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
2020 ◽  
Vol 94 (10) ◽  
Author(s):  
Guobang Li ◽  
Xiaoxia Liu ◽  
Mengyuan Yang ◽  
Guangshun Zhang ◽  
Zhengyang Wang ◽  
...  

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.


2021 ◽  
Author(s):  
Navid Bavi ◽  
Michael D Clark ◽  
Gustavo F Contreras ◽  
Rong Shen ◽  
Bharat Reddy ◽  
...  

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.


Trials ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Nathan A. Pearson ◽  
Elizabeth Tutton ◽  
Alexander Joeris ◽  
Stephen Gwilym ◽  
Richard Grant ◽  
...  

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.


1992 ◽  
Vol 118 (6) ◽  
pp. 1465-1475 ◽  
Author(s):  
J A Marrs ◽  
G B Bouck

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.


Biochemistry ◽  
1999 ◽  
Vol 38 (45) ◽  
pp. 15060-15060 ◽  
Author(s):  
Jacek Lubkowski ◽  
Zbigniew Dauter ◽  
Fan Yang ◽  
Jerry Alexandratos ◽  
George Merkel ◽  
...  

2014 ◽  
Vol 70 (a1) ◽  
pp. C1048-C1048
Author(s):  
Chiara Lee ◽  
Hae Joo Kang ◽  
Christoph von Ballmoos ◽  
Simon Newstead ◽  
Povilas Uzdavinys ◽  
...  

Sodium/proton (Na+/H+) antiporters, located at the plasma membrane in every cell, are vital for cell homeostasis. In humans, their dysfunction has been linked to diseases, such as hypertension, heart failure and epilepsy, and they are well-established drug targets. The best understood model system for Na+/H+ antiport is NhaA from Escherichia coli, for which both electron microscopy and crystal structures are available. NhaA is made up of two distinct domains: a core domain and a dimerization domain. In the NhaA crystal structure a cavity is located between the two domains, providing access to the ion-binding site from the inward-facing surface of the protein. Like many Na+/H+ antiporters, the activity of NhaA is regulated by pH, only becoming active above pH 6.5, at which point a conformational change is thought to occur. The only reported NhaA crystal structure so far is of the low pH inactivated form. Here we describe the active-state structure of a Na+/H+ antiporter, NapA from Thermus thermophilus, at 3 Å resolution, solved from crystals grown at pH 7.8. In the NapA structure, the core and dimerization domains are in different positions to those seen in NhaA, and a negatively charged cavity has now opened to the outside. The extracellular cavity allows access to a strictly conserved aspartate residue thought to coordinate ion binding directly, a role supported here by molecular dynamics simulations. To alternate access to this ion-binding site, however, requires a surprisingly large rotation of the core domain, some 200against the dimerization interface. We conclude that despite their fast transport rates of up to 1,500 ions per second, Na+/H+ antiporters operate by a two-domain rocking bundle model, revealing themes relevant to secondary-active transporters in general.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 700-700
Author(s):  
Yunzhe Lu ◽  
Alicia Rivera ◽  
Athar Chishti

Abstract Dematin is a critical component of the membrane junctional complex in red blood cells. It tethers the spectrin cytoskeleton proteins to the membrane and its genetic deletion in mice causes dissociation of the spectrin, actin and β-adducin from the membrane resulting in the collapse of the red blood cells (RBCs). As dematin lacks a transmembrane domain, it is still unclear how this critical component of the junctional complex is anchored to the RBC membrane. Our previous studies have shown that the multi-transmembrane glucose transporter-1 (GLUT1) interacts with dematin and β-adducin in human RBCs, suggesting a potential role for GLUT1 in recruiting dematin to the membrane. However, as mouse RBCs do not express a GLUT1 homologue, an equivalent membrane receptor for dematin and/or adducin in mice remains to be determined. Using multiple in vitro and in vivo biochemical assays, here we demonstrate that the ubiquitously expressed plasma membrane Na+/H+ exchanger, NHE1 (Slc9a1), is one of the receptors for dematin and β-adducin in mature mouse red blood cells. NHE1 directly interacts with the core domain of dematin. Moreover, the dematin headpiece domain mutant S381E, which binds to the core domain with a higher affinity than the wild type, abolished the biochemical interaction between dematin and NHE1. This observation suggests that NHE1 and dematin headpiece domain compete for the same binding site(s) on the core domain. Furthermore, this finding highlights a molecular mechanism whereby an intermolecular switch of dematin regulates its interaction with NHE1 by phosphorylation. Dematin and β-adducin directly interact with NHE1 at its membrane-proximal cytoplasmic domain, which in turn regulates NHE1 activity in response to growth factor stimuli and intracellular pH alterations. Accordingly,we observed an increased cellular sodium content in erythrocytes of dematin headpiece and adducin double knockout mice (DAKO), suggesting a higher NHE1 activity in DAKO erythrocytes. Unlike GLUT1, NHE1 is expressed in both mouse and human RBCs. Thus, our results provide a novel mechanism for linking NHE1 to membrane skeleton and multiple cell signaling pathways through dematin and adducin (Figure 1). Since NHE1 is one of the major regulators of intracellular pH and hypertonic stress, our findings raise the possibility that the dematin-adducin-NHE1 complex may modulate these functions in RBCs as well as in other cell types with broad impact on the regulation of the actin cytoskeleton and cell migration. Figure 1 Dematin and adducin link erythrocyte junctional complex to membrane via multiple receptors. A, WT RBC cytoskeleton. B, Mutant (DAKO) RBC cytoskeleton. Images show a grossly deranged membrane skeleton in DAKO as compared to wild type. Red arrows show enlarged pores and yellow arrows indicate the presence of aggregates. Bars correspond to 0.2 µM. C, Schematic diagram of dematin, adducin, and NHE1 linking the complex to multiple signaling pathways. D, Proposed new model of the erythrocyte junctional complex. Figure 1. Dematin and adducin link erythrocyte junctional complex to membrane via multiple receptors. A, WT RBC cytoskeleton. B, Mutant (DAKO) RBC cytoskeleton. Images show a grossly deranged membrane skeleton in DAKO as compared to wild type. Red arrows show enlarged pores and yellow arrows indicate the presence of aggregates. Bars correspond to 0.2 µM. C, Schematic diagram of dematin, adducin, and NHE1 linking the complex to multiple signaling pathways. D, Proposed new model of the erythrocyte junctional complex. Disclosures No relevant conflicts of interest to declare.


Nature ◽  
2003 ◽  
Vol 424 (6944) ◽  
pp. 35-41 ◽  
Author(s):  
Soichi Takeda ◽  
Atsuko Yamashita ◽  
Kayo Maeda ◽  
Yuichiro Maéda

Sign in / Sign up

Export Citation Format

Share Document