• We have established homology models of the human TWIST1 homodimer and heterodimers (formed with the E12 partner) bound to their target DNA sequences. (proteopedia.org)
  • The established homology models (including DNA sequences) were visualized with the VMD 1.9.1 software. (proteopedia.org)
  • In this work, homology models of both proteins were constructed and analyzed for a number of structural properties. (nih.gov)
  • HSSP (Homology-derived Secondary Structure of Proteins) is a database that combines structural and sequence information about proteins. (wikipedia.org)
  • This database has the information of the alignment of all available homologs of proteins from the PDB database As a result of this, HSSP is also a database of homology-based implied protein structures. (wikipedia.org)
  • Based on the genome sequencing results, an analysis of structural proteins and prediction of putative microRNAs of Hz-2V was performed. (umass.edu)
  • The viral genome encodes four structural capsid proteins (VP1 to VP4) and seven nonstructural (NS) proteins, the leader Lb/ab protease, and proteins encoded in the P2 (2B and 2C) and P3 (3A, 3B, 3C, and 3D) regions ( 9 ). (asm.org)
  • The structural models of the IF proteins were generated by homology modelling. (uni-duesseldorf.de)
  • Nearly all proteins have structural similarities with other proteins, and in some of these cases, share a common evolutionary origin. (berkeley.edu)
  • The Structural Classification of Proteins - extended ( SCOPe ) knowledgebase aims to provide an accurate, detailed, and comprehensive description of the structural and evolutionary relationships amongst all proteins of known structure, along with resources for analyzing the protein structures and their sequences. (berkeley.edu)
  • SCOPe: Structural Classification of Proteins - extended. (berkeley.edu)
  • Cryo-EM is exceptionally well suited for molecular systems traditionally challenging for structural characterization, including membrane proteins and large and heterogeneous assemblies. (emory.edu)
  • Their N-terminal hydrophilic domains may interact with cytoskeletal proteins and therefore play a cell structural role. (tcdb.org)
  • The results show that nonnative proteins are more structured and less solvent exposed than commonly believed. (lu.se)
  • Inferences about hydration have usually been indirect (where the ous structural and dynamic information about the internal peptide chain is not, there is solvent) or have relied on uncertain (buried) and external (surface) hydration of globular proteins in premises. (lu.se)
  • The resulting accumulation of proteins impairs microtubule function, leading to problems with cell division and migration. (medlineplus.gov)
  • Our results advance our understanding of PI3K biology and pave the way for the development of specific inhibitors of class II PI3K function with wide applications in biomedicine. (nature.com)
  • The project should involve both studies of protein function by the applicant researchers and structural studies by the PSI:Biology network. (nih.gov)
  • The Liang Laboratory is keen to exploit our structural biology (cryo-EM & x-ray crystallography) and biochemistry expertise to elucidate the molecular machinery and associated mechanisms of traditionally challenging and exciting biological systems through collaboration. (emory.edu)
  • He is the Professor of Medical Structural Biology at Lund University. (lu.se)
  • Interstingly, Hz-2V showed 93.5% of sequence homology with Hz-1V and with other nudiviruses, hytrosaviruses, and polydnaviruses. (umass.edu)
  • Our long-term goal is to create residue-level structural models using the cryoEM images, sequence information, and all-atom simulations, building on our modeling studies of RNA folding intermediates. (openwetware.org)
  • PlGF and VEGF share primary structural as well as limited amino acid sequence homology with the A and B chains of PDGF. (reliatech.de)
  • We describe the predatory sequence of P. phalangioides when using gumfoot lines, and discuss possible behavioural homologies between pholcids and araneoids. (bvsalud.org)
  • Including such artifacts can result in similarity between non-homologous sequences. (berkeley.edu)
  • The homology model suggests a high structural similarity with human PRX3. (bvsalud.org)
  • A more optimized cavity system and amino acid replacements resulting in increased conformational rigidity may also contribute to the higher stability of HydSL. (nih.gov)
  • However, even within one related group (bacteria, yeasts and fungi, mammals), DAAOs show very low homology between amino acid sequences. (actanaturae.ru)
  • As a result of alternative splicing, three PlGF RNAs encoding monomeric human PlGF-1, PlGF-2 and PlGF-3 isoform precursors containing 149, 179 and 219 amino acid residues, respectively, have been described. (reliatech.de)
  • The PfTRAMP homologue in P. vivax , here denoted as PvTRAMP, is a 340-amino-acid long antigen encoded by a single exon that could have a potential role in cytoadherence, as indicated by the presence of a thrombospondin structural homology repeat (TSR) domain. (biomedcentral.com)
  • Mauno Vihinen is well-known for his experience and interest in investigating variations and their effects whether they emerge at molecular levels (DNA, RNA protein), in structural context or in the cellular networks and pathways. (lu.se)
  • He has contributed significantly to the state-of-the-art by frequently presenting novel ideas, methods and results and have pioneered several important proof-of-concepts relevant for the project, including the conceptualization of DNA, RNA and protein variation to Variation Ontology (Vihinen, Genome Res . (lu.se)
  • In addition, a homology model of Raf-1 was also constructed using the crystal structure of the kinase domain of B-Raf isoform with one of the most active Raf-1 inhibitors (48) inside the active site. (unboundmedicine.com)
  • Glioblastoma (GBM), a very aggressive and incurable tumor, often results from constitutive activation of EGFR (epidermal growth factor receptor) and of phosphoinositide 3-kinase (PI3K). (sdbonline.org)
  • IKK epsilon is an IKK-related kinase with 30% structural homology to IKK alpha and beta, and is present in a subset of IKK complexes. (rndsystems.com)
  • Results: Data addressing the function of vectors harbouring genes specifically encoding ricin, saporin, lunasin , linamarase, and tomato thymidine kinase 1 under the control of different promoters are summarised here. (weeksmd.com)
  • 11] The resultant mutations were interpreted to result in local structural changes in the ACVR1 protein, as revealed by interrogating homology models of the native and mutated ACVR1 kinase domains. (medscape.com)
  • The comparison of the models reveals that the higher stability of HydSL can be attributed to increased inter-subunit electrostatic interactions: the homology models reliably predict that HydSL contains at least five more inter-subunit ion pairs than HupSL. (nih.gov)
  • The results are in accord with the general observation that with increasing temperature, the role of electrostatic interactions in protein stability increases. (nih.gov)
  • The current view of protein folding and stability is largely based on SAXS and DLS data13-16 and the extensive exposure of hydropho- a generic structural classification into native (N), compact dena- bic residues suggested by the finding that the heat capacity of the tured or molten globule (MG), and unfolded or denatured (D) MG state is midway between that of the N and D states7 have been conformational states1-10. (lu.se)
  • We are also predicting protein structures by simulating folding pathways, taking advantage of our experimental results and an approach that dynamically integrates local and global information. (openwetware.org)
  • In addition, we are refining crystal structures and homology models using our new move-set and statistical potentials. (openwetware.org)
  • In conclusion, our data support the view that interhelical loops within the bHLH play a determining role in maintaining TWIST1-DNA complex structures and provide a structural explanation for the loss of function associated with several TWIST1 mutations/insertions observed in SC patients. (proteopedia.org)
  • Using a homology search, we obtained a set of candidate sequences, modelled the tertiary structure of the selected enzymes, and compared them with experimental and model structures of known DAAOs. (actanaturae.ru)
  • The search for structural correlates of idiotypes could not be framed in a simple picture, but our data suggest that similar idiotopes may result from different interacting primary structures, leading to structural homologies that should be visualized at three-dimensional level. (rupress.org)
  • Homologies were found to 38 of the 113 ORFs predicted for genes with known functions. (umass.edu)
  • Four of structural genes, p11.7, p15.1, p28.4, and p31.7 were identified by matrix assisted laser desorption/ionization time-of-flight mass spectroscopy. (umass.edu)
  • As a result, many (if not most) DAAO genes remain either unannotated or incorrectly annotated. (actanaturae.ru)
  • Analysis of the protein sequences of the three CpHsps indicated the presence of 83 amino acids with homology to the a-crystallin domain. (usda.gov)
  • Although the C-terminal sequences adjacent to the bHLH domain, constitute a protein interaction site essential for TWIST function [4] [5] , we reasoned that a structural model restricted to the bHLH domains should provide additional insights into the TWIST-DNA interface and highlight functional differences between TWIST1 complexes. (proteopedia.org)
  • We unravel a coincident mechanism of lipid-induced activation of PI3KC2α at membranes that involves large-scale repositioning of its Ras-binding and lipid-binding distal Phox-homology and C-C2 domains, and can serve as a model for the entire class II PI3K family. (nature.com)
  • Whereas many of the structural characteristics, homology and cross reactivity of food allergens have been explained, specific immunological and biophysical properties of the allergens that contribute to IgE antibody formation are not fully understood. (usda.gov)
  • However, their structural characteristics are unknown, and possible inhibitors have not been proposed. (bvsalud.org)
  • The aim was to describe in detail some structural characteristics of TcMPX and compare it with several PRXs to find possible similarities and repositioning the antibiotic Thiostrepton as a potential inhibitor molecule. (bvsalud.org)
  • Results murella species helped clarify its clinical characteristics of WGS analysis of TY48 were deposited in BioProject and epidemiology. (cdc.gov)
  • Specific structural features and functional similarities, such as protease activity, have also been associated with both food and inhaled allergens (i.e. pollen, cat, dog, dust mite, etc). (usda.gov)
  • This is also important in order to hypothesize primary homologies ( sensu de Pinna, 1991, 1997), that is, topographical similarities based on Remane's criteria of homology (adapted to the behavioural domain - see Greene, 1994). (bvsalud.org)
  • Myosin-1A targets to microvilli using multiple membrane binding motifs in the tail homology 1 (TH1) domain. (nih.gov)
  • This is indeed a problem about a basic question in evolutionary analyses, that is, the statement of homology. (bvsalud.org)
  • We also constructed, by homology modeling, a theoretical structure of the pUL105 N-terminal domain which indicates that the mutated conserved amino acids in this domain could be involved in ATP hydrolysis. (frontiersin.org)
  • For each of the CpHsps, the a-crystallin domain was surrounded by divergent N- and C-terminal regions, consistent with the conserved structural features of sHsps. (usda.gov)
  • CDK8 can directly interact with Mad in vitro through the linker region between the DNA-binding MH1 (Mad homology 1) domain and the carboxy terminal MH2 (Mad homology 2) transactivation domain. (sdbonline.org)
  • The N-terminal Cu binding domain (CuBD-I) of APP shows structural homology to the Cu binding domain of Cu chaperons (Barnham et al. (springer.com)
  • Stress-Induced Accumulation of DcAOX1 and DcAOX2a Transcripts Coincides with Critical Time Point for Structural Biomass Prediction in Carrot Primary Cultures (Daucus carota L. (frontiersin.org)
  • PredictProtein--an open resource for online prediction of protein structural and functional features. (rostlab.org)
  • Homology-based inference sets the bar high for protein function prediction. (rostlab.org)
  • Conversely, the transcription of COX-2 yields a 4.5-kb mRNA that encodes a 70-kd protein with roughly 70-75% homology to the COX-1 protein. (medscape.com)
  • In the light of published experimental results, structural analysis of the transmembrane cavity suggests that the TM287-288-based CFTR model could correspond to a commonly occupied closed state, while the McjD-based model could represent an open state. (ucl.ac.uk)
  • Various software resources are also required to enable users to conveniently connect their experimental results with publicly, and application specific, bioinformatics databases and tools. (lu.se)
  • Nevertheless, while Q44R led to recovery of viruses that maintained the mutation, Q44D resulted in selection of infective viruses with substitution D44E with acidic charge but with structural features similar to those of the parental virus, suggesting that Q44 is involved in functions other than 3A dimerization. (asm.org)
  • Results of the mutation analysis on 181 pathogenic and 46 neutral variants by 11 different methods. (biomedcentral.com)
  • A minimally hypomorphic mutation in Btk resulting in reduced B cell numbers but no clinical disease. (lu.se)
  • The required atomic structural models were received in case of the KBD-B by the completion of a missing loop region in the crystal structure 1LM7. (uni-duesseldorf.de)
  • Using a homology strategy, in silico models based on the murine NEUROD1/E47 X-ray structure were established and also subjected to dynamics simulations. (proteopedia.org)
  • The models capture the important role played by Phe337 as a filter/gating residue and provide structural information on the conformational transition from closed to open channel. (ucl.ac.uk)
  • In this work, we explored possible conformational states of the CFTR gating cycle by means of homology modeling. (ucl.ac.uk)
  • The classical active IKK complex, composed of IKK alpha, IKK beta, and two forms of processed IKK gamma, phosphorylates and inactivates IkB, resulting in the release and nuclear translocation of active NFkB. (rndsystems.com)
  • Our results demonstrate a novel mechanistic model for ROS-mediated inhibition of Orai1 and identify a candidate residue for pharmaceutical intervention. (nature.com)
  • Activation of AMPK by low energy supply and phosphorylation of LKB1 results in an inhibition of mTOR , thus decreasing energy-consuming processes, in particular translation and, thus, cell growth. (sdbonline.org)
  • In a carrot primary culture system (PCS), this tool allowed identifying an early peak related with structural biomass formation during lag phase of growth, around the 4th day of culture. (frontiersin.org)
  • and probable cases of primary structural homology. (fapesp.br)
  • The results of best 3D-QSAR model were compared with structure-based studies using the Raf-1 homology model. (unboundmedicine.com)
  • It is expected that the results from these collaborations will contribute to understanding many basic and biomedically important research problems as well as to our fundamental understanding of protein structure. (nih.gov)
  • Although these loops do not have a structural organization strictly speaking, H-bond formation can stiffen their structure. (proteopedia.org)
  • We explored the structure of DNAJB6 using a combination of structural methods. (lu.se)
  • The resulting first hypothesis for the interaction region on the KBD B was based on a „computational chemistry " aided approach. (uni-duesseldorf.de)
  • Despite a number of findings supporting the hypothesis of environmental Cu modulating AD, our results demonstrate that oral Cu intake has neither a detrimental nor a promoting effect on the progression of AD. (springer.com)
  • From the RNA standpoint, recent discoveries of the diverse roles structural RNAs play in gene expression, such as riboswitches, illustrate the importance of understanding their dynamics and folding as well. (openwetware.org)
  • This work opens up a whole new avenue of structural studies on non-coding RNAs. (openwetware.org)
  • The results of 3D-QSAR and docking studies validate each other and provided insight into the structural requirements for activity of this class of molecules as Raf-1 inhibitors. (unboundmedicine.com)
  • Once the study is available, the studies with the structural analogue will be replaced with the extended OECD 422 study using Delta Damascone. (europa.eu)
  • The results of this work support conducting further studies with PvTRAMP to evaluate its immunogenicity and protection-inducing ability in the Aotus animal model. (biomedcentral.com)
  • Structural studies of the D and MG states have naturally focused ed in controversy23. (lu.se)
  • Mammalian PI3Ks are grouped into three classes based on their structural organization. (nature.com)
  • Complexes of Vps34, the sole class III PI3K member, produce PI 3-phosphate (PI(3)P) in the endolysosomal system and during autophagy to regulate vesicle-mediated sorting en route to lysosomes 1 . (nature.com)
  • These results demonstrated that DspF residues L32, E39, E44, H55 and F78 are important for virulence, and yeast-two-hybrid experiments showed that DspF residues E39, E44 and H55 are required for binding to DspE. (actahort.org)
  • Lysine-specific crosslinking mass spectrometry provided distance constraints to select a homology model of the DNAJB6 monomer, which was subsequently used in crosslink-assisted docking to generate a dimer model, revealing that a peptide-binding cleft lined with S/T-residues is formed at the monomer-monomer interface. (lu.se)
  • The results will be compared between the species and their different types of ligules, being subsequently confronted with the available data in the literature and discussed inside Poaceae. (fapesp.br)
  • These results suggest that CDK8 and CycC, together with a few other subunits of the MED complex, may coordinate with other transcription cofactors in regulating Mad-dependent transcription during wing development in Drosophila. (sdbonline.org)
  • We have previously reported that post-transplant lymphoma patients have an acquired deficiency of signal transducer and activator of transcription 4, which results in defective IFNγ production during clinical immunotherapy. (weeksmd.com)
  • To further characterize the DspE-DspF interaction, computational methods were used to create a homology-based structural model of DspF. (actahort.org)
  • The lack of structural information on PI3KC2α and related class II PI3Ks has also greatly hampered the development of isoform-selective pharmacological inhibitors for clinical applications. (nature.com)
  • Our results show that Thiostrepton reduces the proliferation of T. cruzi epimastigotes, cell-derived trypomastigotes, and blood trypomastigotes with low cytotoxicity on Vero cells. (bvsalud.org)
  • Regardless of the etiology, a deficiency of cyclooxygenase (COX), a key regulatory enzyme in the synthetic pathway of eicosanoid production, results in beneficial and detrimental physiologic conditions relative to imbalances of the eicosanoids. (medscape.com)
  • Lack of structural data hampers a global understanding of CFTR, and thus the development of rational approaches directly targeting defective CFTR. (ucl.ac.uk)
  • These results suggest that MASP49 can be considered a virulence factor in T. cruzi, and a better understanding of its role in the infection process is necessary. (bvsalud.org)
  • These throat abnormalities can cause difficulty swallowing or breathing, in some cases resulting in recurrent pneumonia or life-threatening breathing problems. (medlineplus.gov)
  • By exploiting the nano-structural ~17 nm repeat pattern typical of myelin sheath, which gives rise to a distinct small angle scattering pattern, tomographic myelin maps in macroscopic tissue volumes were derived ( Fig. 1 ). (stanford.edu)
  • Interestingly, the resulting hyperplastic glia express high levels of key components of the lysosomal-autophagic compartment, including vacuolar-type H(+)-ATPase (V-ATPase) subunits and ref(2)P (refractory to Sigma P), the Drosophila homolog of SQSTM1/p62. (sdbonline.org)
  • Results showed that the first 51 amino acids of DspE were sufficient for minimal protein translocation into the host cell and that translocation levels increased with increasing DspE fragment length. (actahort.org)
  • In a 90-day oral study with its structural analogue Alpha-iso-methylionone, a NOAEL of 30 mg/kg bw/day was established based on increases in plasma levels of creatinine, total protein and cholesterol (indicators of liver effects), increases in absolute and relative weights of the kidneys and spleen, and microscopic changes in thyroid and bone marrow at the next dose level. (europa.eu)
  • Due to the structural and biochemical homology between IGF-2 and insulin, elevated levels of IGF-2 can result in hypoglycemia. (medscape.com)
  • Each year during the 1990s and early 2000s, rotavirus resulted in approximately 410,000 physician visits, 205,000-272,000 emergency department visits, and 55,000-70,000 hospitalizations among U.S. infants and children, with total annual direct and indirect costs of approximately $1 billion. (cdc.gov)
  • the majority had gastroenteritis, resulting annually during the 1990s and early 2000s in approximately 410,000 physician visits, 205,000-272,000 emergency department (ED) visits, 55,000-70,000 hospitalizations, and total annual direct and indirect costs of approximately $1 billion ( 5--9 ) ( Figure 1 ). (cdc.gov)
  • Based on this large body of available data, recent research in P. vivax malaria has made use of bioinformatics tools to identify and characterize new potential anti-malarial vaccine candidates by homology comparison (e.g. (biomedcentral.com)
  • Also, we employ x-ray crystallography and fluorescence light microscopy to provide complementary structural and dynamic information for challenging systems of significant biological importance. (emory.edu)