pulling speed of 400 nm/s, indicating their lower mechanical stability. The mechanical stabilities of SUMO proteins and ubiquitin are well correlated with the number of interresidue contacts present in their structures. From pulling speed-dependent mechanical unfolding experiments and Monte Carlo simulations, we find that the unfolding potential widths of SUMO1 (∼0.51 nm) and SUMO2 (∼0.33 nm) are much larger than that of ubiquitin (∼0.19 nm), indicating that SUMO1 is six times and SUMO2 is three times mechanically more flexible than ubiquitin. These findings might also be important in understanding the functional differences between ubiquitin and SUMOs.
Collapse
Affiliation(s)
- Hema Chandra Kotamarthi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | | | | |
Collapse
|
27
|
De Franceschi N, Wild K, Schlacht A, Dacks JB, Sinning I, Filippini F. Longin and GAF domains: structural evolution and adaptation to the subcellular trafficking machinery. Traffic 2013; 15:104-21. [PMID: 24107188 DOI: 10.1111/tra.12124] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 09/18/2013] [Accepted: 09/23/2013] [Indexed: 11/28/2022]
Abstract
Endomembrane trafficking is one of the most prominent cytological features of eukaryotes. Given their widespread distribution and specialization, coiled-coil domains, coatomer domains, small GTPases and Longin domains are considered primordial 'building blocks' of the membrane trafficking machineries. Longin domains are conserved across eukaryotes and were likely to be present in the Last Eukaryotic Common Ancestor. The Longin fold is based on the α-β-α sandwich architecture and a unique topology, possibly accounting for the special adaptation to the eukaryotic trafficking machinery. The ancient Per ARNT Sim (PAS) and cGMP-specific phosphodiesterases, Adenylyl cyclases and FhlA (GAF) family domains show a similar architecture, and the identification of prokaryotic counterparts of GAF domains involved in trafficking provides an additional connection for the endomembrane system back into the pre-eukaryotic world. Proteome-wide, comparative bioinformatic analyses of the domains reveal three binding regions (A, B and C) mediating either specific or conserved protein-protein interactions. While the A region mediates intra- and inter-molecular interactions, the B region is involved in binding small GTPases, thus providing an evolutionary connection among major building blocks in the endomembrane system. Finally, we propose that the peculiar interaction surface of the C region of the Longin domain allowed it to extensively integrate into the endomembrane trafficking machinery in the earliest stages of building the eukaryotic cell.
Collapse
Affiliation(s)
- Nicola De Franceschi
- Molecular Biology and Bioinformatics Unit, Department of Biology, University of Padova, Padova, Italy; Current address: Centre for Biotechnology, University of Turku, Turku, Finland
| | | | | | | | | | | |
Collapse
|
28
|
Andreini C, Cavallaro G, Rosato A, Valasatava Y. MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acids. J Chem Inf Model 2013; 53:3064-75. [PMID: 24117467 DOI: 10.1021/ci400459w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We developed a new software tool, MetalS(2), for the structural alignment of Minimal Functional Sites (MFSs) in metal-binding biological macromolecules. MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. On our example data sets, MetalS(2) unveiled structural similarities that other programs for protein structure comparison do not consistently point out and overall identified a larger number of structurally similar MFSs. MetalS(2) supports the comparison of MFSs harboring different metals and/or with different nuclearity and is available both as a stand-alone program and a Web tool ( http://metalweb.cerm.unifi.it/tools/metals2/).
Collapse
Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM) - University of Florence , Via L. Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | | | | | | |
Collapse
|
29
|
Kilian P, Valdes JJ, Lecina-Casas D, Chrudimský T, Růžek D. The variability of the large genomic segment of Ťahyňa orthobunyavirus and an all-atom exploration of its anti-viral drug resistance. INFECTION GENETICS AND EVOLUTION 2013; 20:304-11. [PMID: 24090866 DOI: 10.1016/j.meegid.2013.09.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 09/19/2013] [Accepted: 09/21/2013] [Indexed: 11/30/2022]
Abstract
Ťahyňa virus (TAHV), a member of the Bunyaviridae family (California complex), is an important but neglected human mosquito-borne pathogen. The virus genome is composed of three segments, i.e., small (S), medium (M), and large (L). Previous studies on genetic variability of viruses within the California complex were focused on S and M segments, but the L segment remains relatively unstudied. To assess the genetic variation and the relation to virus phenotype we analyzed the L segment sequences of biologically diverse TAHV strains isolated in the Czech Republic and Slovakia. Phylogenetic analysis covering all available sequences of the L segment of TAHV clearly revealed two distinguished lineages, tentatively named as "European" and "Asian". The L segment strains within the European lineage are highly conserved (identity 99.3%), whilst Asian strains are more genetically diverse (identity 97%). Based on sequence comparison with other bunyaviruses, several non-synonymous nucleotide substitutions unique for TAHV in the L segment were identified. We also identified specific residue substitutions in the endonuclease domain of TAHV compared with the La Crosse virus. Since the endonuclease domain of the La Crosse virus has been resolved, we employed an all energy landscape algorithm to analyze the ligand migration of a viral polymerase inhibitor. This allowed us to demonstrate, at the atomic level, that this viral polymerase inhibitor randomly explored the specific residue substitutions in the endonuclease domain of the TAHV L segment.
Collapse
Affiliation(s)
- Patrik Kilian
- Faculty of Science, University of South Bohemia, Branišovská 31, CZ-37005 České Budějovice, Czech Republic; Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
| | | | | | | | | |
Collapse
|
30
|
Pauli I, dos Santos RN, Rostirolla DC, Martinelli LK, Ducati RG, Timmers LFSM, Basso LA, Santos DS, Guido RVC, Andricopulo AD, Norberto de Souza O. Discovery of new inhibitors of Mycobacterium tuberculosis InhA enzyme using virtual screening and a 3D-pharmacophore-based approach. J Chem Inf Model 2013; 53:2390-401. [PMID: 23889525 DOI: 10.1021/ci400202t] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis InhA (MtInhA) is an attractive enzyme to drug discovery efforts due to its validation as an effective biological target for tuberculosis therapy. In this work, two different virtual-ligand-screening approaches were applied in order to identify new InhA inhibitors' candidates from a library of ligands selected from the ZINC database. First, a 3-D pharmacophore model was built based on 36 available MtInhA crystal structures. By combining structure-based and ligand-based information, four pharmacophoric points were designed to select molecules able to satisfy the binding features of MtInhA substrate-binding cavity. The second approach consisted of using four well established docking programs, with different search algorithms, to compare the binding mode and score of the selected molecules from the aforementioned library. After detailed analyses of the results, six ligands were selected for in vitro analysis. Three of these molecules presented a satisfactory inhibitory activity with IC50 values ranging from 24 (±2) μM to 83 (±5) μM. The best compound presented an uncompetitive inhibition mode to NADH and 2-trans-dodecenoyl-CoA substrates, with Ki values of 24 (±3) μM and 20 (±2) μM, respectively. These molecules were not yet described as antituberculars or as InhA inhibitors, making its novelty interesting to start efforts on ligand optimization in order to identify new effective drugs against tuberculosis having InhA as a target. More studies are underway to dissect the discovered uncompetitive inhibitor interactions with MtInhA.
Collapse
Affiliation(s)
- Ivani Pauli
- Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas - LABIO, Faculdade de Informática, PUCRS , Brazil
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Topham CM, Rouquier M, Tarrat N, André I. Adaptive Smith-Waterman residue match seeding for protein structural alignment. Proteins 2013; 81:1823-39. [DOI: 10.1002/prot.24327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 04/22/2013] [Accepted: 05/15/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Christopher M. Topham
- Université de Toulouse, INSA, UPS, INP, LISBP; 135 Avenue de Rangueil F-31077 Toulouse France
- CNRS, UMR5504; F-31400 Toulouse France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés; F-31400 Toulouse France
| | - Mickaël Rouquier
- Université de Toulouse, INSA, UPS, INP, LISBP; 135 Avenue de Rangueil F-31077 Toulouse France
- CNRS, UMR5504; F-31400 Toulouse France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés; F-31400 Toulouse France
| | - Nathalie Tarrat
- Université de Toulouse, INSA, UPS, INP, LISBP; 135 Avenue de Rangueil F-31077 Toulouse France
- CNRS, UMR5504; F-31400 Toulouse France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés; F-31400 Toulouse France
| | - Isabelle André
- Université de Toulouse, INSA, UPS, INP, LISBP; 135 Avenue de Rangueil F-31077 Toulouse France
- CNRS, UMR5504; F-31400 Toulouse France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés; F-31400 Toulouse France
| |
Collapse
|
32
|
Parra RG, Espada R, Sánchez IE, Sippl MJ, Ferreiro DU. Detecting repetitions and periodicities in proteins by tiling the structural space. J Phys Chem B 2013; 117:12887-97. [PMID: 23758291 PMCID: PMC3807821 DOI: 10.1021/jp402105j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
The
notion of energy landscapes provides conceptual tools for understanding
the complexities of protein folding and function. Energy landscape
theory indicates that it is much easier to find sequences that satisfy
the “Principle of Minimal Frustration” when the folded
structure is symmetric (Wolynes, P. G. Symmetry and the Energy Landscapes
of Biomolecules. Proc. Natl. Acad. Sci. U.S.A.1996, 93, 14249–14255). Similarly,
repeats and structural mosaics may be fundamentally related to landscapes
with multiple embedded funnels. Here we present analytical tools to
detect and compare structural repetitions in protein molecules. By
an exhaustive analysis of the distribution of structural repeats using
a robust metric, we define those portions of a protein molecule that
best describe the overall structure as a tessellation of basic units.
The patterns produced by such tessellations provide intuitive representations
of the repeating regions and their association toward higher order
arrangements. We find that some protein architectures can be described
as nearly periodic, while in others clear separations between repetitions
exist. Since the method is independent of amino acid sequence information,
we can identify structural units that can be encoded by a variety
of distinct amino acid sequences.
Collapse
Affiliation(s)
- R Gonzalo Parra
- Protein Physiology Lab, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN , Buenos Aires, Argentina
| | | | | | | | | |
Collapse
|
33
|
Chakraborty S, Rao BJ, Baker N, Asgeirsson B. Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator. INTRINSICALLY DISORDERED PROTEINS 2013; 1. [PMID: 25364645 PMCID: PMC4212511 DOI: 10.4161/idp.25463] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Phylogenetic analysis of proteins using multiple sequence alignment (MSA) assumes an underlying evolutionary relationship in these proteins which occasionally remains undetected due to considerable sequence divergence. Structural alignment programs have been developed to unravel such fuzzy relationships. However, none of these structure based methods have used electrostatic properties to discriminate between spatially equivalent residues. We present a methodology for MSA of a set of related proteins with known structures using electrostatic properties as an additional discriminator (STEEP). STEEP first extracts a profile, then generates a multiple structural superimposition providing a consolidated spatial framework for comparing residues and finally emits the MSA. Residues that are aligned differently by including or excluding electrostatic properties can be targeted by directed evolution experiments to transform the enzymatic properties of one protein into another. We have compared STEEP results to those obtained from a MSA program (ClustalW) and a structural alignment method (MUSTANG) for chymotrypsin serine proteases. Subsequently, we used PhyML to generate phylogenetic trees for the serine and metallo-β-lactamase superfamilies from the STEEP generated MSA, and corroborated the accepted relationships in these superfamilies. We have observed that STEEP acts as a functional classifier when electrostatic congruence is used as a discriminator, and thus identifies potential targets for directed evolution experiments. In summary, STEEP is unique among phylogenetic methods for its ability to use electrostatic congruence to specify mutations that might be the source of the functional divergence in a protein family. Based on our results, we also hypothesize that the active site and its close vicinity contains enough information to infer the correct phylogeny for related proteins.
Collapse
Affiliation(s)
- Sandeep Chakraborty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
| | - Basuthkar J Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
| | - Nathan Baker
- Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington 99354, United States
| | - Bjarni Asgeirsson
- Science Institute, Department of Biochemistry, University of Iceland, Dunhaga 3, IS-107 Reykjavik, Iceland
| |
Collapse
|
34
|
Li F, Wu QY, Wang XY. The amino acid residue L113 is involved in arginine kinase activity and structural stability. Int J Biol Macromol 2013; 52:198-205. [DOI: 10.1016/j.ijbiomac.2012.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 09/13/2012] [Accepted: 09/14/2012] [Indexed: 10/27/2022]
|
35
|
Wu QY, Li F, Wang XY, Xu KL. Evidence that the amino acid residue Ile121 is involved in arginine kinase activity and structural stability. Int J Biol Macromol 2012; 51:369-77. [DOI: 10.1016/j.ijbiomac.2012.05.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 05/17/2012] [Accepted: 05/21/2012] [Indexed: 10/28/2022]
|
36
|
Ritchie DW, Ghoorah AW, Mavridis L, Venkatraman V. Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity. Bioinformatics 2012; 28:3274-81. [DOI: 10.1093/bioinformatics/bts618] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
37
|
Slater AW, Castellanos JI, Sippl MJ, Melo F. Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments. Bioinformatics 2012; 29:47-53. [PMID: 23060612 DOI: 10.1093/bioinformatics/bts600] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Pairwise alignment of protein structures is a fundamental task in structural bioinformatics. There are numerous computer programs in the public domain that produce alignments for a given pair of protein structures, but the results obtained by the various programs generally differ substantially. Hence, in the application of such programs the question arises which of the alignment programs are the most trustworthy in the sense of overall performance, and which programs provide the best result for a given pair of proteins. The major problem in comparing, evaluating and judging alignment results is that there is no clear notion of the optimality of an alignment. As a consequence, the numeric criteria and scores reported by the individual structure alignment programs are largely incomparable. RESULTS Here we report on the development and application of a new approach for the evaluation of structure alignment results. The method uses the translation vector and rotation matrix to generate the superposition of two structures but discards the alignment reported by the individual programs. The optimal alignment is then generated in standardized form based on a suitably implemented dynamic programming algorithm where the length of the alignment is the single most informative parameter. We demonstrate that some of the most popular programs in protein structure research differ considerably in their overall performance. In particular, each of the programs investigated here produced in at least in one case the best and the worst alignment compared with all others. Hence, at the current state of development of structure comparison techniques, it is advisable to use several programs in parallel and to choose the optimal alignment in the way reported here. AVAILABILITY AND IMPLEMENTATION The computer software that implement the method described here is freely available at http://melolab.org/stovca.
Collapse
Affiliation(s)
- Alex W Slater
- Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy, Portugal 49, Santiago, CP 8330025, Chile
| | | | | | | |
Collapse
|
38
|
Kumar D, Gautam A, Hosur RV. A unified NMR strategy for high-throughput determination of backbone fold of small proteins. ACTA ACUST UNITED AC 2012; 13:201-12. [DOI: 10.1007/s10969-012-9144-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 09/18/2012] [Indexed: 11/30/2022]
|
39
|
Henen M, Coudevylle N, Geist L, Konrat R. Toward rational fragment-based lead design without 3D structures. J Med Chem 2012; 55:7909-19. [PMID: 22889313 PMCID: PMC3557921 DOI: 10.1021/jm301016m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Indexed: 01/21/2023]
Abstract
Fragment-based lead discovery (FBLD) has become a prime component of the armamentarium of modern drug design programs. FBLD identifies low molecular weight ligands that weakly bind to important biological targets. Three-dimensional structural information about the binding mode is provided by X-ray crystallography or NMR spectroscopy and is subsequently used to improve the lead compounds. Despite tremendous success rates, FBLD relies on the availability of high-resolution structural information, still a bottleneck in drug discovery programs. To overcome these limitations, we recently demonstrated that the meta-structure approach provides an alternative route to rational lead identification in cases where no 3D structure information about the biological target is available. Combined with information-rich NMR data, this strategy provides valuable information for lead development programs. We demonstrate with several examples the feasibility of the combined NMR and meta-structure approach to devise a rational strategy for fragment evolution without resorting to highly resolved protein complex structures.
Collapse
Affiliation(s)
- Morkos
A. Henen
- Department of Structural and Computational Biology,
Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, A-1030 Vienna, Austria
| | - Nicolas Coudevylle
- Department of Structural and Computational Biology,
Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, A-1030 Vienna, Austria
| | - Leonhard Geist
- Department of Structural and Computational Biology,
Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, A-1030 Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology,
Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, A-1030 Vienna, Austria
| |
Collapse
|
40
|
Eibl C, Grigoriu S, Hessenberger M, Wenger J, Puehringer S, Pinheiro AS, Wagner RN, Proell M, Reed JC, Page R, Diederichs K, Peti W. Structural and functional analysis of the NLRP4 pyrin domain. Biochemistry 2012; 51:7330-41. [PMID: 22928810 PMCID: PMC3445046 DOI: 10.1021/bi3007059] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
NLRP4 is a member of the nucleotide-binding and leucine-rich
repeat
receptor (NLR) family of cytosolic receptors and a member of an inflammation
signaling cascade. Here, we present the crystal structure of the NLRP4
pyrin domain (PYD) at 2.3 Å resolution. The NLRP4 PYD is a member
of the death domain (DD) superfamily and adopts a DD fold consisting
of six α-helices tightly packed around a hydrophobic core, with
a highly charged surface that is typical of PYDs. Importantly, however,
we identified several differences between the NLRP4 PYD crystal structure
and other PYD structures that are significant enough to affect NLRP4
function and its interactions with binding partners. Notably, the
length of helix α3 and the α2−α3 connecting
loop in the NLRP4 PYD are unique among PYDs. The apoptosis-associated
speck-like protein containing a CARD (ASC) is an adaptor protein whose
interactions with a number of distinct PYDs are believed to be critical
for activation of the inflammatory response. Here, we use co-immunoprecipitation,
yeast two-hybrid, and nuclear magnetic resonance chemical shift perturbation
analysis to demonstrate that, despite being important for activation
of the inflammatory response and sharing several similarities with
other known ASC-interacting PYDs (i.e., ASC2), NLRP4 does not interact
with the adaptor protein ASC. Thus, we propose that the factors governing
homotypic PYD interactions are more complex than the currently accepted
model, which states that complementary charged surfaces are the main
determinants of PYD–PYD interaction specificity.
Collapse
Affiliation(s)
- Clarissa Eibl
- Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Tan KW, Jobichen C, Ong TC, Gao YF, Tiong YS, Wong KN, Chew FT, Sivaraman J, Mok YK. Crystal structure of Der f 7, a dust mite allergen from Dermatophagoides farinae. PLoS One 2012; 7:e44850. [PMID: 22970319 PMCID: PMC3435378 DOI: 10.1371/journal.pone.0044850] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 08/07/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Der f 7 is the group 7 allergen from the dust mite Dermatophagoides farinae, homologous to the major allergen Der p 7 from D. pteronyssinus. Monoclonal antibody that bind to residues Leu48 and Phe50 was found to inhibit IgE binding to residue Asp159, which is important for the cross-reactivity between Der f 7 and Der p 7. METHODOLOGY/PRINCIPAL FINDINGS Here, we report the crystal structure of Der f 7 that shows an elongated and curved molecule consisting of two anti-parallel β-sheets--one 4-stranded and the other 5-stranded--that wrap around a long C-terminal helix. The overall fold of Der f 7 is similar to Der p 7 but key difference was found in the β1-β2 loop region. In Der f 7, Leu48 and Phe50 are in close proximity to Asp159, explaining why monoclonal antibody binding to Leu48 and Phe50 can inhibit IgE binding to Asp159. Both Der f 7 and Der p 7 bind weakly to polymyxin B via a similar binding site that is formed by the N-terminal helix, the 4-stranded β-sheet and the C-terminal helix. The thermal stability of Der f 7 is significantly lower than that of Der p 7, and the stabilities of both allergens are highly depend on pH. CONCLUSION/SIGNIFICANCE Der f 7 is homologous to Der p 7 in terms of the amino acid sequence and overall 3D structure but with significant differences in the region proximal to the IgE epitope and in thermal stability. The crystal structure of Der f 7 provides a basis for studying the function and allergenicity of this group of allergens.
Collapse
Affiliation(s)
- Kang Wei Tan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Chacko Jobichen
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Tan Ching Ong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yun Feng Gao
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yuen Sung Tiong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kang Ning Wong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - J. Sivaraman
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yu Keung Mok
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- * E-mail:
| |
Collapse
|
42
|
Tan KW, Ong TC, Gao YF, Tiong YS, Wong KN, Chew FT, Mok YK. NMR structure and IgE epitopes of Blo t 21, a major dust mite allergen from Blomia tropicalis. J Biol Chem 2012; 287:34776-85. [PMID: 22887997 DOI: 10.1074/jbc.m112.348730] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Blo t 21 is a paralogue of the group 5 allergen, Blo t 5, a major allergen from the dust mite Blomia tropicalis. Blo t 21 has moderate sequence identity (40.7%) to Blo t 5 and low to moderate cross-reactivity to Blo t 5. In B. tropicalis, the most prevalent and allergenic allergens are in the order of Blo t 21, Blo t 5, and Blo t 7. Here, we determined the NMR solution structure of Blo t 21, which represents the first structure of the group 21 dust mite allergen. The structure of Blo t 21 closely resembles the structures of Blo t 5 and Der p 5, comprising three anti-parallel α-helices arranged in a helical bundle. Using site-directed mutagenesis and specific IgE binding ELISA, Blo t 21 was found to contain both conserved and unique charged IgE epitope residues at the L2 loop region and on helix α3. Cross-inhibition assays confirmed that Blo t 21 has a low to moderate cross-reactivity with Blo t 5 and Der p 5 and represents a novel group of major allergen in B. tropicalis. In addition to group 5 allergens, Blo t 21 has also a low to moderate cross-reactivity with group 21 allergens from Dermatophagoides mites, confirming that B. tropicalis is a major and distinct source of dust mite allergens.
Collapse
Affiliation(s)
- Kang Wei Tan
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | | | | | | | | | | | | |
Collapse
|
43
|
Chakraborty S. An automated flow for directed evolution based on detection of promiscuous scaffolds using spatial and electrostatic properties of catalytic residues. PLoS One 2012; 7:e40408. [PMID: 22811760 PMCID: PMC3394801 DOI: 10.1371/journal.pone.0040408] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 06/06/2012] [Indexed: 12/25/2022] Open
Abstract
The aspiration to mimic and accelerate natural evolution has fueled interest in directed evolution experiments, which endow or enhance functionality in enzymes. Barring a few de novo approaches, most methods take a template protein having the desired activity, known active site residues and structure, and proceed to select a target protein which has a pre-existing scaffold congruent to the template motif. Previously, we have established a computational method (CLASP) based on spatial and electrostatic properties to detect active sites, and a method to quantify promiscuity in proteins. We exploit the prospect of promiscuous active sites to serve as the starting point for directed evolution and present a method to select a target protein which possesses a significant partial match with the template scaffold (DECAAF). A library of partial motifs, constructed from the active site residues of the template protein, is used to rank a set of target proteins based on maximal significant matches with the partial motifs, and cull out the best candidate from the reduced set as the target protein. Considering the scenario where this ‘incubator’ protein lacks activity, we identify mutations in the target protein that will mirror the template motif by superimposing the target and template protein based on the partial match. Using this superimposition technique, we analyzed the less than expected gain of activity achieved by an attempt to induce β-lactamase activity in a penicillin binding protein (PBP) (PBP-A from T. elongatus), and attributed this to steric hindrance from neighboring residues. We also propose mutations in PBP-5 from E. coli, which does not have similar steric constraints. The flow details have been worked out in an example which aims to select a substitute protein for human neutrophil elastase, preferably related to grapevines, in a chimeric anti-microbial enzyme which bolsters the innate immune defense system of grapevines.
Collapse
Affiliation(s)
- Sandeep Chakraborty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India.
| |
Collapse
|
44
|
Gurrola GB, Hernández-López RA, Rodríguez de la Vega RC, Varga Z, Batista CVF, Salas-Castillo SP, Panyi G, del Río-Portilla F, Possani LD. Structure, function, and chemical synthesis of Vaejovis mexicanus peptide 24: a novel potent blocker of Kv1.3 potassium channels of human T lymphocytes. Biochemistry 2012; 51:4049-61. [PMID: 22540187 DOI: 10.1021/bi300060n] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Animal venoms are rich sources of ligands for studying ion channels and other pharmacological targets. Proteomic analyses of the soluble venom from the Mexican scorpion Vaejovis mexicanus smithi showed that it contains more than 200 different components. Among them, a 36-residue peptide with a molecular mass of 3864 Da (named Vm24) was shown to be a potent blocker of Kv1.3 of human lymphocytes (K(d) ∼ 3 pM). The three-dimensional solution structure of Vm24 was determined by nuclear magnetic resonance, showing the peptide folds into a distorted cystine-stabilized α/β motif consisting of a single-turn α-helix and a three-stranded antiparallel β-sheet, stabilized by four disulfide bridges. The disulfide pairs are formed between Cys6 and Cys26, Cys12 and Cys31, Cys16 and Cys33, and Cys21 and Cys36. Sequence analyses identified Vm24 as the first example of a new subfamily of α-type K(+) channel blockers (systematic number α-KTx 23.1). Comparison with other Kv1.3 blockers isolated from scorpions suggests a number of structural features that could explain the remarkable affinity and specificity of Vm24 toward Kv1.3 channels of lymphocytes.
Collapse
Affiliation(s)
- Georgina B Gurrola
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 2001 Cuernavaca, Mor. 62210, Mexico
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Perez A, Yang Z, Bahar I, Dill KA, MacCallum JL. FlexE: Using elastic network models to compare models of protein structure. J Chem Theory Comput 2012; 8:3985-3991. [PMID: 25530735 DOI: 10.1021/ct300148f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
It is often valuable to compare protein structures to determine how similar they are. Structure comparison methods such as RMSD and GDT-TS are based solely on fixed geometry and do not take into account the intrinsic flexibility or energy landscape of the protein. We propose a method, which we call FlexE, that is based on a simple elastic network model and uses the deformation energy as measure of the similarity between two structures. FlexE can distinguish biologically relevant conformational changes from random changes, while existing geometry-based methods cannot. Additionally, FlexE incorporates the concept of thermal energy, which provides a rational way to determine when two models are "the same". FlexE provides a unique measure of the similarity between protein structures that is complementary to existing methods.
Collapse
Affiliation(s)
- Alberto Perez
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252
| | - Zheng Yang
- Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, 3064 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
| | - Ivet Bahar
- Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, 3064 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
| | - Ken A Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252
| | - Justin L MacCallum
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252
| |
Collapse
|
46
|
Analyzing of expression of novel polypeptide complexes consisting of Shiga toxin B subunit and Adherence Fimbriae of Escherichia coli based on in silico modeling. J Mol Model 2012; 18:4131-9. [PMID: 22527278 DOI: 10.1007/s00894-012-1414-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 03/26/2012] [Indexed: 10/28/2022]
Abstract
Enterohemorrhagic (EHEC) and enteroaggregative (EAEC) are two pathotypes of diarrheagenic Escherichia coli. EAEC strains express adhesins called aggregate adherence fimbriae (AAFs) which the bacteria use to adhere to intestinal mucosa. EHEC virulence factor is Shiga toxin which belongs to the AB5 toxin family. B subunit, the nontoxic part of Shiga toxin (StxB), forms a homo pentamer and is responsible for binding to target cells. StxB has recently been proven to have adjuvant activity. In the current study we fused StxB encoding gene to 3' end of genes encoding two variants of AAFs, i.e., AAF/I and AAF/II. The in silico studies on tertiary structure and biochemical characteristics of Shiga toxin A subunit (StxA) revealed more resemblance to AAF/II than AAF/I. The constructs were prepared in a way that StxB could imitate its natural structure (pentamer formation) and its position (C-terminus) in the native toxin complex. The expression of these constructs showed the formation of AAF/II-B as a protein complex but with lower molecular mass than its expected size. In contrast, the AAF/I-B complex was not formed. Overall, the results of in silico studies and expression experiments together revealed that despite AAF/II-B expression, StxB failed to form pentamer. Therefore the observed protein complex has lower molecular mass. Since StxB is bound to AAF/II through disulfide bond, this bond prevents pentamer formation of StxB. However, due to the lack of disulfide bond between AAF/I and StxB, no protein complex is formed, thus StxB maintains its pentamer structure.
Collapse
|
47
|
Real space refinement of crystal structures with canonical distributions of electrons. Structure 2012; 19:1739-43. [PMID: 22153496 PMCID: PMC3234344 DOI: 10.1016/j.str.2011.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 09/28/2011] [Accepted: 10/10/2011] [Indexed: 11/21/2022]
Abstract
Recurring groups of atoms in molecules are surrounded by specific canonical distributions of electrons. Deviations from these distributions reveal unrealistic molecular geometries. Here, we show how canonical electron densities can be combined with classical electron densities derived from X-ray diffraction experiments to drive the real space refinement of crystal structures. The refinement process generally yields superior molecular models with reduced excess electron densities and improved stereochemistry without compromising the agreement between molecular models and experimental data.
Collapse
|
48
|
Sippl MJ, Wiederstein M. Detection of spatial correlations in protein structures and molecular complexes. Structure 2012; 20:718-28. [PMID: 22483118 PMCID: PMC3320710 DOI: 10.1016/j.str.2012.01.024] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 01/09/2012] [Accepted: 01/31/2012] [Indexed: 10/28/2022]
Abstract
Protein structures are frequently related by spectacular and often surprising similarities. Structural correlations among protein chains are routinely detected by various structure-matching techniques, but the comparison of oligomers and molecular complexes is largely uncharted territory. Here we solve the structure-matching problem for oligomers and large molecular aggregates, including the largest molecular complexes known today. We provide several challenging examples that cannot be handled by conventional structure-matching techniques and we report on a number of remarkable correlations. The examples cover the cell-puncturing device of bacteriophage T4, the secretion system of P. aeruginosa, members of the dehydrogenase family, DNA clamps, ferredoxin iron-storage cages, and virus capsids.
Collapse
Affiliation(s)
- Manfred J Sippl
- Division of Bioinformatics, Department of Molecular Biology, University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria.
| | | |
Collapse
|
49
|
Computer-based annotation of putative AraC/XylS-family transcription factors of known structure but unknown function. J Biomed Biotechnol 2012; 2012:103132. [PMID: 22505803 PMCID: PMC3312330 DOI: 10.1155/2012/103132] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 12/09/2011] [Accepted: 12/13/2011] [Indexed: 12/12/2022] Open
Abstract
Currently, about 20 crystal structures per day are released and deposited in the Protein Data Bank. A significant fraction of these structures is produced by research groups associated with the structural genomics consortium. The biological function of many of these proteins is generally unknown or not validated by experiment. Therefore, a growing need for functional prediction of protein structures has emerged. Here we present an integrated bioinformatics method that combines sequence-based relationships and three-dimensional (3D) structural similarity of transcriptional regulators with computer prediction of their cognate DNA binding sequences. We applied this method to the AraC/XylS family of transcription factors, which is a large family of transcriptional regulators found in many bacteria controlling the expression of genes involved in diverse biological functions. Three putative new members of this family with known 3D structure but unknown function were identified for which a probable functional classification is provided. Our bioinformatics analyses suggest that they could be involved in plant cell wall degradation (Lin2118 protein from Listeria innocua, PDB code 3oou), symbiotic nitrogen fixation (protein from Chromobacterium violaceum, PDB code 3oio), and either metabolism of plant-derived biomass or nitrogen fixation (protein from Rhodopseudomonas palustris, PDB code 3mn2).
Collapse
|
50
|
Kovalchuk N, Smith J, Bazanova N, Pyvovarenko T, Singh R, Shirley N, Ismagul A, Johnson A, Milligan AS, Hrmova M, Langridge P, Lopato S. Characterization of the wheat gene encoding a grain-specific lipid transfer protein TdPR61, and promoter activity in wheat, barley and rice. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2025-40. [PMID: 22213809 DOI: 10.1093/jxb/err409] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The TaPR61 gene from bread wheat encodes a lipid transfer protein (LTP) with a hydrophobic signal peptide, predicted to direct the TaPR61 protein to the apoplast. Modelling of TaPR61 revealed the presence of an internal cavity which can accommodate at least two lipid molecules. The full-length gene, including the promoter sequence of a TaPR61 orthologue, was cloned from a BAC library of Triticum durum. Quantitative RT-PCR analysis revealed the presence of TaPR61 and TdPR61 mainly in grain. A transcriptional TdPR61 promoter-GUS fusion was stably transformed into wheat, barley, and rice. The strongest GUS expression in all three plants was found in the endosperm transfer cells, the embryo surrounding region (ESR), and in the embryo. The promoter is strong and has similar but not identical spatial patterns of activity in wheat, barley, and rice. These results suggest that the TdPR61 promoter will be a useful tool for improving grain quality by manipulating the quality and quantity of nutrient/lipid uptake to the endosperm and embryo. Mapping of regions important for the promoter function using transient expression assays in developing embryos resulted in the identification of two segments important for promoter activation in embryos. The putative cis-elements from the distal segment were used as bait in a yeast 1-hybrid (Y1H) screen of a cDNA library prepared from the liquid part of the wheat multinucleate syncytium. A transcription factor isolated in the screen is similar to BES1/BLZ1 from Arabidopsis, which is known to be a key transcriptional regulator of the brassinosteroid signalling pathway.
Collapse
Affiliation(s)
- Nataliya Kovalchuk
- Australian Centre for Plant Functional Genomics, University of Adelaide, South Australia, Australia
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|