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Katharine A Michie, Ann H Kwan, Chang-Shung Tung, J Mitchell Guss, Jill Trewhella
The nuclear magnetic resonance (NMR) structure of the tri-helix bundle (THB) of the m-domain plus C2 (ΔmC2) of myosin-binding protein C (MyBP-C) has revealed a highly flexible seven-residue linker between the structured THB and C2. Bioinformatics shows significant patterns of conservation across the THB-linker sequence, with the linker containing a strictly conserved serine in all MyBP-C isoforms. Clinically linked mutations further support the functional significance of the THB-linker region. NMR, small-angle X-ray scattering, and binding studies show the THB-linker plus the first ten residues of C2 undergo dramatic changes when ΔmC2 binds Ca(2+)-calmodulin, with the linker and C2 N-terminal residues contributing significantly to the affinity...
October 4, 2016: Structure
Tamas Yelland, Snezana Djordjevic
Neuropilins (NRPs) are single-pass transmembrane receptors involved in several signaling pathways that regulate key physiological processes such as vascular morphogenesis and axon guidance. The MAM domain of NRP, which has previously been implicated in receptor multimerization, was the only portion of the ectopic domain of the NRPs for which the structure, until now, has been elusive. Using site-directed mutagenesis in the linker region preceding the MAM domain we generated a protein construct amenable to crystallization...
October 3, 2016: Structure
Artem Zhmurov, Anna D Protopopova, Rustem I Litvinov, Pavel Zhukov, Alexander R Mukhitov, John W Weisel, Valeri Barsegov
Fibrin is a filamentous network made in blood to stem bleeding; it forms when fibrinogen is converted into fibrin monomers that self-associate into oligomers and then to polymers. To gather structural insights into fibrin formation and properties, we combined high-resolution atomic force microscopy of fibrin(ogen) oligomers and molecular modeling of crystal structures of fibrin(ogen) and its fragments. We provided a structural basis for the intermolecular flexibility of single-stranded fibrin(ogen) oligomers and identified a hinge region at the D:D inter-monomer junction...
September 28, 2016: Structure
Meytal Galilee, Elena Britan-Rosich, Sarah L Griner, Serdar Uysal, Viola Baumgärtel, Don C Lamb, Anthony A Kossiakoff, Moshe Kotler, Robert M Stroud, Ailie Marx, Akram Alian
HIV-1 integrase (IN) catalyzes viral DNA integration into the host genome and facilitates multifunctional steps including virus particle maturation. Competency of IN to form multimeric assemblies is functionally critical, presenting an approach for anti-HIV strategies. Multimerization of IN depends on interactions between the distinct subunit domains and among the flanking protomers. Here, we elucidate an overlooked docking cleft of IN core domain that anchors the N-terminal helix-turn-helix (HTH) motif in a highly preserved and functionally critical configuration...
September 28, 2016: Structure
Radu Huculeci, Elisa Cilia, Agatha Lyczek, Lieven Buts, Klaartje Houben, Markus A Seeliger, Nico van Nuland, Tom Lenaerts
Src kinase activity is controlled by various mechanisms involving a coordinated movement of kinase and regulatory domains. Notwithstanding the extensive knowledge related to the backbone dynamics, little is known about the more subtle side-chain dynamics within the regulatory domains and their role in the activation process. Here, we show through experimental methyl dynamic results and predicted changes in side-chain conformational couplings that the SH2 structure of Fyn contains a dynamic network capable of propagating binding information...
September 28, 2016: Structure
Roland G Huber, Irina Kulemzina, Keven Ang, Alap P Chavda, Sasikala Suranthran, Jun-Thing Teh, Dimitar Kenanov, Gaowen Liu, Giulia Rancati, Radoslaw Szmyd, Philipp Kaldis, Peter J Bond, Dmitri Ivanov
The cohesin ring, which is composed of the Smc1, Smc3, and Scc1 subunits, topologically embraces two sister chromatids from S phase until anaphase to ensure their precise segregation to the daughter cells. The opening of the ring is required for its loading on the chromosomes and unloading by the action of Wpl1 protein. Both loading and unloading are dependent on ATP hydrolysis by the Smc1 and Smc3 "head" domains, which engage to form two composite ATPase sites. Based on the available structures, we modeled the Saccharomyces cerevisiae Smc1/Smc3 head heterodimer and discovered that the Smc1/Smc3 interfaces at the two ATPase sites differ in the extent of protein contacts and stability after ATP hydrolysis...
September 27, 2016: Structure
Fernando Corrêa, Jason Key, Brian Kuhlman, Kevin H Gardner
Hypoxia-inducible factors (HIFs) are heterodimeric transcription factors central to hypoxia response and cancer development. Within the HIF-2 complex, one domain (HIF-2α PAS-B) contains a large (290 Å(3)) buried cavity filled with water molecules within its hydrophobic core. Such cavities are uncommon except in the case of ligand-binding proteins, leading to the hypothesis that HIF-2α can be regulated by small molecules. The development of artificial HIF-2α inhibitors validates this hypothesis but raises questions about the impact of this cavity on HIF-2α PAS-B structure and function...
September 20, 2016: Structure
Andrei Fokine, Michael G Rossmann
Many large viruses, including tailed dsDNA bacteriophages and herpesviruses, assemble their capsids via formation of precursors, called procapsids or proheads. The prohead has an internal core, made of scaffolding proteins, and an outer shell, formed by the major capsid protein. The prohead usually contains a protease, which is activated during capsid maturation to destroy the inner core and liberate space for the genome. Here, we report a 2.0 Å resolution structure of the pentameric procapsid protease of bacteriophage T4, gene product (gp)21...
September 20, 2016: Structure
James M Fay, Cheng Zhu, Elizabeth A Proctor, Yazhong Tao, Wenjun Cui, Hengming Ke, Nikolay V Dokholyan
The majority of amyotrophic lateral sclerosis (ALS)-related mutations in the enzyme Cu,Zn superoxide dismutase (SOD1), as well as a post-translational modification, glutathionylation, destabilize the protein and lead to a misfolded oligomer that is toxic to motor neurons. The biophysical role of another physiological SOD1 modification, T2-phosphorylation, has remained a mystery. Here, we find that a phosphomimetic mutation, T2D, thermodynamically stabilizes SOD1 even in the context of a strongly SOD1-destabilizing mutation, A4V, one of the most prevalent and aggressive ALS-associated mutations in North America...
September 17, 2016: Structure
Jinwei Zhu, Yuan Shang, Yitian Xia, Rongguang Zhang, Mingjie Zhang
The membrane-associated guanylate kinase (MAGUK) scaffold proteins share a signature guanylate kinase (GK) domain. Despite their diverse functional roles in cell polarity control and synaptic signaling, the currently known mode of action of MAGUK GK is via its binding to phosphorylated short peptides from target proteins. Here, we discover that the GK domain of DLG MAGUK binds to an unphosphorylated and autonomously folded domain within the stalk region (MAGUK binding stalk [MBS] domain) of a kinesin motor KIF13B with high specificity and affinity...
September 15, 2016: Structure
Jordan M Mancl, Wesley P Black, Howard Robinson, Zhaomin Yang, Florian D Schubot
Type IV pili (T4P) mediate bacterial motility and virulence. The PilB/GspE family ATPases power the assembly of T4P and type 2 secretion systems. We determined the structure of the ATPase region of PilB (PilBATP) in complex with ATPγS to provide a model of a T4P assembly ATPase and a view of a PilB/GspE family hexamer at better than 3-Å resolution. Spatial positioning and conformations of the protomers suggest a mechanism of force generation. All six PilBATP protomers contain bound ATPγS. Two protomers form a closed conformation poised for ATP hydrolysis...
September 13, 2016: Structure
Vinod K Batra, William A Beard, Lars C Pedersen, Samuel H Wilson
High-fidelity DNA synthesis requires that polymerases display a strong preference for right nucleotide insertion. When the wrong nucleotide is inserted, the polymerase deters extension from the mismatched DNA terminus. Twenty-three crystallographic structures of DNA polymerase β with terminal template-primer mismatches were determined as binary DNA and ternary pre-catalytic substrate complexes. These structures indicate that the mismatched termini adopt various distorted conformations that attempt to satisfy stacking and hydrogen-bonding interactions...
September 13, 2016: Structure
Jason Koo, Ryan P Lamers, John L Rubinstein, Lori L Burrows, P Lynne Howell
Type IVa pili (T4aP) function as bacterial virulence factors. T4aP pass through the outer membranes of Gram-negative bacteria via homo-oligomeric secretins. We present a 7.4 Å cryoelectron microscopy structure of the Pseudomonas aeruginosa PilQ secretin. Peripheral and internal features show that the secretin is composed of 14 subunits with C7 symmetry. The channel is a ribbed cylinder with central peripheral spokes and a central gate closed on the periplasmic side. The structure suggests that during pilus extrusion, the central gate is displaced to the interior walls and that no additional conformational changes are required, as the internal diameter can accommodate the pilus...
October 4, 2016: Structure
Roland Seifert
The cyclic purine nucleotide cIMP and the cyclic pyrimidine nucleotides cCMP and cUMP are emerging second messengers. These cNMPs show different biological effects, but the molecular mechanisms remain elusive. In this issue of Structure, Ng et al. (2016) provide structural evidence for distinct interactions of cIMP, cCMP, and cUMP with ion channels.
October 4, 2016: Structure
Sebastian Guettler
The poly(ADP-ribose)polymerase (PARP) Tankyrase uses ankyrin repeat modules to capture substrates via Tankyrase-binding peptide motifs. In this issue of Structure, Eisemann et al. (2016) describe how the signaling protein AXIN can access and conformationally adapt the multivalent ankyrin repeat region of Tankyrase and discuss potential implications for enzymatic substrate modification.
October 4, 2016: Structure
Nishant K Singh, Brian M Baker
Recognition of antigens by T cell receptors (TCRs) underlies cellular immunity. By comparing how different TCRs recognize the key antigens associated with celiac disease, Petersen et al. (2016), in this issue of Structure, show how celiac antigen properties select immunologically distinct yet structurally and physically compatible TCRs, ultimately driving autoimmunity.
October 4, 2016: Structure
Vladimir Baytshtok, Xue Fei, Robert A Grant, Tania A Baker, Robert T Sauer
The I domain of HslU sits above the AAA+ ring and forms a funnel-like entry to the axial pore, where protein substrates are engaged, unfolded, and translocated into HslV for degradation. The L199Q I-domain substitution, which was originally reported as a loss-of-function mutation, resides in a segment that appears to adopt multiple conformations as electron density is not observed in HslU and HslUV crystal structures. The L199Q sequence change does not alter the structure of the AAA+ ring or its interactions with HslV but increases I-domain susceptibility to limited endoproteolysis...
October 4, 2016: Structure
Kai Yang, De-Feng Li, Xi'e Wang, Jinzhao Liang, Roberto Sitia, Chih-Chen Wang, Xi Wang
ERp44 controls the localization and transport of diverse proteins in the early secretory pathway. The mechanisms that allow client recognition and the source of the oxidative power for forming intermolecular disulfides are as yet unknown. Here we present the structure of ERp44 bound to a client, peroxiredoxin 4. Our data reveal that ERp44 binds the oxidized form of peroxiredoxin 4 via thiol-disulfide interchange reactions. The structure explains the redox-dependent recognition and characterizes the essential non-covalent interactions at the interface...
October 4, 2016: Structure
Chengfei Yan, Xianjin Xu, Xiaoqin Zou
Protein-peptide interactions play an important role in many cellular processes. In silico prediction of protein-peptide complex structure is highly desirable for mechanistic investigation of these processes and for therapeutic design. However, predicting all-atom structures of protein-peptide complexes without any knowledge about the peptide binding site and the bound peptide conformation remains a big challenge. Here, we present a docking-based method for predicting protein-peptide complex structures, referred to as MDockPeP, which starts with the peptide sequence and globally docks the all-atom, flexible peptide onto the protein structure...
October 4, 2016: Structure
Mengying Zhang, Hejun Liu, Yongxiang Gao, Zhongliang Zhu, Zijun Chen, Peiyi Zheng, Lu Xue, Jixi Li, Maikun Teng, Liwen Niu
Histone chaperones are critical for guiding specific post-transcriptional modifications of histones, safeguarding the histone deposition (or disassociation) of nucleosome (dis)assembly, and regulating chromatin structures to change gene activities. HAT1-interacting factor 1 (Hif1) has been reported to be an H3-H4 chaperone and to be involved in telomeric silencing and nucleosome (dis)assembly. However, the structural basis for the interaction of Hif1 with histones remains unknown. Here, we report the complex structure of Hif1 binding to H2A-H2B for uncovering the chaperone specificities of Hif1 on binding to both the H2A-H2B dimer and the H3-H4 tetramer...
October 4, 2016: Structure
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