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Membrane protein crystal structure

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https://www.readbyqxmd.com/read/28430426/the-rosetta-all-atom-energy-function-for-macromolecular-modeling-and-design
#1
Rebecca Faye Alford, Andrew Leaver-Fay, Jeliazko R Jeliazkov, Matthew J O'Meara, Frank P DiMaio, Hahnbeom Park, Maxim V Shapovalov, P Douglas Renfrew, Vikram Khipple Mulligan, Kalli Kappel, Jason W Labonte, Michael Steven Pacella, Richard Bonneau, Philip Bradley, Roland L Dunbrack, Rhiju Das, David Baker, Brian Kuhlman, Tanja Kortemme, Jeffrey J Gray
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta's success is the energy function: a model parameterized from small molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta Energy Function, REF15...
April 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28420706/common-structural-features-of-cholesterol-binding-sites-in-crystallized-soluble-proteins
#2
Anna N Bukiya, Alejandro M Dopico
Cholesterol-protein interactions are essential for the architectural organization of cell membranes and for lipid metabolism. While cholesterol-sensing motifs in transmembrane proteins have been identified, little is known about cholesterol recognition by soluble proteins. We reviewed the structural characteristics of binding sites for cholesterol and cholesterol sulfate from crystallographic structures available in the Protein Data Bank. This analysis unveiled key features of cholesterol-binding sites that are present in either all or the majority of sites: i) the cholesterol molecule is generally positioned between protein domains that have an organized secondary structure; ii) the cholesterol hydroxyl/sulfo group is often partnered by Asn, Gln and/or Tyr while the hydrophobic part of cholesterol interacts with Leu, Ile, Val and/or Phe; iii) cholesterol hydrogen-bonding partners are often found on alpha-helices while amino acids that interact with cholesterol hydrophobic core have a slight preference for beta-strands and secondary structure-lacking protein areas; iv) the steroid C21 and 26 constitute the ″hot spots″ most often seen for steroid-protein hydrophobic interactions; v) common ″cold spots″ are C8, 9, 10, 13 and 17, at which contacts with the proteins were not detected...
April 18, 2017: Journal of Lipid Research
https://www.readbyqxmd.com/read/28398555/biophysical-and-functional-characterization-of-hippocalcin-mutants-responsible-for-human-dystonia
#3
Nordine Helassa, Svetlana V Antonyuk, Lu-Yun Lian, Lee P Haynes, Robert D Burgoyne
Dystonia is a neurological movement disorder that forces the body into twisting, repetitive movements or sometimes painful abnormal postures. With the advent of next-generation sequencing technologies, the homozygous mutations T71N and A190T in the neuronal calcium sensor (NCS) hippocalcin were identified as the genetic cause of primary isolated dystonia (DYT2 dystonia). However, the effect of these mutations on the physiological role of hippocalcin has not yet been elucidated. Using a multidisciplinary approach, we demonstrated that hippocalcin oligomerises in a calcium-dependent manner and binds to voltage-gated calcium channels...
April 7, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28394325/structural-basis-for-lipopolysaccharide-extraction-by-abc-transporter-lptb2fg
#4
Qingshan Luo, Xu Yang, Shan Yu, Huigang Shi, Kun Wang, Le Xiao, Guangyu Zhu, Chuanqi Sun, Tingting Li, Dianfan Li, Xinzheng Zhang, Min Zhou, Yihua Huang
After biosynthesis, bacterial lipopolysaccharides (LPS) are transiently anchored to the outer leaflet of the inner membrane (IM). The ATP-binding cassette (ABC) transporter LptB2FG extracts LPS molecules from the IM and transports them to the outer membrane. Here we report the crystal structure of nucleotide-free LptB2FG from Pseudomonas aeruginosa. The structure reveals that lipopolysaccharide transport proteins LptF and LptG each contain a transmembrane domain (TMD), a periplasmic β-jellyroll-like domain and a coupling helix that interacts with LptB on the cytoplasmic side...
April 10, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28393915/allosteric-inhibition-of-aminopeptidase-n-functions-related-to-tumor-growth-and-virus-infection
#5
César Santiago, Gaurav Mudgal, Juan Reguera, Rosario Recacha, Sébastien Albrecht, Luis Enjuanes, José M Casasnovas
Cell surface aminopeptidase N (APN) is a membrane-bound ectoenzyme that hydrolyzes proteins and peptides and regulates numerous cell functions. APN participates in tumor cell expansion and motility, and is a target for cancer therapies. Small drugs that bind to the APN active site inhibit catalysis and suppress tumor growth. APN is also a major cell entry receptor for coronavirus, which binds to a region distant from the active site. Three crystal structures that we determined of human and pig APN ectodomains defined the dynamic conformation of the protein...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28375549/homology-based-modeling-of-rhodopsin-like-family-members-in-the-inactive-state-structural-analysis-and-deduction-of-tips-for-modeling-and-optimization
#6
Matteo Pappalardo, Mahmoud Rayan, Saleh Abu-Lafi, Martha E Leonardi, Danilo Milardi, Salvatore Guccione, Anwar Rayan
Modeling G-Protein Coupled Receptors (GPCRs) is an emergent field of research, since utility of high-quality models in receptor structure-based strategies might facilitate the discovery of interesting drug candidates. The findings from a quantitative analysis of eighteen resolved structures of rhodopsin family "A" receptors crystallized with antagonists and 153 pairs of structures are described. A strategy termed endeca-amino acids fragmentation was used to analyze the structures models aiming to detect the relationship between sequence identity and Root Mean Square Deviation (RMSD) at each trans-membrane-domain...
April 4, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/28370548/formation-of-a-cubic-liquid-crystalline-nanostructure-with-%C3%AF-conjugated-fluorinated-rods-on-the-gyroid-minimal-surface
#7
Marko Poppe, Changlon Chen, Feng Liu, Silvio Poppe, Carsten Tschierske
Bicontinuous cubic phases are of significant importance for numerous applications, for example, for the crystallization of membrane proteins, as photonic materials and as templates for porous silica. A new variant of bicontinuous cubic liquid crystalline phase with Ia3¯d lattice is reported here for X-shaped bolapolyphiles. It is shown that in this class of compounds cubic phase induction can be achieved by proper aromatic core fluorination; in addition, the first cubic phases having π-conjugated oligo(phenylene ethynylene) rods on the gyroid minimal surface were obtained...
March 29, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28369529/human-apo-srp72-and-srp68-72-complex-structures-reveal-the-molecular-basis-of-protein-translocation
#8
Yina Gao, Qi Zhang, Yue Lang, Yang Liu, Xiaofei Dong, Zhenhang Chen, Wenli Tian, Jun Tang, Wei Wu, Yufeng Tong, Zhongzhou Chen
The co-translational targeting or insertion of secretory and membrane proteins into the endoplasmic reticulum (ER) is a key biological process mediated by the signal recognition particle (SRP). In eukaryotes, the SRP68-SRP72 (SRP68/72) heterodimer plays an essential role in protein translocation. However, structural information on the two largest SRP proteins, SRP68 and SRP72, is limited, especially regarding their interaction. Herein, we report the first crystal structures of human apo-SRP72 and the SRP68/72 complex at 2...
March 20, 2017: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/28368278/crystallization-and-x-ray-analysis-of-the-extracellular-adhesion-domain-of-helicobacter-pylori-adhesin-a-the-significance-of-the-cation-composition-in-the-crystallization-precipitant
#9
Ling Guo, Jinyong Zhang, Liwei Cui, Dong Liu, Bo Ma, Shufeng Wang, Haibo Li, Yuzhang Wu, Wei Liu
Adherence to host cells is a crucial step in the process of bacterial infection, which is usually mediated by a number of outer membrane proteins identified as adhesins. Helicobacter pylori adhesin A (HpaA) is a member of the adhesin family that mediates the adherence of Helicobacter pylori to gastric epithelial cells, and consequently assists the bacteria in becoming a life-long colonizer of the human stomach. In this study, two constructs were made for the production of truncated HpaA proteins comprising residues 31-260 and 53-260, respectively...
April 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28348076/the-crystal-structure-of-a-membrane-bound-multi-domain-protease-inhibitor-reveals-the-mechanism-of-its-auto-inhibition
#10
Min Liu, Cai Yuan, Jan Jensen, Baoyu Zhao, Yunbin Jiang, Longguang Jiang, Mindong Huang
Hepatocyte growth factor activator inhibitor 1 (HAI-1) is a membrane-bound multi-domain protein essential to the integrity of the basement membrane during placental development and is also important in maintaining postnatal homeostasis in many tissues. HAI-1 is a Kunitz-type serine protease inhibitor, and soluble fragments of HAI-1 with variable lengths have been identified in vivo. The full-length extracellular portion of HAI-1 (sHAI-1) shows weaker inhibitory activity toward target proteases than do the smaller fragments, suggesting auto-inhibition of HAI-1...
March 27, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28343125/structural-modeling-of-human-organic-cation-transporters
#11
Tikam Chand Dakal, Rajender Kumar, Dindial Ramotar
Human organic cation transporters (hOCTs) belong to solute carriers (SLC) 22 family of membrane proteins that play a central role in transportation of chemotherapeutic drugs for several clinical and pathological conditions, including cancer and diabetes. These transporters mediate drug transport; however, the precise mechanism of drug-binding and transport by them is not fully uncovered yet, partly due to unavailability of any crystal structure record. In this work, we performed a multi-phasic approach to compute the 3D structural models of seven human organic cation transporters (hOCTs) starting from primary protein sequence...
March 18, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28329765/structural-insights-into-adiponectin-receptors-suggest-ceramidase-activity
#12
Ieva Vasiliauskaité-Brooks, Remy Sounier, Pascal Rochaix, Gaëtan Bellot, Mathieu Fortier, François Hoh, Luigi De Colibus, Chérine Bechara, Essa M Saied, Christoph Arenz, Cédric Leyrat, Sébastien Granier
Adiponectin receptors (ADIPORs) are integral membrane proteins that control glucose and lipid metabolism by mediating, at least in part, a cellular ceramidase activity that catalyses the hydrolysis of ceramide to produce sphingosine and a free fatty acid (FFA). The crystal structures of the two receptor subtypes, ADIPOR1 and ADIPOR2, show a similar overall seven-transmembrane-domain architecture with large unoccupied cavities and a zinc binding site within the seven transmembrane domain. However, the molecular mechanisms by which ADIPORs function are not known...
April 6, 2017: Nature
https://www.readbyqxmd.com/read/28319136/structural-insights-into-the-regulation-of-bacillus-subtilis-sigw-activity-by-anti-sigma-rsiw
#13
Shankar Raj Devkota, Eunju Kwon, Sung Chul Ha, Hyeun Wook Chang, Dong Young Kim
Bacillus subtilis SigW is localized to the cell membrane and is inactivated by the tight interaction with anti-sigma RsiW under normal growth conditions. Whereas SigW is discharged from RsiW binding and thus initiates the transcription of its regulon under diverse stress conditions such as antibiotics and alkaline shock. The release and activation of SigW in response to extracytoplasmic signals is induced by the regulated intramembrane proteolysis of RsiW. As a ZAS (Zinc-containing anti-sigma) family protein, RsiW has a CHCC zinc binding motif, which implies that its anti-sigma activity may be regulated by the state of zinc coordination in addition to the proteolytic cleavage of RsiW...
2017: PloS One
https://www.readbyqxmd.com/read/28315353/crystal-structure-of-the-extracellular-domain-of-the-human-dendritic-cell-surface-marker-cd83
#14
Christiane S Heilingloh, Stefan Klingl, Claudia Egerer-Sieber, Benedikt Schmid, Sigrid Weiler, Petra Mühl-Zürbes, Jörg Hofmann, Joachim D Stump, Heinrich Sticht, Mirko Kummer, Alexander Steinkasserer, Yves A Muller
CD83 is a type-I membrane protein and an efficient marker for identifying mature dendritic cells. Whereas membrane-bound, full-length CD83 co-stimulates the immune system, a soluble variant (sCD83), consisting of the extracellular domain only, displays strong immune-suppressive activities. Besides a prediction that sCD83 adopts a V-set Ig-like fold, however, little is known about the molecular architecture of CD83 and the mechanism by which CD83 exerts its function on dendritic cells and additional immune cells...
March 15, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28303107/localization-and-ordering-of-lipids-around-aquaporin-0-protein-and-lipid-mobility-effects
#15
Rodolfo Briones, Camilo Aponte-Santamaría, Bert L de Groot
Hydrophobic matching, lipid sorting, and protein oligomerization are key principles by which lipids and proteins organize in biological membranes. The Aquaporin-0 channel (AQP0), solved by electron crystallography (EC) at cryogenic temperatures, is one of the few protein-lipid complexes of which the structure is available in atomic detail. EC and room-temperature molecular dynamics (MD) of dimyristoylglycerophosphocholine (DMPC) annular lipids around AQP0 show similarities, however, crystal-packing and temperature might affect the protein surface or the lipids distribution...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28302513/expression-purification-and-enzymatic-characterization-of-undecaprenyl-pyrophosphate-phosphatase-from-vibrio-vulnificus
#16
Hsin-Yang Chang, Chia-Cheng Chou, Mao-Lun Wu, Andrew H J Wang
Undecaprenyl pyrophosphate phosphatase (UppP), a cell membrane integral enzyme, catalyzes the dephosphorylation of undecaprenyl pyrophosphate to undecaprenyl phosphate, which is an essential carrier lipid in bacterial cell wall synthesis. We previously purified E. coli UppP and concluded that its catalytic site is likely located in the periplasm. To search for additional natural UppP homologs to elucidate what constitutes a common catalytic mechanism and to gain a better chance of obtaining high-resolution crystal structural information, we expressed and purified recombinant Vibrio vulnificus UppP using E...
March 14, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28299732/structural-studies-of-matrix-metalloproteinase-by-x-ray-diffraction
#17
Elena Decaneto, Wolfgang Lubitz, Hideaki Ogata
Matrix Metalloproteinases (MMPs) are a family of proteolytic enzymes whose endopeptidase activity is dependent on the presence of specific metal ions. MT1-MMP (or MMP-14), which has been implicated in tumor progression and cellular invasion, contains a membrane-spanning region located C-terminal to a hemopexin-like domain and an N-terminal catalytic domain. We recombinantly expressed the catalytic domain of human MT1-MMP in E. coli and purified it from inclusion bodies using a refolding protocol that yielded significant quantities of active protein...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28291748/the-crystal-structure-of-mouse-lc3b-in-complex-with-the-fyco1-lir-reveals-the-importance-of-the-flanking-region-of-the-lir-motif
#18
Shunya Sakurai, Taisuke Tomita, Toshiyuki Shimizu, Umeharu Ohto
FYVE and coiled-coil domain-containing protein 1 (FYCO1), a multidomain autophagy adaptor protein, mediates microtubule plus-end-directed autophagosome transport by interacting with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7 and phosphatidylinositol 3-phosphate (PI3P). To establish the structural basis for the recognition of FYCO1 by LC3, the crystal structure of mouse LC3B in complex with the FYCO1 LC3-interacting region (LIR) motif peptide was determined...
March 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28286332/two-alternative-binding-mechanisms-connect-the-protein-translocation-sec71-sec72-complex-with-heat-shock-proteins
#19
Arati Tripathi, Elisabet C Mandon, Reid Gilmore, Tom A Rapoport
The biosynthesis of many eukaryotic proteins requires accurate targeting to and translocation across the endoplasmic reticulum (ER) membrane. Post-translational protein translocation in yeast requires both the Sec61 translocation channel, and a complex of four additional proteins: Sec63, Sec62, Sec71, and Sec72. The structure and function of these proteins are largely unknown. This pathway also requires the cytosolic Hsp70 protein Ssa1, but whether Ssa1 associates with the translocation machinery to target protein substrates to the membrane is unclear...
March 12, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28272640/mutual-relationships-between-structural-and-functional-changes-in-a-psbm-deletion-mutant-of-photosystem-ii
#20
S Uto, K Kawakami, Y Umena, M Iwai, M Ikeuchi, J-R Shen, N Kamiya
Photosystem II (PSII) is a membrane protein complex that performs light-induced electron transfer and oxygen evolution from water. PSII consists of 19 or 20 subunits in its crystal form and binds various cofactors such as chlorophyll a, plastoquinone, carotenoid, and lipids. After initial light excitation, the charge separation produces an electron, which is transferred to a plastoquinone molecule (QA) and then to another plastoquinone (QB). PsbM is a low-molecular-weight subunit with one transmembrane helix, and is located in the monomer-monomer interface of the PSII dimer...
March 8, 2017: Faraday Discussions
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