Detecting Internally Symmetric Protein Structures Changhoon Kim1,2, Jodi Basner1, Byungkook Lee1*
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A Gene Co-Expression Network Model Identifies Yield-Related Vicinity
www.nature.com/scientificreports OPEN A gene co-expression network model identifes yield-related vicinity networks in Jatropha curcas Received: 7 February 2018 Accepted: 4 June 2018 shoot system Published: xx xx xxxx Nisha Govender1,2, Siju Senan1, Zeti-Azura Mohamed-Hussein2,3 & Ratnam Wickneswari1 The plant shoot system consists of reproductive organs such as inforescences, buds and fruits, and the vegetative leaves and stems. In this study, the reproductive part of the Jatropha curcas shoot system, which includes the aerial shoots, shoots bearing the inforescence and inforescence were investigated in regard to gene-to-gene interactions underpinning yield-related biological processes. An RNA-seq based sequencing of shoot tissues performed on an Illumina HiSeq. 2500 platform generated 18 transcriptomes. Using the reference genome-based mapping approach, a total of 64 361 genes was identifed in all samples and the data was annotated against the non-redundant database by the BLAST2GO Pro. Suite. After removing the outlier genes and samples, a total of 12 734 genes across 17 samples were subjected to gene co-expression network construction using petal, an R library. A gene co-expression network model built with scale-free and small-world properties extracted four vicinity networks (VNs) with putative involvement in yield-related biological processes as follow; heat stress tolerance, foral and shoot meristem diferentiation, biosynthesis of chlorophyll molecules and laticifers, cell wall metabolism and epigenetic regulations. Our VNs revealed putative key players that could be adapted in breeding strategies for J. curcas shoot system improvements. Jatropha curcas L. or the physic nut is an environmentally friendly and cost-efective feedstock for sustainable biofuel production. -
Non-Cellulosomal Cohesin- and Dockerin-Like Modules in the Three Domains of Life Ayelet Peera, Steven P
1 Non-cellulosomal Cohesin- and Dockerin-like Modules in the Three Domains of Life Ayelet Peera, Steven P. Smithb, Edward A. Bayerc,*, Raphael Lameda and Ilya Borovoka aDepartment of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978 Israel bDepartment of Biochemistry, Queen’s University Kingston Ontario Canada K7L 3N6 cDepartment of Biological Sciences, Weizmann Institute of Science, Rehovot 76100 Israel *Corresponding author: Edward A. Bayer Tel: (+972) -8-934-2373 Fax: (+972)-8-946-8256 Email: [email protected] Supplementary Table S1. Compendium of cohesins and dockerins in the three domains of life. In order to discover new putative cohesin/dockerin-containing proteins, we used sequences of all the classical cohesin and dockerin modules from C. thermocellum, C. cellulovorans, C. cellulolyticum, B. cellulosolvens and Acetivibrio cellulolyticus as well as cohesins and dockerins recently discovered in rumen bacteria, Ruminococcus albus and R. flavefaciens as BlastP queries for the main NCBI Blast server against all non- redundant protein sequences deposited in GenBank/EMBL/DDBJ databases. We also performed extensive searches using the TblastN algorithm through all publicly available microbial genome databases including those attached to the NCBI BLAST server for bacterial genomes (http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi?), as well as several additional microbial genome databases – Microbial Genomics at the DOE Joint Genome Institute (http://genome.jgi-psf.org/mic_home.html), the Rumenomics database at TIGR/JCVI (http://tigrblast.tigr.org/rumenomics/index.cgi) and Bacterial Genomes at the Sanger Centre (http://www.sanger.ac.uk/Projects/Microbes/). Once a putative cohesin or dockerin-encoding gene product was identified, gene-walking techniques were employed to analyze and locate possible cellulosome-like gene clusters. -
STACK: a Toolkit for Analysing Β-Helix Proteins
STACK: a toolkit for analysing ¯-helix proteins Master of Science Thesis (20 points) Salvatore Cappadona, Lars Diestelhorst Abstract ¯-helix proteins contain a solenoid fold consisting of repeated coils forming parallel ¯-sheets. Our goal is to formalise the intuitive notion of a ¯-helix in an objective algorithm. Our approach is based on first identifying residues stacks — linear spatial arrangements of residues with similar conformations — and then combining these elementary patterns to form ¯-coils and ¯-helices. Our algorithm has been implemented within STACK, a toolkit for analyzing ¯-helix proteins. STACK distinguishes aromatic, aliphatic and amidic stacks such as the asparagine ladder. Geometrical features are computed and stored in a relational database. These features include the axis of the ¯-helix, the stacks, the cross-sectional shape, the area of the coils and related packing information. An interface between STACK and a molecular visualisation program enables structural features to be highlighted automatically. i Contents 1 Introduction 1 2 Biological Background 2 2.1 Basic Concepts of Protein Structure ....................... 2 2.2 Secondary Structure ................................ 2 2.3 The ¯-Helix Fold .................................. 3 3 Parallel ¯-Helices 6 3.1 Introduction ..................................... 6 3.2 Nomenclature .................................... 6 3.2.1 Parallel ¯-Helix and its ¯-Sheets ..................... 6 3.2.2 Stacks ................................... 8 3.2.3 Coils ..................................... 8 3.2.4 The Core Region .............................. 8 3.3 Description of Known Structures ......................... 8 3.3.1 Helix Handedness .............................. 8 3.3.2 Right-Handed Parallel ¯-Helices ..................... 13 3.3.3 Left-Handed Parallel ¯-Helices ...................... 19 3.4 Amyloidosis .................................... 20 4 The STACK Toolkit 24 4.1 Identification of Structural Elements ....................... 24 4.1.1 Stacks ................................... -
The Relationship Between Protein Structure and Function: a Comprehensive Survey with Application to the Yeast Genome Hedi Hegyi and Mark Gerstein*
Article No. jmbi.1999.2661 available online at http://www.idealibrary.com on J. Mol. Biol. (1999) 000, 1±18 The Relationship Between Protein Structure and Function: A Comprehensive Survey with Application to the Yeast Genome Hedi Hegyi and Mark Gerstein* Department of Molecular For most proteins in the genome databases, function is predicted via Biophysics & Biochemistry sequence comparison. In spite of the popularity of this approach, the Yale University, 266 Whitney extent to which it can be reliably applied is unknown. We address this Avenue, PO Box 208114 issue by systematically investigating the relationship between protein New Haven, CT, 06520 USA function and structure. We focus initially on enzymes classi®ed by the Enzyme Commission (EC) and relate these to structurally classi®ed pro- teins in the SCOP database. We ®nd that the major SCOP fold classes have different propensities to carry out certain broad categories of func- tions. For instance, alpha/beta folds are disproportionately associated with enzymes, especially transferases and hydrolases, and all-alpha and small folds with non-enzymes, while alpha beta folds have an equal tendency either way. These observations for the database overall are lar- gely true for speci®c genomes. We focus, in particular, on yeast, analyz- ing it with many classi®cations in addition to SCOP and EC (i.e. COGs, CATH, MIPS), and ®nd clear tendencies for fold-function association, across a broad spectrum of functions. Analysis with the COGs scheme also suggests that the functions of the most ancient proteins are more evenly distributed among different structural classes than those of more modern ones. -
Folding-TIM Barrel
Protein Folding Practical September 2011 Folding up the TIM barrel Preliminary Examine the parallel beta barrel that you constructed, noting the stagger of the strands that was needed to connect the ends of the 8-stranded parallel beta sheet into the 8-stranded beta barrel. Notice that the stagger dictates which side of the sheet is on the inside and which is on the outside. This will be key information in folding the complete TIM linear peptide into the TIM barrel. Assembling the full linear peptide 1. Make sure the white beta strands are extended correctly, and the 8 yellow helices (with the green loops at each end) are correctly folded into an alpha helix (right handed with H-bonds to the 4th ahead in the chain). 2. starting with a beta strand connect an alpha helix and green loop to make the blue-red connecting peptide bond. Making sure that you connect the carbonyl (red) end of the beta strand to the amino (blue) end of the loop-helix-loop. Secure the just connected peptide bond bond with a twist-tie as shown. 3. complete step 2 for all beta strand/loop-helix-loop pairs, working in parallel with your partners 4. As pairs are completed attach the carboxy end of the strand- loop-helix-loop to the amino end of the next strand-loop-helix-loop module and secure the new peptide bond with a twist-tie as before. Repeat until the full linear TIM polypeptide chain is assembled. Make sure all strands and helices are still in the correct conformations. -
Supplemental Table 7. Every Significant Association
Supplemental Table 7. Every significant association between an individual covariate and functional group (assigned to the KO level) as determined by CPGLM regression analysis. Variable Unit RelationshipLabel See also CBCL Aggressive Behavior K05914 + CBCL Emotionally Reactive K05914 + CBCL Externalizing Behavior K05914 + K15665 K15658 CBCL Total K05914 + K15660 K16130 KO: E1.13.12.7; photinus-luciferin 4-monooxygenase (ATP-hydrolysing) [EC:1.13.12.7] :: PFAMS: AMP-binding enzyme; CBQ Inhibitory Control K05914 - K12239 K16120 Condensation domain; Methyltransferase domain; Thioesterase domain; AMP-binding enzyme C-terminal domain LEC Family Separation/Social Services K05914 + K16129 K16416 LEC Poverty Related Events K05914 + K16124 LEC Total K05914 + LEC Turmoil K05914 + CBCL Aggressive Behavior K15665 + CBCL Anxious Depressed K15665 + CBCL Emotionally Reactive K15665 + K05914 K15658 CBCL Externalizing Behavior K15665 + K15660 K16130 KO: K15665, ppsB, fenD; fengycin family lipopeptide synthetase B :: PFAMS: Condensation domain; AMP-binding enzyme; CBCL Total K15665 + K12239 K16120 Phosphopantetheine attachment site; AMP-binding enzyme C-terminal domain; Transferase family CBQ Inhibitory Control K15665 - K16129 K16416 LEC Poverty Related Events K15665 + K16124 LEC Total K15665 + LEC Turmoil K15665 + CBCL Aggressive Behavior K11903 + CBCL Anxiety Problems K11903 + CBCL Anxious Depressed K11903 + CBCL Depressive Problems K11903 + LEC Turmoil K11903 + MODS: Type VI secretion system K01220 K01058 CBCL Anxiety Problems K11906 + CBCL Depressive -
Tertiary Structure
Comments Structural motif v sequence motif polyproline (“PXXP”) motif for SH3 binding “RGD” motif for integrin binding “GXXXG” motif within the TM domain of membrane protein Most common type I’ beta turn sequences: X – (N/D/G)G – X Most common type II’ beta turn sequences: X – G(S/T) – X 1 Putting it together Alpha helices and beta sheets are not proteins—only marginally stable by themselves … Extremely small “proteins” can’t do much 2 Tertiary structure • Concerns with how the secondary structure units within a single polypeptide chain associate with each other to give a three- dimensional structure • Secondary structure, super secondary structure, and loops come together to form “domains”, the smallest tertiary structural unit • Structural domains (“domains”) usually contain 100 – 200 amino acids and fold stably. • Domains may be considered to be connected units which are to varying extents independent in terms of their structure, function and folding behavior. Each domain can be described by its fold, i.e. how the secondary structural elements are arranged. • Tertiary structure also includes the way domains fit together 3 Domains are modular •Because they are self-stabilizing, domains can be swapped both in nature and in the laboratory PI3 kinase beta-barrel GFP Branden & Tooze 4 fluorescence localization experiment Chimeras Recombinant proteins are often expressed and purified as fusion proteins (“chimeras”) with – glutathione S-transferase – maltose binding protein – or peptide tags, e.g. hexa-histidine, FLAG epitope helps with solubility, stability, and purification 5 Structural Classification All classifications are done at the domain level In many cases, structural similarity implies a common evolutionary origin – structural similarity without evolutionary relationship is possible – but no structural similarity means no evolutionary relationship Each domain has its corresponding “fold”, i.e. -
Allostery in the Ferredoxin Protein Motif Does Not Involve a Conformational Switch
Allostery in the ferredoxin protein motif does not involve a conformational switch Rachel Nechushtaia, Heiko Lammertb, Dorit Michaelia, Yael Eisenberg-Domovicha, John A. Zurisc, Maria A. Lucac, Dominique T. Capraroc, Alex Fisha, Odelia Shimshona, Melinda Royc, Alexander Schugb,d, Paul C. Whitforde, Oded Livnaha, José N. Onuchicb,1, and Patricia A. Jenningsc,1 aLife Science Institute and The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel; bCenter for Theoretical Biological Physics and the Department of Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0375; cDepartment of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093- 0375; dDepartment of Chemistry, Umeå University, Umeå, Sweden; and eLos Alamos National Laboratory, Theoretical Biology and Biophysics, MS K710, Los Alamos, NM 87545 Contributed by José N. Onuchic, December 28, 2010 (sent for review December 11, 2010) Regulation of protein function via cracking, or local unfolding substantial theoretical (9–13) and experimental (14, 15) work and refolding of substructures, is becoming a widely recognized has aimed at revealing the details of the functionally relevant mechanism of functional control. Oftentimes, cracking events are transition-state ensembles. These investigations have shown localized to secondary and tertiary structure interactions between that rearrangements may involve a degree of cracking, or loca- domains that control the optimal position for catalysis and/or the lized unfolding and refolding, which serves to reduce the asso- formation of protein complexes. Small changes in free energy ciated free-energy barriers (16, 17). -
BMC Structural Biology Biomed Central
BMC Structural Biology BioMed Central Research article Open Access Natural history of S-adenosylmethionine-binding proteins Piotr Z Kozbial*1 and Arcady R Mushegian1,2 Address: 1Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA and 2Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA Email: Piotr Z Kozbial* - [email protected]; Arcady R Mushegian - [email protected] * Corresponding author Published: 14 October 2005 Received: 21 July 2005 Accepted: 14 October 2005 BMC Structural Biology 2005, 5:19 doi:10.1186/1472-6807-5-19 This article is available from: http://www.biomedcentral.com/1472-6807/5/19 © 2005 Kozbial and Mushegian; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: S-adenosylmethionine is a source of diverse chemical groups used in biosynthesis and modification of virtually every class of biomolecules. The most notable reaction requiring S- adenosylmethionine, transfer of methyl group, is performed by a large class of enzymes, S- adenosylmethionine-dependent methyltransferases, which have been the focus of considerable structure-function studies. Evolutionary trajectories of these enzymes, and especially of other classes of S-adenosylmethionine-binding proteins, nevertheless, remain poorly understood. We addressed this issue by computational comparison of sequences and structures of various S- adenosylmethionine-binding proteins. Results: Two widespread folds, Rossmann fold and TIM barrel, have been repeatedly used in evolution for diverse types of S-adenosylmethionine conversion. -
Molecular Modeling 2021 Lecture 3 -- Tues Feb 2
Molecular Modeling 2021 lecture 3 -- Tues Feb 2 Protein classification SCOP TOPS Contact maps domains Domains To a cell biologist a domain is a sequential unit within a gene, usually with a specific function. To a structural biologist a domain is a compact globular unit within a protein, classified by its 3D structure. 2 A domain is... • ... an autonomously-folding substructure of a protein. • ... > 30 residues, but typically < 200. May be bigger. • ...usually has a single hydrophobic core • ... usually composed of one chain (occasionally composed of multiple chains) • ...is usually composed on one contiguous segment (occasionally made of discontiguous segments of the same chain) 3 SARS-CoV-2 spike protein — a multi domain protein 4 SCOPe -- classification of domains !http://scop.berkeley.edu similar secondary structure (1) class content (2) fold vague structural homology (3) superfamily Clear structural homology (4) family increasing structural similarity structural increasing (5) protein Clear sequence homology (6) species nearly identical sequences individual structures SCOPe -- class 1. all α (289) classes of domains 2. all β (178) 3. α/β (148) 4. α+β (388) 5. multidomain (71) 6. membrane (60) 7. small (98) Not true classes of globular 8. coiled coil (7) protein domains 9. low-resolution (25) 10. peptides (148) 11. designed proteins (44) 12. artifacts (1) Proteins of the same class conserve secondary structure content SCOPe -- fold level within α/β proteins -- Mainly parallel beta sheets (beta-alpha-beta units) TIM-barrel (22) swivelling beta/beta/alpha domain (5) Many folds have historical spoIIaa-like (2) names. “TIM” barrel was flavodoxin-like (10) first seen in TIM. -