journal
MENU ▼
Read by QxMD icon Read
search

Proteins

journal
https://www.readbyqxmd.com/read/28646497/geometrical-principles-of-homomeric-%C3%AE-barrels-and-%C3%AE-helices-application-to-modelling-amyloid-protofilaments
#1
Steven Hayward, E James Milner-White
Examples of homomeric β-helices and β-barrels have recently emerged. Here we generalise the theory for the shear number in β-barrels to encompass β-helices and homomeric structures. We introduce the concept of the "β-strip", the set of parallel or antiparallel neighbouring strands, from which the whole helix can be generated giving it n-fold rotational symmetry. In this context the shear number is interpreted as the sum around the helix of the fixed register shift between neighbouring identical β-strips...
June 24, 2017: Proteins
https://www.readbyqxmd.com/read/28643349/a-qm-mm-study-of-the-catalytic-mechanism-of-sam-methyltransferase-rlmn-from-escherichia-coli
#2
Chenxiao Zhao, Lihua Dong, Yongjun Liu
RlmN is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the C2 methylation of adenosine 2503 (A2503) in 23S rRNA and adenosine 37 (A37) in several Escherichia coli transfer RNAs (tRNA). The catalytic reaction of RlmN is distinctly different from that of typical SAM-dependent methyltransferases that employs an SN 2 mechanism, but follows a ping-pong mechanism which involves the intermediate methylation of a conserved cysteine residue. Recently, the x-ray structure of a key intermediate in the RlmN reaction has been reported, allowing us to perform combined quantum mechanics and molecular mechanics (QM/MM) calculations to delineate the reaction details of RlmN at atomic level...
June 23, 2017: Proteins
https://www.readbyqxmd.com/read/28643343/alpha-beta-hydrolases-a-unique-structural-motif-coordinates-catalytic-acid-residue-in-40-protein-fold-families
#3
Polytimi S Dimitriou, Alexander Denesyuk, Seiji Takahashi, Satoshi Yamashita, Mark S Johnson, Toru Nakayama, Konstantin Denessiouk
The alpha/beta-hydrolases (ABH) are a family of acid-base-nucleophile catalytic triad enzymes with a common fold, but using a wide variety of substrates, having different pH optima, catalyzing unique catalytic reactions and often showing improved chemical and thermo stability. The ABH enzymes are prime targets for protein engineering. Here, we have classified active sites from 51 representative members of 40 structural ABH fold families into eight distinct conserved geometries. We demonstrate the occurrence of a common structural motif, the catalytic acid zone, at the catalytic triad acid turn...
June 23, 2017: Proteins
https://www.readbyqxmd.com/read/28639287/exploration-of-conformational-changes-in-lactose-permease-upon-sugar-binding-and-proton-transfer-through-coarse-grained-simulations
#4
Yead Jewel, Prashanta Dutta, Jin Liu
Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H(+) symport process. Lactose/H(+) symport is a highly complex process that involves sugar translocation, H(+) transfer, as well as large-scale protein conformational changes. The complete picture of lactose/H(+) symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid...
June 22, 2017: Proteins
https://www.readbyqxmd.com/read/28614901/x-ray-crystal-structures-of-the-pheromone-binding-domains-of-two-quorum-hindered-transcription-factors-yenr-of-yersinia-enterocolitica-and-cepr2-of-burkholderia-cenocepacia
#5
Youngchang Kim, Gekleng Chhor, Ching-Sung Tsai, Gabriel Fox, Chia-Sui Chen, Nathan J Winans, Robert Jedrzejczak, Andrzej Joachimiak, Stephen C Winans
The ability of LuxR-type proteins to regulate transcription is controlled by bacterial pheromones, N-acylhomoserine lactones (AHLs). Most LuxR-family proteins require their cognate AHLs for activity, and some of them require AHLs for folding and stability, and for protease-resistance. However, a few members of this family are able to fold, dimerize, bind DNA, and regulate transcription in the absence of AHLs; moreover, these proteins are antagonized by their cognate AHLs. One such protein is YenR of Yersinia enterocolitica, which is antagonized by N-3-oxohexanoyl-l-homoserine lactone (OHHL)...
June 14, 2017: Proteins
https://www.readbyqxmd.com/read/28612368/crystal-structure-of-non-specific-lipid-transfer-protein-from-solanum-melongena
#6
Abha Jain, Dinakar M Salunke
Lipids are considered to protect protein allergens from proteolysis and are generally seen to exist in a bound form. One of the well-known plant protein families with bound lipids is non-specific lipid transfer proteins (nsLTPs). Structure-function relationships in the case of the members of non-specific lipid transfer protein family are not clearly understood. As part of exploring the seed proteome, we have analyzed the proteome of a member of Solanaceae family, Solanum melongena (eggplant) and a non-specific lipid transfer protein from S...
June 13, 2017: Proteins
https://www.readbyqxmd.com/read/28612358/%C3%AE-chymotrypsin-in-water-acetone-and-water-dimethyl-sulfoxide-mixtures-effect-of-preferential-solvation-and-hydration
#7
Vladimir A Sirotkin, Alexandra A Kuchierskaya
We investigated water/organic solvent sorption and residual enzyme activity to simultaneously monitor preferential solvation/hydration of protein macromolecules in the entire range of water content at 25°C. We applied this approach to estimate protein destabilization/stabilization due to the preferential interactions of bovine pancreatic α-chymotrypsin with water-acetone (moderate-strength H-bond acceptor) and water-DMSO (strong H-bond acceptor) mixtures. There are three concentration regimes for the dried α-chymotrypsin...
June 13, 2017: Proteins
https://www.readbyqxmd.com/read/28598584/camels-in-silico-prediction-of-calmodulin-binding-proteins-and-their-binding-sites
#8
Wajid Arshad Abbasi, Amina Asif, Saiqa Andleeb, Fayyaz Ul Amir Afsar Minhas
Due to Ca(2+) -dependent binding and the sequence diversity of Calmodulin (CaM) binding proteins, identifying CaM interactions and binding sites in the wet-lab is tedious and costly. Therefore, computational methods for this purpose are crucial to the design of such wet-lab experiments. We present an algorithm suite called CaMELS (CalModulin intEraction Learning System) for predicting proteins that interact with CaM as well as their binding sites using sequence information alone. CaMELS offers state of the art accuracy for both CaM interaction and binding site prediction and can aid biologists in studying CaM binding proteins...
June 9, 2017: Proteins
https://www.readbyqxmd.com/read/28598579/validation-of-protein-structure-models-using-network-similarity-score
#9
Sambit Ghosh, Vasundhara Gadiyaram, Saraswathi Vishveshwara
Accurate structural validation of proteins is of extreme importance in studies like protein structure prediction, analysis of molecular dynamic simulation trajectories and finding subtle changes in very similar structures. The benchmarks for today's structure validation are scoring methods like Global Distance Test-Total Structure (GDT-TS), TM-Score and Root Mean Square Deviations (RMSD). However, there is a lack of methods that look at both the protein backbone and side chain structures at the global connectivity level and provide information about the differences in connectivity...
June 9, 2017: Proteins
https://www.readbyqxmd.com/read/28598514/the-finite-number-of-global-motion-patterns-available-to-symmetric-protein-complexes
#10
Guang Song
In PDB, more than half of the entries are structure complexes and of these complexes, most are symmetric, composed of identical subunits. Complex formation is the way through which larger structures and even molecular machines are assembled and built in nature. In this work, we apply group theory and carry out a comprehensive study of the global motion patterns of protein complexes of various symmetries. The work presents for the first time a comprehensive list of all the symmetric, aesthetically pleasing, global motion patterns available to complexes of cyclic, dihedral, tetrahedral, and octahedral symmetry...
June 9, 2017: Proteins
https://www.readbyqxmd.com/read/28597979/on-the-relationship-between-residue-structural-environment-and-sequence-conservation-in-proteins
#11
Jen-Wei Liu, Jau-Ji Lin, Chih-Wen Cheng, Yu-Feng Lin, Jenn-Kang Hwang, Tsun-Tsao Huang
Residues that are crucial to protein function or structure are usually evolutionarily conserved. In order to identify the important residues in protein, sequence conservation is estimated, and current methods rely upon the unbiased collection of homologous sequences. Surprisingly, our previous studies have shown that the sequence conservation is closely correlated with the weighted contact number (WCN), a measure of packing density for residue's structural environment, calculated only based on the Cα positions of a protein structure...
June 9, 2017: Proteins
https://www.readbyqxmd.com/read/28597937/frustration-guided-motion-planning-reveals-conformational-transitions-in-proteins
#12
Dominik Budday, Rasmus Fonseca, Sigrid Leyendecker, Henry van den Bedem
Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here, we present a new, robotics-inspired motion planning procedure called dCC-RRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration...
June 9, 2017: Proteins
https://www.readbyqxmd.com/read/28547871/sequence-based-analysis-of-protein-degradation-rates-a-computational-study-of-protein-degradation
#13
Miguel Correa Marrero, Aalt D J van Dijk, Dick de Ridder
Protein turnover is a key aspect of cellular homeostasis and proteome dynamics. However, there is little consensus on which properties of a protein determine its lifetime in the cell. In this work, we exploit two reliable datasets of experimental protein degradation rates to learn models and uncover determinants of protein degradation, with particular focus on properties that can be derived from the sequence. Our work shows that simple sequence features suffice to obtain predictive models of which the output correlates reasonably well with the experimentally measured values...
May 25, 2017: Proteins
https://www.readbyqxmd.com/read/28547780/advances-in-molecular-engineering-of-carbohydrate-binding-modules
#14
REVIEW
Silvia Armenta, Silvia Moreno-Mendieta, Zaira Sánchez-Cuapio, Sergio Sánchez, Romina Rodríguez-Sanoja
Carbohydrate-binding modules (CBMs) are non-catalytic domains that are generally appended to carbohydrate-active enzymes. CBMs have a broadly conserved structure that allows recognition of a notable variety of carbohydrates, in both their soluble and insoluble forms, as well as in their alpha and beta conformations and with different types of bonds or substitutions. This versatility suggests a high functional plasticity that is not yet clearly understood, in spite of the important number of studies relating protein structure and function...
May 25, 2017: Proteins
https://www.readbyqxmd.com/read/28547747/deciphering-common-recognition-principles-of-nucleoside-mono-di-and-tri-phosphates-binding-in-diverse-proteins-via-structural-matching-of-their-binding-sites
#15
Raghu Bhagavat, Narayanaswamy Srinivasan, Nagasuma Chandra
Nucleoside triphosphate (NTP) ligands are of high biological importance and essential for all life forms. A pre-requisite for them to participate in diverse biochemical processes is their recognition by diverse proteins. It is thus of great interest to understand the basis for such recognition in different proteins. Towards this, we have employed a structural bioinformatics approach and analyse structures of 4677 NTP complexes available in PDB. Binding sites were extracted and compared exhaustively by using PocketMatch, a sensitive in-house site comparison algorithm, which resulted in grouping the entire dataset into 27 site-types...
May 25, 2017: Proteins
https://www.readbyqxmd.com/read/28544098/crystal-structure-of-the-sensor-domain-of-baes-from-serratia-marcescens-fs14
#16
Ya Zhang, Shenshen Qiu, Shanshan Jia, Dongqing Xu, Tingting Ran, Weiwu Wang
The sensor histidine kinases of two-component signal-transduction systems (TCSs) are essential for bacteria to adapt to variable environmental conditions. The two-component regulatory system BaeS/R increases multidrug and metal resistance in Salmonella and Escherichia coli. In this study, we report the X-ray structure of the periplasmic sensor domain of BaeS from Serratia marcescens FS14. The BaeS sensor domain (34-160) adopts a mixed α/β-fold containing a central four-stranded antiparallel β-sheet flanked by a long N-terminal α-helix and additional loops and a short C-terminal α-helix on each side...
May 24, 2017: Proteins
https://www.readbyqxmd.com/read/28544090/functional-tuning-of-the-catalytic-residue-pka-in-a-de-novo-designed-esterase
#17
Katharina Hiebler, Zsófia Lengyel, Carlos A Castañeda, Olga V Makhlynets
AlleyCatE is a de novo designed esterase that can be allosterically regulated by calcium ions. This artificial enzyme has been shown to hydrolyze p-nitrophenyl acetate (pNPA) and 4-nitrophenyl-(2-phenyl)-propanoate (pNPP) with high catalytic efficiency. AlleyCatE was created by introducing a single histidine residue (His(144) ) into a hydrophobic pocket of calmodulin. In this work, we explore the determinants of catalytic properties of AlleyCatE. We obtained the pKa value of the catalytic histidine using experimental measurements by NMR and pH rate profile and compared these values to those predicted from electrostatics pKa calculations (from both empirical and continuum electrostatics calculations)...
May 24, 2017: Proteins
https://www.readbyqxmd.com/read/28543853/crystal-structure-of-lipoate-bound-lipoate-ligase-1-lipl1-from-plasmodium-falciparum
#18
Alfredo J Guerra, Gustavo A Afanador, Sean T Prigge
Plasmodium falciparum lipoate protein ligase 1 (PfLipL1) is an ATP-dependent ligase that belongs to the biotin/lipoate A/B protein ligase family (PFAM PF03099). PfLipL1 is the only known canonical lipoate ligase in Pf and functions as a redox switch between two lipoylation routes in the parasite mitochondrion. Here, we report the crystal structure of a deletion construct of PfLipL1 (PfLipL1Δ243-279 ) bound to lipoate, and validate the lipoylation activity of this construct in both an in vitro lipoylation assay and a cell based lipoylation assay...
May 24, 2017: Proteins
https://www.readbyqxmd.com/read/28543724/predicting-binding-modes-of-reversible-peptide-based-inhibitors-of-falcipain-2-consistent-with-structure-activity-relationships
#19
Jorge Enrique Hernández González, Lilian Hernández Alvarez, Pedro Geraldo Pascutti, Pedro Alberto Valiente
Falcipain-2 (FP-2) is a major hemoglobinase of Plasmodium falciparum, considered an important drug target for the development of antimalarials. A previous study reported a novel series of twenty reversible peptide-based inhibitors of FP-2. However, the lack of tridimensional structures of the complexes hinders further optimization strategies to enhance the inhibitory activity of the compounds. Here we report the prediction of the binding modes of the aforementioned inhibitors to FP-2. A computational approach combining previous knowledge on the determinants of binding to the enzyme, docking and post-docking refinement steps, is employed...
May 24, 2017: Proteins
https://www.readbyqxmd.com/read/28543443/structural-review-of-ppar%C3%AE-in-complex-with-ligands-cartesian-and-dihedral-angle-principal-component-analyses-of-x-ray-crystallographic-data
#20
Åsmund Kaupang, Tuomo Laitinen, Antti Poso, Trond Vidar Hansen
Two decades of research into the ligand-dependent modulation of the activity of the peroxisome proliferator-activated receptor γ (PPARγ) have demonstrated the heterogeneous modes of action of PPARγ ligands, in terms of their interaction surfaces in the ligand-binding pocket, binding stoichiometry and ability to interact with functionally important parts of the receptor, through both direct and allosteric mechanisms. These findings signal the complex mechanistic bases of the distinct biological effects of different classes of PPARγ ligands...
May 24, 2017: Proteins
journal
journal
29413
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"