Journal of Molecular Biology

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  • RING E3-Catalyzed E2 Self-Ubiquitination Attenuates the Activity of Ube2E Ubiquitin-Conjugating Enzymes
    [Jul 2015]

    Publication date: 3 July 2015
    Source:Journal of Molecular Biology, Volume 427, Issue 13

    Author(s): Prerana Agarwal Banka, Adaitya Prasad Behera, Sayani Sarkar, Ajit B. Datta

    Ubiquitination of a target protein is accomplished through sequential actions of the E1, E2s, and the E3s. E2s dictate the modification topology while E3 ligases confer substrate specificity and recruit the cognate E2. Human genome codes for ~35 different E2 proteins; all of which contain the characteristic ubiquitin-conjugating UBC core domain sufficient for catalysis. Many of these E2 enzymes also have N- or C-terminal extensions; roles of which are not very well understood. We show that the N-terminal extension of Ube2E1 undergoes intramolecular auto-ubiquitination. This self-ubiquitination activity is enhanced in the presence of interacting RING E3 ligases and results in a progressive attenuation of the E2 activity toward substrate/E3 modification. We also find that the N-terminal ubiquitination sites are conserved in all the three Ube2Es and replacing them with arginine renders all three full-length Ube2Es equally active as their core UBC domains. Based on these results, we propose that E3-catalyzed self-ubiquitination acts as a key regulatory mechanism that controls the activity of Ube2E class of ubiquitin E2s.
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    Categories: Journal Articles
  • E. coli Gyrase Fails to Negatively Supercoil Diaminopurine-Substituted DNA
    [Jul 2015]

    Publication date: 3 July 2015
    Source:Journal of Molecular Biology, Volume 427, Issue 13

    Author(s): Mónica Fernández-Sierra, Qing Shao, Chandler Fountain, Laura Finzi, David Dunlap

    Type II topoisomerases modify DNA supercoiling, and crystal structures suggest that they sharply bend DNA in the process. Bacterial gyrases are a class of type II topoisomerases that can introduce negative supercoiling by creating a wrap of DNA before strand passage. Isoforms of these essential enzymes were compared to reveal whether they can bend or wrap artificially stiffened DNA. Escherichia coli gyrase and human topoisomerase IIα were challenged with normal DNA or stiffer DNA produced by polymerase chain reaction reactions in which diaminopurine (DAP) replaced adenine deoxyribonucleotide triphosphates. On single DNA molecules twisted with magnetic tweezers to create plectonemes, the rates or pauses during relaxation of positive supercoils in DAP-substituted versus normal DNA were distinct for both enzymes. Gyrase struggled to bend or perhaps open a gap in DAP-substituted DNA, and segments of wider DAP DNA may have fit poorly into the N-gate of the human topoisomerase IIα. Pauses during processive activity on both types of DNA exhibited ATP dependence consistent with two pathways leading to the strand-passage-competent state with a bent gate segment and a transfer segment trapped by an ATP-loaded and latched N-gate. However, E. coli DNA gyrase essentially failed to negatively supercoil 35% stiffer DAP DNA.
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    Categories: Journal Articles
  • Antiparallel β-Sheet Structure within the C-Terminal Region of 42-Residue Alzheimer's Amyloid-β Peptides When They Form 150-kDa Oligomers
    [Jul 2015]

    Publication date: 3 July 2015
    Source:Journal of Molecular Biology, Volume 427, Issue 13

    Author(s): Danting Huang, Maxwell I. Zimmerman, Patricia K. Martin, A.Jeremy Nix, Terrone L. Rosenberry, Anant K. Paravastu

    Understanding the molecular structures of amyloid-β (Aβ) oligomers and underlying assembly pathways will advance our understanding of Alzheimer's disease (AD) at the molecular level. This understanding could contribute to disease prevention, diagnosis, and treatment strategies, as oligomers play a central role in AD pathology. We have recently presented a procedure for production of 150-kDa oligomeric samples of Aβ(1-42) (the 42-residue variant of the Aβ peptide) that are compatible with solid-state nuclear magnetic resonance (NMR) analysis, and we have shown that these oligomers and amyloid fibrils differ in intermolecular arrangement of β-strands. Here we report new solid-state NMR constraints that indicate antiparallel intermolecular alignment of β-strands within the oligomers. Specifically, 150-kDa Aβ(1-42) oligomers with uniform 13C and 15N isotopic labels at I32, M35, G37, and V40 exhibit β-strand secondary chemical shifts in 2-dimensional (2D) finite-pulse radiofrequency-driven recoupling NMR spectra, spatial proximities between I32 and V40 as well as between M35 and G37 in 2D dipolar-assisted rotational resonance spectra, and close proximity between M35 Hα and G37 Hα in 2D CHHC spectra. Furthermore, 2D dipolar-assisted rotational resonance analysis of an oligomer sample prepared with 30% labeled peptide indicates that the I32-V40 and M35-G37 contacts are between residues on different molecules. We employ molecular modeling to compare the newly derived experimental constraints with previously proposed geometries for arrangement of Aβ molecules into oligomers.
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  • Catalytic role of the substrate defines specificity of therapeutic L-asparaginase (L-ASP)
    [Jul 2015]

    Publication date: Available online 2 July 2015
    Source:Journal of Molecular Biology

    Author(s): Andriy Anishkin, Juan M. Vanegas, David M. Rogers, Philip L. Lorenzi, Wai Kin Chan, Preeti Purwaha, John N. Weinstein, Sergei Sukharev, Susan B. Rempe

    Type II bacterial L-asparaginases (L-ASP) have played an important therapeutic role in cancer treatment for over four decades, yet their exact reaction mechanism remains elusive. L-ASP from E. coli deamidates asparagine (Asn) and glutamine, with a ~104 higher specificity (k cat/K m) for asparagine despite only one methylene difference in length. Through a sensitive kinetic approach, we quantify competition among the substrates and interpret its clinical role. To understand specificity, we use molecular simulations characterize enzyme interactions with substrates and a product (aspartate). We present evidence that the aspartate product in the crystal structure of L-ASP exists in an unusual α-COOH protonation state. Consequently, the set of enzyme-product interactions found in the crystal structure, which guided prior mechanistic interpretations, differs from those observed in dynamic simulations of the enzyme with the substrates. Finally, we probe the initial nucleophilic attack with ab initio simulations. The unusual protonation state reappears, suggesting that crystal structures (wild-type and a T89V mutant) represent intermediate steps rather than initial binding. Also, a proton transfers spontaneously to Asn, advancing a new hypothesis that the substrate’s α-carboxyl serves as a proton acceptor and activates one of the catalytic threonines during L-ASP’s nucleophilic attack on the amide carbon. That hypothesis explains for the first time why proximity of the substrate α-COO- group to the carboxamide is absolutely required for catalysis. The substrate’s catalytic role is likely the determining factor in enzyme specificity as it constrains the allowed distance between the backbone carboxyl and the amide carbon of any L-ASP substrate.
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    Categories: Journal Articles
  • One-Dimensional Sliding of p53 Along DNA Is Accelerated in the Presence of Ca2+ or Mg2+ at Millimolar Concentrations
    [Jul 2015]

    Publication date: Available online 2 July 2015
    Source:Journal of Molecular Biology

    Author(s): Agato Murata, Yuji Ito, Risa Kashima, Saori Kanbayashi, Kei Nanatani, Chihiro Igarashi, Masaki Okumura, Kenji Inaba, Takashi Tokino, Satoshi Takahashi, Kiyoto Kamagata

    One-dimensional (1D) sliding of the tumor suppressor p53 along DNA is an essential dynamics required for its efficient search for the binding sites in the genome. To address how the search process of p53 is affected by the changes in the concentration of Mg2+ and Ca2+ after the cell damages, we investigated its sliding dynamics at different concentrations of the divalent cations. The 1D sliding trajectories of p53 along the stretched DNA were measured by using single-molecule fluorescence microscopy. The averaged diffusion coefficient calculated from the mean square displacement of p53 on DNA increased significantly at the higher concentration of Mg2+ or Ca2+, indicating that the divalent cations accelerate the sliding likely by weakening the DNA–p53 interaction. In addition, two distributions were identified in the displacement of the observed trajectories of p53, demonstrating the presence of the fast and slow sliding modes having large and small diffusion coefficients, respectively. A coreless mutant of p53, in which the core domain was deleted, showed only a single mode whose diffusion coefficient is about twice that of the fast mode for the full-length p53. Thus, the two modes are likely the result of the tight and loose interactions between the core domain of p53 and DNA. These results demonstrated clearly that the 1D sliding dynamics of p53 is strongly dependent on the concentration of Mg2+ and Ca2+, which maintains the search distance of p53 along DNA in cells that lost homeostatic control of the divalent cations.
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    Categories: Journal Articles
  • Structure of Hepatitis C Virus Envelope Glycoprotein E1 Antigenic Site 314–324 in Complex with Antibody IGH526
    [Jul 2015]

    Publication date: Available online 30 June 2015
    Source:Journal of Molecular Biology

    Author(s): Leopold Kong, Rameshwar U. Kadam, Erick Giang, Tinashe B. Ruwona, Travis Nieusma, Jeffrey C. Culhane, Robyn L. Stanfield, Philip E. Dawson, Ian A. Wilson, Mansun Law

    Hepatitis C virus (HCV) is a positive-strand RNA virus within the Flaviviridae family. The viral “spike” of HCV is formed by two envelope glycoproteins, E1 and E2, which together mediate viral entry by engaging host receptors and undergoing conformational changes to facilitate membrane fusion. While E2 can be readily produced in the absence of E1, E1 cannot be expressed without E2 and few reagents, including monoclonal antibodies (mAbs), are available for study of this essential HCV glycoprotein. A human mAb to E1, IGH526, was previously reported to cross-neutralize different HCV isolates, and therefore, we sought to further characterize the IGH526 neutralizing epitope to obtain information for vaccine design. We found that mAb IGH526 bound to a discontinuous epitope, but with a major component corresponding to E1 residues 314–324. The crystal structure of IGH526 Fab with this E1 glycopeptide at 1.75Å resolution revealed that the antibody binds to one face of an α-helical peptide. Single mutations on the helix substantially lowered IGH526 binding but did not affect neutralization, indicating either that multiple mutations are required or that additional regions are recognized by the antibody in the context of the membrane-associated envelope oligomer. Molecular dynamics simulations indicate that the free peptide is flexible in solution, suggesting that it requires stabilization for use as a candidate vaccine immunogen.
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    Categories: Journal Articles
  • C-terminal threonine reduces Aβ43 amyloidogenicity compared with Aβ42
    [Jul 2015]

    Publication date: Available online 26 June 2015
    Source:Journal of Molecular Biology

    Author(s): Saketh Chemuru, Ravindra Kodali, Ronald Wetzel

    Aβ43, a product of the proteolysis of the amyloid precursor protein APP, is related to Aβ42 by an additional Thr residue at the C-terminus. Aβ43 is typically generated at low levels compared with the predominant Aβ42 and Aβ40 forms, but it has been suggested that this longer peptide might have an impact on Aβ aggregation and Alzheimer’s disease that is out of proportion to its brain content. Here we report that Aβ42 and Aβ43 both spontaneously aggregate into mature amyloid fibrils via sequential appearance of the same series of oligomeric and protofibrillar intermediates, the earliest of which appears to lack β-structure. In spite of the additional β-branched amino acid at the C-terminus, Aβ43 fibrils have fewer strong backbone H-bonds than Aβ42 fibrils, some of which are lost at the C-terminus. In contrast to previous reports, we found that Aβ43 spontaneously aggregates more slowly than Aβ42. In addition, Aβ43 fibrils are very inefficient at seeding Aβ42 amyloid formation, even though Aβ42 fibrils efficiently seed amyloid formation by Aβ43 monomers. Finally, mixtures of Aβ42 and Aβ43 aggregate more slowly than Aβ42 alone. Both in this Aβ42/Aβ43 co-aggregation reaction and in cross-seeding by Aβ42 fibrils, the structure of the Aβ43 in the product fibrils is influenced by the presence of Aβ42. The results provide new details of amyloid structure and assembly pathways, an example of structural plasticity in prion-like replication, and data showing that low levels of Aβ43 in the brain are unlikely to favorably impact the aggregation of Aβ42.





    Categories: Journal Articles
  • Motility, Chemotaxis and Aerotaxis Contribute to Competitiveness during Bacterial Pellicle Biofilm Development
    [Jul 2015]

    Publication date: Available online 26 June 2015
    Source:Journal of Molecular Biology

    Author(s): Theresa Hölscher, Benjamin Bartels, Yu-Cheng Lin, Ramses Gallegos-Monterrosa, Alexa Price-Whelan, Roberto Kolter, Lars E.P. Dietrich, Ákos T. Kovács

    Biofilm formation is a complex process involving various signaling pathways and changes in gene expression. Many of the sensory mechanisms and regulatory cascades involved have been defined for biofilms formed by diverse organisms attached to solid surfaces. By comparison, our knowledge on the basic mechanisms underlying the formation of biofilms at air–liquid interfaces, that is, pellicles, is much less complete. In particular, the roles of flagella have been studied in multiple solid-surface biofilm models but remain largely undefined for pellicles. In this work, we characterize the contributions of flagellum-based motility, chemotaxis and oxygen sensing to pellicle formation in the Gram-positive Bacillus subtilis. We confirm that flagellum-based motility is involved in, but is not absolutely essential for, B. subtilis pellicle formation. Further, we show that flagellum-based motility, chemotaxis and oxygen sensing are important for successful competition during B. subtilis pellicle formation. We report that flagellum-based motility similarly contributes to pellicle formation and fitness in competition assays in the Gram-negative Pseudomonas aeruginosa. Time-lapse imaging of static liquid cultures demonstrates that, in both B. subtilis and P. aeruginosa, a turbulent flow forms in the tube and a zone of clearing appears below the air–liquid interface just before the formation of the pellicle but only in strains that have flagella.
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    Categories: Journal Articles
  • Signaling Control of Differentiation of Embryonic Stem Cells toward Mesendoderm
    [Jul 2015]

    Publication date: Available online 25 June 2015
    Source:Journal of Molecular Biology

    Author(s): Lu Wang, Ye-Guang Chen

    Mesendoderm (ME) refers to the primitive streak in mammalian embryos, which has the ability to further differentiate into mesoderm and endoderm. A better understanding on the regulatory networks of ME differentiation of embryonic stem (ES) cells would provide important insights on early embryo patterning and a possible guidance for ES applications in regenerative medicine. Studies on developmental biology and embryology have offered a great deal of knowledge about key signaling pathways involved in primitive streak formation. Recently, various chemically defined recipes have been formulated to induce differentiation of ES cells toward ME in vitro, which greatly facilitate the elucidation of the regulatory mechanisms of different signals involved in ME specification. Among the extrinsic signals, transforming growth factor-β/Activin signaling and Wnt signaling have been shown to be the most critical ones. On another side, intrinsic epigenetic regulation has been indicated to be important in ME determination. In this review, we summarize the current understanding on the extrinsic and intrinsic regulations of ES cells-to-ME differentiation and the crosstalk among them, aiming to get a general overview on ME specification and primitive streak formation.
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    Categories: Journal Articles
  • ClickSeq: Fragmentation-Free Next-Generation Sequencing via Click Ligation of Adaptors to Stochastically Terminated 3′-Azido cDNAs
    [Jul 2015]

    Publication date: Available online 24 June 2015
    Source:Journal of Molecular Biology

    Author(s): Andrew Routh, Steven R. Head, Phillip Ordoukhanian, John E. Johnson

    We present a simple method called “ClickSeq” for NGS (next-generation sequencing) library synthesis that uses click chemistry rather than enzymatic reactions for the ligation of Illumina sequencing adaptors. In ClickSeq, randomly primed reverse transcription reactions are supplemented with azido-2′,3′-dideoxynucleotides that randomly terminate DNA synthesis and release 3′-azido-blocked cDNA fragments in a process akin to dideoxy-Sanger sequencing. Purified fragments are “click ligated” via copper-catalyzed alkyne-azide cycloaddition to DNA oligos modified with a 5′-alkyne group. This generates ssDNA molecules containing an unnatural triazole-linked DNA backbone that is sufficiently biocompatible for PCR amplification to generate a cDNA library for RNAseq. Here, we analyze viral RNAs and mRNA to demonstrate that ClickSeq produces unbiased NGS libraries with low error rates comparable to standard methods. Importantly, ClickSeq is robust against common artifacts of NGS such as chimera formation and artifactual recombination with fewer than 3 aberrant events detected per million reads.
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    Categories: Journal Articles
  • Snapshots of Conformational Changes Shed Light into the NtrX Receiver Domain Signal Transduction Mechanism
    [Jul 2015]

    Publication date: Available online 23 June 2015
    Source:Journal of Molecular Biology

    Author(s): Ignacio Fernández, Lisandro H. Otero, Sebastián Klinke, Mariela del Carmen Carrica, Fernando A. Goldbaum

    Brucella abortus is an important pathogenic bacterium that has to overcome oxygen deficiency in order to achieve a successful infection. Previously, we proved that a two-component system formed by the histidine kinase NtrY and the response regulator NtrX is essential to achieve an adaptive response to low oxygen tension conditions. Even though the relevance of this signaling pathway has already been demonstrated in other microorganisms, its molecular activation mechanism has not yet been described in detail. In this article, we report the first crystal structures from different conformations of the NtrX receiver domain from B. abortus, and we propose a sequence of events to explain the structural rearrangements along the activation process. The analysis of the structures obtained in the presence of the phosphoryl group analog beryllofluoride led us to postulate that changes in the interface formed by the α4 helix and the β5 strand are important for the activation, producing a reorientation of the α5 helix. Also, a biochemical characterization of the NtrX receiver domain enzymatic activities was performed, describing its autophosphorylation and autodephosphorylation kinetics. Finally, the role of H85, an important residue, was addressed by site-directed mutagenesis. Overall, these results provide significant structural basis for understanding the response regulator activation in this bacterial two-component system.
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    Categories: Journal Articles
  • Exposed: The Many and Varied Roles of Phospholipase C γ SH2 Domains
    [Jul 2015]

    Publication date: Available online 23 June 2015
    Source:Journal of Molecular Biology

    Author(s): Paul C. Driscoll







    Categories: Journal Articles
  • The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N6-Threonylcarbamoyladenosine Dehydratase Activity
    [Jul 2015]

    Publication date: Available online 21 June 2015
    Source:Journal of Molecular Biology

    Author(s): Sunmin Kim, Hyuk Lee, SangYoun Park

    Escherichia coli TcdA (also known as CsdL) was previously shown to catalyze the ATP-dependent dehydration/cyclization of hypermodified tRNA N 6-threonylcarbamoyladenosine into further cyclic N 6-threonylcarbamoyladenosine. In this study, we report the X-ray crystal structures of E. coli TcdA with either AMP or ATP bound. The AMP/ATP-bound N-terminal sub-domain of TcdA resembles the ATP-binding Rossmann fold of E. coli ThiF and MoeB that are enzymes respectively taking part in the biosynthesis of thiamine and molybdopterin; however, the remaining C-terminal sub-domain of TcdA adopts a structure unrelated to any other known folds. In TcdA, the ATP-utilizing adenylation of tRNA N 6-threonylcarbamoyladenosine and a subsequent thioester formation via an active cysteine, similar to the mechanisms in ThiF and MoeB, could take place for the dehydratase function. Analysis of the structure with sequence alignment suggests the disordered Cys234 of TcdA as the most likely catalytic residue. The structure further indicates that the C-terminal sub-domain can provide a binding interface for the tRNA substrate. Binding study using the surface mutants of TcdA and tRNA reveals that the positively charged regions of mainly the C-terminal sub-domain are important for the tRNA recognition.
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    Categories: Journal Articles
  • Over-Expression Analysis of All Eight Subunits of the Molecular Chaperone CCT in Mammalian Cells Reveals a Novel Function for CCTdelta
    [Jul 2015]

    Publication date: Available online 21 June 2015
    Source:Journal of Molecular Biology

    Author(s): Matthias Spiess, Meriem Echbarthi, Andreas Svanström, Roger Karlsson, Julie Grantham

    Chaperonin containing tailless complex polypeptide 1 (CCT) forms a classical chaperonin barrel structure where two rings of subunits surround a central cavity. Each ring consists of eight distinct subunits, creating a complex binding interface that makes CCT unique among the chaperonins. In addition to acting as a multimeric chaperonin, there is increasing evidence indicating that the CCT subunits, when monomeric, possess additional functions. Here we assess the role of the CCT subunits individually, using a GFP (green fluorescent protein) tagging approach to express each of the subunits in their monomeric form in cultured mammalian cells. Over-expression of CCTdelta, but not the other seven CCT subunits, results in the appearance of numerous protrusions at the cell surface. Two point mutations, one in the apical domain and one in the ATP binding pocket of CCTdelta, that abolish protrusion formation have been identified, consistent with the apical domain containing a novel interaction site that is influenced by the ATPase activity in the equatorial domain. Structured illumination microscopy, together with sub-cellular fractionation, reveals that only the wild-type CCTdelta is associated with the plasma membrane, thus connecting spatial organization with surface protrusion formation. Expression of the equivalent subunit in yeast, GFP-Cct4, rescues growth of the temperature-sensitive strain cct4-1 at the non-permissive temperature, indicative of conserved subunit-specific activities for CCTdelta.
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    Categories: Journal Articles
  • Using Molecular Dynamics Simulations as an Aid in the Prediction of Domain Swapping of Computationally Designed Protein Variants
    [Jul 2015]

    Publication date: Available online 21 June 2015
    Source:Journal of Molecular Biology

    Author(s): Yun Mou, Po-Ssu Huang, Leonard M. Thomas, Stephen L. Mayo

    In standard implementations of computational protein design, a positive-design approach is used to predict sequences that will be stable on a given backbone structure. Possible competing states are typically not considered, primarily because appropriate structural models are not available. One potential competing state, the domain-swapped dimer, is especially compelling because it is often nearly identical with its monomeric counterpart, differing by just a few mutations in a hinge region. Molecular dynamics (MD) simulations provide a computational method to sample different conformational states of a structure. Here, we tested whether MD simulations could be used as a post-design screening tool to identify sequence mutations leading to domain-swapped dimers. We hypothesized that a successful computationally designed sequence would have backbone structure and dynamics characteristics similar to that of the input structure and that, in contrast, domain-swapped dimers would exhibit increased backbone flexibility and/or altered structure in the hinge-loop region to accommodate the large conformational change required for domain swapping. While attempting to engineer a homodimer from a 51-amino-acid fragment of the monomeric protein engrailed homeodomain (ENH), we had instead generated a domain-swapped dimer (ENH_DsD). MD simulations on these proteins showed increased B-factors derived from MD simulation in the hinge loop of the ENH_DsD domain-swapped dimer relative to monomeric ENH. Two point mutants of ENH_DsD designed to recover the monomeric fold were then tested with an MD simulation protocol. The MD simulations suggested that one of these mutants would adopt the target monomeric structure, which was subsequently confirmed by X-ray crystallography.
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    Categories: Journal Articles
  • Dividing and Conquering the Family of RNA Recognition Motifs: A Representative Case Based on hnRNP L
    [Jul 2015]

    Publication date: Available online 20 June 2015
    Source:Journal of Molecular Biology

    Author(s): Sarah Loerch, Clara L. Kielkopf







    Categories: Journal Articles
  • Editorial Board
    [Jul 2015]

    Publication date: 19 June 2015
    Source:Journal of Molecular Biology, Volume 427, Issue 12









    Categories: Journal Articles
  • Contents List
    [Jul 2015]

    Publication date: 19 June 2015
    Source:Journal of Molecular Biology, Volume 427, Issue 12









    Categories: Journal Articles
  • Sallimus and the Dynamics of Sarcomere Assembly in Drosophila Flight Muscles
    [Jul 2015]

    Publication date: 19 June 2015
    Source:Journal of Molecular Biology, Volume 427, Issue 12

    Author(s): Zacharias Orfanos, Kevin Leonard, Chris Elliott, Anja Katzemich, Belinda Bullard, John Sparrow

    The Drosophila indirect flight muscles (IFM) can be used as a model for the study of sarcomere assembly. Here we use a transgenic line with a green fluorescent protein (GFP) exon inserted into the Z-disc-proximal portion of sallimus (Sls), also known as Drosophila titin, to observe sarcomere assembly during IFM development. Firstly, we confirm that Sls-GFP can be used in the heterozygote state without an obvious phenotype in IFM and other muscles. We then use Sls-GFP in the IFM to show that sarcomeres grow individually and uniformly throughout the fibre, growing linearly in length and in diameter. Finally, we show that limiting the amounts of Sls in the IFM using RNAi leads to sarcomeres with smaller Z-discs in their core, whilst the thick/thin filament lattice can form peripherally without a Z-disc. Thick filament preparations from those muscles show that although the Z-disc-containing core has thick filaments of a regular length, filaments from the peripheral lattice are longer and asymmetrical around the bare zone. Therefore, the Z-disc and Sls are required for thick filament length specification but not for the assembly of the thin/thick filament lattice.
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    Categories: Journal Articles
  • The Response of Greek Key Proteins to Changes in Connectivity Depends on the Nature of Their Secondary Structure
    [Jul 2015]

    Publication date: 19 June 2015
    Source:Journal of Molecular Biology, Volume 427, Issue 12

    Author(s): Katherine R. Kemplen, David De Sancho, Jane Clarke

    What governs the balance between connectivity and topology in regulating the mechanism of protein folding? We use circular permutation to vary the order of the helices in the all-α Greek key protein FADD (Fas-associated death domain) to investigate this question. Unlike all-β Greek key proteins, where changes in the order of secondary structure cause a shift in the folding nucleus, the position of the nucleus in FADD is unchanged, even when permutation reduces the complexity significantly. We suggest that this is because local helical contacts are so dominant that permutation has little effect on the entropic cost of forming the folding nucleus whereas, in all-β Greek key proteins, all interactions in the nucleus are long range. Thus, the type of secondary structure modulates the sensitivity of proteins to changes in connectivity.
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    Categories: Journal Articles