scholarly journals Identification of a novel fold type in CPA/AT transporters by ab-initio structure prediction

2020 ◽  
Author(s):  
Claudio Bassot ◽  
Sudha Govindarajan ◽  
John Lamb ◽  
Arne Elofsson
Keyword(s):  
Structure Prediction ◽  
Repeat Unit ◽  
Transmembrane Helix ◽  
Core Domain ◽  
Biologically Relevant ◽  
The Core ◽  
External Loop ◽  
Central Helix ◽  
Fold Type ◽  
Ab Initio Structure

AbstractMembers of the CPA/AT transporter superfamily show significant structural variability. All previously known members consist of an inverted duplicated repeat unit that folds into two separate domains, the core and the scaffold domain. Crucial for its transporting function, the central helix in the core domain is a noncanonical transmembrane helix, which can either be in the form of a broken helix or a reentrant helix. Here, we expand the structural knowledge of the CPA/AT family by using contact-prediction-based protein modelling. We show that the N-terminal domains of the Pfam families; PSE (Cons_hypoth698 PF03601), Lysine exporter (PF03956) and LrgB (PF04172) families have a previously unseen reentrant-helix-reentrant fold. The close homology between PSE and the Sodium-citrate symporter (2HCT) suggests that the new fold originates from the truncation of an ancestral reentrant protein, caused by the loss of the C-terminal reentrant helix. To compensate for the lost reentrant helix one external loop moves into the membrane to form the second reentrant helix, highlighting the adaptability of the CPA/AT transporters. This study also demonstrates that the most recent deep-learning-based modelling methods have become a useful tool to gain biologically relevant structural, evolutionary and functional insights about protein families.

scholarly journals The Core Domain of Chemokines Binds CCR5 Extracellular Domains while Their Amino Terminus Interacts with the Transmembrane Helix Bundle

2002 ◽  
Vol 278 (7) ◽  
pp. 5179-5187 ◽  
Author(s):  
Cédric Blanpain ◽  
Benjamin J. Doranz ◽  
Antoine Bondue ◽  
Cédric Govaerts ◽  
Anne De Leener ◽  
...  
Keyword(s):  
Transmembrane Helix ◽  
Amino Terminus ◽  
Core Domain ◽  
Helix Bundle ◽  
The Core ◽  
Extracellular Domains

scholarly journals Investigation of the Wilson gene ATP7B transcriptional start site and the effect of core promoter alterations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Clemens Höflich ◽  
Angela Brieger ◽  
Stefan Zeuzem ◽  
Guido Plotz
Keyword(s):  
Wilson Disease ◽  
Transcription Initiation ◽  
Transcriptional Activity ◽  
Core Promoter ◽  
Transcriptional Start Site ◽  
Copper Metabolism ◽  
Biologically Relevant ◽  
The Core ◽  
Translational Start

AbstractPathogenic genetic variants in the ATP7B gene cause Wilson disease, a recessive disorder of copper metabolism showing a significant variability in clinical phenotype. Promoter mutations have been rarely reported, and controversial data exist on the site of transcription initiation (the core promoter). We quantitatively investigated transcription initiation and found it to be located in immediate proximity of the translational start. The effects human single-nucleotide alterations of conserved bases in the core promoter on transcriptional activity were moderate, explaining why clearly pathogenic mutations within the core promoter have not been reported. Furthermore, the core promoter contains two frequent polymorphisms (rs148013251 and rs2277448) that could contribute to phenotypical variability in Wilson disease patients with incompletely inactivating mutations. However, neither polymorphism significantly modulated ATP7B expression in vitro, nor were copper household parameters in healthy probands affected. In summary, the investigations allowed to determine the biologically relevant site of ATP7B transcription initiation and demonstrated that genetic variations in this site, although being the focus of transcriptional activity, do not contribute significantly to Wilson disease pathogenesis.

scholarly journals FOLDING ELASTIC TRANSMEMBRANE HELICES TO FIT IN A LOW-RESOLUTION IMAGE BY ELECTRON MICROSCOPY

2011 ◽  
Vol 09 (supp01) ◽  
pp. 37-50 ◽  
Author(s):  
YUTAKA UENO ◽  
KAZUNORI KAWASAKI ◽  
OSAMU SAITO ◽  
MASAFUMI ARAI ◽  
MAKIKO SUWA
Keyword(s):  
Membrane Proteins ◽  
Structure Prediction ◽  
Molecular Model ◽  
Imaging Techniques ◽  
Transmembrane Helix ◽  
Prediction Method ◽  
Molecular Shape ◽  
Coarse Grained ◽  
Transmembrane Helices ◽  
Low Resolution

Structure prediction of membrane proteins could be constrained and thereby improved by introducing data of the observed molecular shape. We studied a coarse-grained molecular model that relied on residue-based dummy atoms to fold the transmembrane helices of a protein in the observed molecular shape. Based on the inter-residue potential, the α-helices were folded to contact each other in a simulated annealing protocol to search optimized conformation. Fitting the model into a three-dimensional volume was tested for proteins with known structures and resulted in a fairly reasonable arrangement of helices. In addition, the constraint to the packing transmembrane helix with the two-dimensional region was tested and found to work as a very similar folding guide. The obtained models nicely represented α-helices with the desired slight bend. Our structure prediction method for membrane proteins well demonstrated reasonable folding results using a low-resolution structural constraint introduced from recent cell-surface imaging techniques.

scholarly journals Crystal Structure of African Swine Fever Virus pS273R Protease and Implications for Inhibitor Design

2020 ◽  
Vol 94 (10) ◽  
Author(s):  
Guobang Li ◽  
Xiaoxia Liu ◽  
Mengyuan Yang ◽  
Guangshun Zhang ◽  
Zhengyang Wang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structural Information ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Hydrolytic Activity ◽  
Viral Disease ◽  
Fever Virus ◽  
Dna Virus ◽  
Core Domain ◽  
The Core

ABSTRACT African swine fever (ASF) is a highly contagious hemorrhagic viral disease of domestic and wild pigs that is responsible for serious economic and production losses. It is caused by the African swine fever virus (ASFV), a large and complex icosahedral DNA virus of the Asfarviridae family. Currently, there is no effective treatment or approved vaccine against the ASFV. pS273R, a specific SUMO-1 cysteine protease, catalyzes the maturation of the pp220 and pp62 polyprotein precursors into core-shell proteins. Here, we present the crystal structure of the ASFV pS273R protease at a resolution of 2.3 Å. The overall structure of the pS273R protease is represented by two domains named the “core domain” and the N-terminal “arm domain.” The “arm domain” contains the residues from M1 to N83, and the “core domain” contains the residues from N84 to A273. A structure analysis reveals that the “core domain” shares a high degree of structural similarity with chlamydial deubiquitinating enzyme, sentrin-specific protease, and adenovirus protease, while the “arm domain” is unique to ASFV. Further, experiments indicated that the “arm domain” plays an important role in maintaining the enzyme activity of ASFV pS273R. Moreover, based on the structural information of pS273R, we designed and synthesized several peptidomimetic aldehyde compounds at a submolar 50% inhibitory concentration, which paves the way for the design of inhibitors to target this severe pathogen. IMPORTANCE African swine fever virus, a large and complex icosahedral DNA virus, causes a deadly infection in domestic pigs. In addition to Africa and Europe, countries in Asia, including China, Vietnam, and Mongolia, were negatively affected by the hazards posed by ASFV outbreaks in 2018 and 2019, at which time more than 30 million pigs were culled. Until now, there has been no vaccine for protection against ASFV infection or effective treatments to cure ASF. Here, we solved the high-resolution crystal structure of the ASFV pS273R protease. The pS273R protease has a two-domain structure that distinguishes it from other members of the SUMO protease family, while the unique “arm domain” has been proven to be essential for its hydrolytic activity. Moreover, the peptidomimetic aldehyde compounds designed to target the substrate binding pocket exert prominent inhibitory effects and can thus be used in a potential lead for anti-ASFV drug development.

scholarly journals Cryo-EM Structures of Prestin and the Molecular Basis of Outer Hair Cell Electromotility

2021 ◽  
Author(s):  
Navid Bavi ◽  
Michael D Clark ◽  
Gustavo F Contreras ◽  
Rong Shen ◽  
Bharat Reddy ◽  
...  
Keyword(s):  
Outer Hair Cell ◽  
Binding Pocket ◽  
Structural Features ◽  
Outer Hair Cells ◽  
Anion Binding ◽  
Structural Basis ◽  
Inhibition Mechanism ◽  
Core Domain ◽  
The Core ◽  
Voltage Dependent

The voltage-dependent motor protein, Prestin (SLC26A5) is responsible for the electromotive behavior of outer hair cells (OHCs). Here, we determined the structure of dolphin Prestin in complex with Cl- and the inhibitor Salicylate using single particle cryo-electron microscopy. These structures establish the specific structural features of mammalian Prestin and reveal small but significant differences with the transporter members of the SLC26 family of membrane proteins. Comparison with SLC26A9 point to conformational differences in the special relationship between the core and gate domains. Importantly, we highlight substantial alterations to the hydrophobic footprint of Prestin as it relates to the membrane, which point to a potential influence of Prestin on its surrounding lipid. The structure of Prestin bound to the inhibitor Salicylate confirms the nature of the anion binding pocket, formed by TM3 and TM10 in the Core domain and a set of anion coordinating residues which include Q97, F101, F137, S398 and R399. The presence of a well-defined density for Salycilate points to an inhibition mechanism based on competition for the anion-binding pocket of Prestin. These observations illuminate the structural basis of Prestin electromotility, a key component in the mammalian cochlear amplifier.

scholarly journals Co-producing a multi-stakeholder Core Outcome Set for distal Tibia and Ankle fractures (COSTA): a study protocol

Trials ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Nathan A. Pearson ◽  
Elizabeth Tutton ◽  
Alexander Joeris ◽  
Stephen Gwilym ◽  
Richard Grant ◽  
...  
Keyword(s):  
Core Outcome Set ◽  
Distal Tibia ◽  
Ankle Fractures ◽  
Core Outcome ◽  
Core Domain ◽  
Outcome Reporting ◽  
The Core ◽  
Outcome Set ◽  
Multi Stakeholder ◽  
Core Domain Set

Abstract Background Ankle fracture is a common injury with a strong evidence base focused on effectiveness of treatments. However, there are no reporting guidelines on distal tibia and ankle fractures. This has led to heterogeneity in outcome reporting and consequently, restricted the contribution of evidence syntheses. Over the past decade, core outcome sets have been developed to address this issue and are available for several common fractures, including those of the hip, distal radius, and open tibial fractures. This protocol describes the process to co-produce—with patient partners and other key stakeholders—a multi-stakeholder derived Core Outcome Set for distal Tibia and Ankle fractures (COSTA). The scope of COSTA will be for clinical trials. Methods The study will have five-stages which will include the following: (i) systematic reviews of existing qualitative studies and outcome reporting in randomised controlled trial studies to inform a developing list of potential outcome domains; (ii) qualitative interviews (including secondary data) and focus groups with patients and healthcare professionals to explore the impact of ankle fracture and the outcomes that really matter; (iii) generation of meaningful outcome statements with the study team, international advisory group and patient partners; (iv) a multi-round, international e-Delphi study to achieve consensus on the core domain set; and (v) an evidence-based consensus on a core measurement set will be achieved through a structured group consensus meeting, recommending best assessment approaches for each of the domains in the core domain set. Discussion Development of COSTA will provide internationally endorsed outcome assessment guidance for clinical trials for distal tibia and ankle fractures. This will enhance comparative reviews of interventions, potentially reducing reporting bias and research waste.

scholarly journals The two major membrane skeletal proteins (articulins) of Euglena gracilis define a novel class of cytoskeletal proteins.

1992 ◽  
Vol 118 (6) ◽  
pp. 1465-1475 ◽  
Author(s):  
J A Marrs ◽  
G B Bouck
Keyword(s):  
Amino Acid ◽  
Fusion Protein ◽  
Euglena Gracilis ◽  
Cytoskeletal Proteins ◽  
Cdna Clones ◽  
Thin Sections ◽  
Core Domain ◽  
The Core ◽  
Amino Acid Repeats ◽  
Peptide Maps

60% of the peripheral membrane skeleton of Euglena gracilis consists of equimolar amounts of two proteins (articulins) with M(r)s in SDS gels of 80 and 86 kD. To understand eventually how these proteins assemble and function in maintaining cell form and membrane integrity we have undertaken a molecular characterization of articulins. A lambda gt11 expression library constructed from Euglena gracilis mRNAs was screened with antibodies against both articulins. Two sets of cDNAs were recovered, and evidence from three independent assays confirmed that both sets encoded articulins: (a) Anti-articulin antibodies recognized a high molecular weight beta-galactosidase (beta-gal) fusion protein expressed in bacteria infected with lambda gt11 cDNA clones. (b) Antibodies generated against the bacterially expressed beta-gal fusion protein identified one or the other articulin in Western blots of Euglena proteins. These antibodies also localized to the membrane skeletal region in thin sections of Euglena. (c) Peptide maps of the beta-gal fusion protein were similar to peptide maps of Euglena articulins. From the nucleotide sequence of the two sets of cDNAs an open reading frame for each articulin was deduced. In addition to 37% amino acid identity and overall structural similarity, both articulins exhibited a long core domain consisting of over 30 12-amino acid repeats with the consensus VPVPV--V--. Homology plots comparing the same or different articulins revealed larger, less regular repeats in the core domain that coincided with predicted turns in extended beta-sheets. Outside the core domain a short hydrophobic region containing four seven-amino acid repeats (consensus: APVTYGA) was identified near the carboxy terminus of the 80-kD articulin, but near the amino terminus of the 86-kD articulin. No extensive sequence similarities were found between articulins and other protein sequences in various databanks. We conclude that the two articulins are related members of a new class of membrane cytoskeletal proteins.

scholarly journals Stability of the core domain of p53: insights from computer simulations

2008 ◽  
Vol 9 (Suppl 1) ◽  
pp. S17 ◽  
Author(s):  
Arumugam Madhumalar ◽  
Derek Smith ◽  
Chandra Verma
Keyword(s):  
Computer Simulations ◽  
Core Domain ◽  
The Core
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