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Dongxiao Hao, Zhiwei Yang, Teng Gao, Zhiqi Tian, Lei Zhang, Shengli Zhang
Current cholesteryl ester transfer protein (CETP) inhibitors are designed based on the unglycosylated crystal structure, and most of them have failed to cure cardiovascular disease (CVD). It is particularly important for us to investigate the glycosylation structure of CETP (CETP-G) and effect of glycans on the structure and function of CETP. Here, we used a total of 3.0-μs molecular dynamics trajectories of nascent structure of CETP (CETP-N) and CETP-G to study their structural differentiations, to shed new light on the CETP-mediated lipid exchange...
May 3, 2018: Proteins
Eva Maria Steiner, Jeppe Lyngsø, Jodie E Guy, Gleb Bourenkov, Ylva Lindqvist, Thomas R Schneider, Jan Skov Pedersen, Gunter Schneider, Robert Schnell
RipA plays a vital role during cell division of Mycobacterium tuberculosis by degrading the cell wall peptidoglycan at the septum, allowing daughter cell separation. The peptidoglycan degrading activity relies on the NlpC/P60 domain, and as it is potentially harmful when deregulated, spatial and temporal control is necessary in this process. The N-terminal domain of RipA has been proposed to play an inhibitory role blocking the C-terminal NlpC/P60 domain. Accessibility of the active site cysteine residue is however not limited by the presence of the N-terminal domain, but by the lid-module of the inter-domain linker, which is situated in the peptide binding groove of the crystal structures of the catalytic domain...
May 2, 2018: Proteins
Jan Komárek, Eva Ivanov Kavková, Josef Houser, Aneta Horáčková, Jitka Ždánská, Gabriel Demo, Michaela Wimmerová
We report the characterization of the dimeric protein AB21 from Agaricus bisporus, one of the most commonly and widely consumed mushrooms in the world. The protein shares no significant sequence similarity with any protein of known function, and it is the first characterized member of its protein family. The coding sequence of the ab21 gene was determined and the protein was expressed in E. coli in a recombinant form. We demonstrated a high thermal and pH stability of AB21 and proved the weak affinity of the protein to divalent ions of some transition metals (nickel, zinc, cadmium and cobalt)...
May 2, 2018: Proteins
Scot Wherland, Israel Pecht
The three-dimensional structure of proteins, especially as determined by X-ray crystallography, is critical to the understanding of their function. However, the X-ray exposure may lead to damage that must be recognized and understood to interpret the crystallographic results. This is especially relevant for proteins with transition metal ions that can be oxidized or reduced. The detailed study of proteins in aqueous solution by the technique of pulse radiolysis has provided a wealth of information on the production and fate of radicals that are the same as those produced by X-ray exposure...
April 30, 2018: Proteins
Pedro Jimenez-Sandoval, Ezequiel A Madrigal-Carrillo, Hugo A Santamaría-Suárez, Daniel Maturana, Itzel Rentería-González, Claudia G Benitez-Cardoza, Alfredo Torres-Larios, Luis G Brieba
Antibodies recognize protein targets with great affinity and specificity. However, posttranslational modifications and the presence of intrinsic disulfide-bonds pose difficulties for their industrial use. The immunoglobulin fold is one of the most ubiquitous folds in nature and it is found in many proteins besides antibodies. An example of a protein family with an immunoglobulin-like fold is the Cysteine Protease Inhibitors (ICP) family I42 of the MEROPs database for protease and protease inhibitors. Members of this protein family are thermostable and do not present internal disulfide bonds...
April 26, 2018: Proteins
Saurav Mallik, Sudipto Basu, Suman Hait, Sudip Kundu
Do coding and regulatory segments of a gene co-evolve with each-other? Seeking answers to this question, here we analyze the case of Escherichia coli ribosomal protein S15, that represses its own translation by specifically binding its messenger RNA (rpsO mRNA) and stabilizing a pseudoknot structure at the upstream untranslated region, thus trapping the ribosome into an incomplete translation initiation complex. In the absence of S15, ribosomal protein S1 recognizes rpsO and promotes translation by melting this very pseudoknot...
April 21, 2018: Proteins
Md Mofijul Islam, Sanjay Saha, Md Mahmudur Rahman, Swakkhar Shatabda, Dewan Md Farid, Abdollah Dehzangi
Glycation is chemical reaction by which sugar molecule bonds with a protein without the help of enzymes. This is often cause to many diseases and therefore the knowledge about glycation is very important. In this paper, we present iProtGly-SS, a protein lysine glycation site identification method based on features extracted from sequence and secondary structural information. In the experiments, we found the best feature groups combination: Amino Acid Composition, Secondary Structure Motifs and Polarity. We used support vector machine classifier to train our model and used an optimal set of features using a group based forward feature selection technique...
April 20, 2018: Proteins
Sha Sha Li, Bao Qiong Li, Jin Jin Liu, Shao Hua Lu, Hong Lin Zhai
Circular dichroism (CD) spectroscopy is a widely used technique for the evaluation of protein secondary structures that has a significant impact for the understanding of molecular biology. However, the quantitative analysis of protein secondary structures based on CD spectra is still a hard work due to the serious overlap of the spectra corresponding to different structural motifs. Here, Tchebichef image moment (TM) approach is introduced for the first time, which can effectively extract the chemical features in CD spectra for the quantitative analysis of protein secondary structures...
April 20, 2018: Proteins
Ingemar André, Sinisa Bjelic
The coiled coil structural motif consists of alpha helices supercoiling around each other to form staggered knobs-into-holes packing. Such structures are deceptively simple, especially as they often can be described with parametric equations, but are known to exist in various conformations. Even the simplest systems, consisting of two monomers, can assemble into a wide range of states. They can form canonical as well as noncanonical coiled coils, be parallel or antiparallel, where helices associate with different degrees of shift, tilt, and rotation...
April 20, 2018: Proteins
Bercem Dutagaci, Lim Heo, Michael Feig
A refinement protocol based on physics-based techniques established for water soluble proteins is tested for membrane protein structures. Initial structures were generated by homology modeling and sampled via molecular dynamics simulations in explicit lipid bilayer and aqueous solvent systems. Snapshots from the simulations were selected based on scoring with either knowledge-based or implicit membrane-based scoring functions and averaged to obtained refined models. The protocol resulted in consistent and significant refinement of the membrane protein structures similar to the performance of refinement methods for soluble proteins...
April 20, 2018: Proteins
Prachi Mehrotra, Vimla Kany G Ami, Narayanaswamy Srinivasan
The overall function of a multi-domain protein is determined by the functional and structural interplay of its constituent domains. Traditional sequence alignment-based methods commonly utilize domain-level information and provide classification only at the level of domains. Such methods are not capable of taking into account the contributions of other domains in the proteins, and domain-linker regions and classify multi-domain proteins. An alignment-free protein sequence comparison tool, CLAP (CLAssification of Proteins) was previously developed in our laboratory to especially handle multi-domain protein sequences without a requirement of defining domain boundaries and sequential order of domains...
April 20, 2018: Proteins
Anni Kauko, Kirsi Lehto
The origin of eukaryotes is one of the central transitions in the history of life; without eukaryotes there would be no complex multicellular life. The most accepted scenarios suggest the endosymbiosis of a mitochondrial ancestor with a complex archaeon, even though the details regarding the host and the triggering factors are still being discussed. Accordingly, phylogenetic analyses have demonstrated archaeal affiliations with key informational systems, while metabolic genes are often related to bacteria, mostly to the mitochondrial ancestor...
April 20, 2018: Proteins
Nathalie Lagarde, Alessandra Carbone, Sophie Sacquin-Mora
Protein-protein interactions control a large range of biological processes and their identification is essential to understand the underlying biological mechanisms. To complement experimental approaches, in silico methods are available to investigate protein-protein interactions. Cross-docking methods, in particular, can be used to predict protein binding sites. However, proteins can interact with numerous partners and can present multiple binding sites on their surface, which may alter the binding site prediction quality...
April 17, 2018: Proteins
Gunasekaran Dhandapani, Thoduvayil Sikha, Aarti Rana, Rahul Brahma, Yusuf Akhter, Madathiparambil Gopalakershnan Madanan
Proteomes of pathogenic Leptospira interrogans and L. borgpetersenii and the saprophytic L. biflexa were filtered through computational tools to identify Outer Membrane Proteins (OMPs) that satisfy the required biophysical parameters for their presence on the outer membrane. A total of 133, 130 and 144 OMPs were identified in L. interrogans, L. borgpetersenii and L. biflexa respectively which forms approximately 4% of proteomes. A holistic analysis of transporting and pathogenic characteristics of OMPs together with Clusters of Orthologous Groups (COGs) among the OMPs and their distribution across three species was made and put forward a set of 21 candidate OMPs specific to pathogenic leptospires...
April 10, 2018: Proteins
Steven T Gossert, Bibek Parajuli, Irwin Chaiken, Cameron F Abrams
The Dual-Action Virolytic Entry Inhibitors, or "DAVEI's," are a class of recombinant fusions of a lectin, a linker polypeptide, and a 15-residue fragment from the membrane-proximal external region (MPER) of HIV-1 gp41. DAVEI's trigger rupture of HIV-1 virions, and the interaction site between DAVEI MPER and HIV-1 lies in the gp41 component of the envelope glycoprotein Env. Here we explore the hypothesis that DAVEI MPER engages Env gp41 in a mode structurally similar to a crystallographic MPER trimer...
April 6, 2018: Proteins
Jia Wang, Jingfei Chen, Jingwen Li, Liaoyuan An, Yefei Wang, Qingshan Huang, Lishan Yao
A combined experimental and computational study is performed for arginine side chain stacking with the protein α-helix. Theremostability measurements of Aristaless homeodomain, a helical protein, suggest that mutating the arginine residue R106, R137 or R141, which has the guanidino side chain stacking with the peptide plane, to alanine, destabilizes the protein. The R-PP stacking has an energy of ∼0.2-0.4 kcal/mol. This stacking interaction mainly comes from dispersion and electrostatics, based on MP2 calculations with the energy decomposition analysis...
March 25, 2018: Proteins
Grigor Arakelov, Vahram Arakelov, Karen Nazaryan
Pyrin protein is the product of the MEFV gene, mutations in which cause manifestation of Familial Mediterranean Fever (FMF). Functions of pyrin are not completely clear. The secondary structure of the pyrin is represented with four domains and two motifs. Mutations p.M680I, p.M694V, p.M694I, p.K695R, p.V726A and p.A744S, which are located in the B30.2 domain of pyrin protein, are responsible for manifestation of the most common and severe forms of FMF. All the domains and the motifs of pyrin, are directly or indirectly, involved in the protein-protein interaction with proteins of apoptosis and regulate the cascade of inflammatory reactions, which is impaired due to pyrin mutations...
March 25, 2018: Proteins
Steven V Molinski, Vijay M Shahani, Adithya S Subramanian, Stephen S MacKinnon, Geoffrey Woollard, Marcon Laforet, Onofrio Laselva, Leonard D Morayniss, Christine E Bear, Andreas Windemuth
Cystic Fibrosis (CF) is caused by mutations in the CFTR gene, of which over 2000 have been reported to date. Mutations have yet to be analyzed in aggregate to assess their distribution across the tertiary structure of the CFTR protein, an approach that could provide valuable insights into the structure-function relationship of CFTR. In addition, the binding site of Class I correctors (VX-809, VX-661, and C18) is not well understood. In this study, exonic CFTR mutations and mutant allele frequencies described in 3 curated databases (ABCMdb, CFTR1, and CFTR2, comprising >130 000 data points) were mapped to 2 different structural models: a homology model of full-length CFTR protein in the open-channel state, and a cryo-electron microscopy core-structure of CFTR in the closed-channel state...
March 23, 2018: Proteins
Laura S Mitchell, Lucy J Colwell
Nanobodies are a class of antigen-binding protein derived from camelids that achieve comparable binding affinities and specificities to classical antibodies, despite comprising only a single 15 kDa variable domain. Their reduced size makes them an exciting target molecule with which we can explore the molecular code that underpins binding specificity - how is such high specificity achieved? Here we use a novel dataset of 90 non-redundant, protein-binding nanobodies with antigen-bound crystal structures to address this question...
March 22, 2018: Proteins
Suvethigaa Shanthirabalan, Jacques Chomilier, Mathilde Carpentier
A structural database of eleven families of chains differing by a single amino acid substitution has been built. Another structural dataset of 5 families with identical sequences has been used for comparison. The RMSD computed after a global superimposition of the mutated protein on each native one is smaller than the RMSD calculated among proteins of identical sequences. The effect of the perturbation is very local, and not necessarily the highest at the position of the mutation. A RMSD between mutated and native proteins is computed over a 3-residue or a 7-residue window at each position...
March 22, 2018: Proteins
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