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https://www.readbyqxmd.com/read/29334318/molecular-dynamics-perspective-on-the-thermal-stability-of-mandelate-racemase
#1
Jiali Gu, Hongfei Tong, Laiyu Sun, Zhijian Lin
Mandelate racemase from Pseudomonas putida is a promising candidate for the dynamic kinetic resolution of α-hydroxy carboxylic acids. In the present study, the thermal stability of mandelate racemase was investigated through molecular dynamics simulations in the temperature range of 303 K to 363 K, which can guide the design of mandelate racemase with higher stability. The basic features such as radius of gyration, surface accessibility, and secondary structure content suggested the instability of mandelate racemase at high temperatures...
January 15, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29330023/unraveling-the-differential-structural-stability-and-dynamics-features-of-t7-endolysin-partially-folded-conformations
#2
Meenakshi Sharma, Dinesh Kumar, Krishna Mohan Poluri
BACKGROUND: Characterization of partially collapsed protein conformations at atomic level is a daunting task due to their inherent flexibility and conformational heterogeneity. T7 bacteriophage endolysin (T7L) is a single-domain amidase that facilitates the lysis of Gram-negative bacteria. T7L exhibits a pH-dependent structural transition from native state to partially folded (PF) conformation. In the pH range 5-3, T7L PF states display differential ANS binding characteristics. METHODS: CD, fluorescence, NMR spectroscopy and lysis assays were used to investigate the structure-stability- dynamics relationships of T7L PF conformations...
January 9, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29325229/dual-drug-targeting-of-mutant-bcr-abl-induces-inactive-conformation-new-strategy-for-the-treatment-of-chronic-myeloid-leukemia-and-overcoming-monotherapy-resistance
#3
Ahmed A El Rashedy, Fisayo A Olotu, Mahmoud E S Soliman
Bcr-Abl is an oncogenic fusion protein which expression enhances tumorigenesis, and has been highly associated with chronic myeloid leukemia (CML). Acquired drug resistance in mutant Bcr-Abl has enhanced pathogenesis with the use of single therapy agents such as Nilotinib. Moreover, allosteric targeting has been identified to consequentially inhibit Bcr-Abl activity, which led to the recent development of ABL-001 (asciminib) that selectively binds the myristoyl pocket. Experimental studies have revealed that the combination of Nilotinib and ABL-001 induced a "bent" conformation in the C-terminal helix of Bcr-Abl; a benchmark of inhibition, thereby exhibiting a greater potency in the treatment of CML, surmounting the setbacks of drug resistance, disease regression and relapse...
January 11, 2018: Chemistry & Biodiversity
https://www.readbyqxmd.com/read/29323921/membrane-anchoring-of-%C3%AE-helical-proteins-role-of-tryptophan
#4
Alan J Situ, So-Min Kang, Benjamin B Frey, Woojin An, Chungho Kim, Tobias S Ulmer
The function of membrane proteins relies on a defined orientation of protein relative to lipid. In apparent correlation to protein anchoring, tryptophan residues are enriched in the lipid headgroup region. To characterize the thermodynamic and structural basis of this relationship in α-helical membrane proteins, we examined the role of three conserved tryptophans in the folding of the heterodimeric integrin αIIbβ3 transmembrane (TM) complex in phospholipid bicelles and mammalian membranes. In the homogenous lipid environment of bicelles, tryptophan was replaceable by residues of distinct polarities...
January 11, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29321962/mutual-influence-of-secondary-and-key-drug-resistance-mutations-on-catalytic-properties-and-thermal-stability-of-tem-type-%C3%AE-lactamases
#5
Vitaly Grigorenko, Igor Uporov, Maya Rubtsova, Irina Andreeva, Dmitrii Shcherbinin, Alexander Veselovsky, Oksana Serova, Maria Ulyashova, Igor Ishtubaev, Alexey Egorov
Highly mutable β-lactamases are responsible for the ability of Gram-negative bacteria to resist β-lactam antibiotics. Using site-directed mutagenesis technique, we have produced in vitro a number of recombinant analogs of naturally occurring TEM-type β-lactamases, bearing the secondary substitution Q39K and key mutations related to the extended-spectrum (E104K, R164S) and inhibitor-resistant (M69V) β-lactamases. The mutation Q39K alone was found to be neutral and hardly affected the catalytic properties of β-lactamases...
January 2018: FEBS Open Bio
https://www.readbyqxmd.com/read/29320723/comparative-study-of-structural-and-functional-characterization-of-bran-protein-concentrates-from-superfine-fine-and-coarse-rice-cultivars
#6
Tajendra Pal Singh, Dalbir Singh Sogi
Rice bran protein concentrates prepared from superfine, fine and coarse cultivars were assessed for their physicochemical, structural, functional properties and digestibility. The protein concentrates differed in structural, thermal and functional properties. Rice bran protein concentrate of fine cultivar (F-RBPC) had relatively more β-sheets (42.81%) and less α-helix (15.03%) and β-turns (21.98%) than that of superfine (SF-RBPC) and coarse (C-RBPC) cultivars. Thermal denaturation temperature (Td) was similar for all cultivars, whereas enthalpy of denaturation (ΔH) was high for F-RBPC...
January 7, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29320682/translational-entropy-and-dna-duplex-stability
#7
Peter L Privalov, Colyn Crane-Robinson
Investigation of folding/unfolding DNA duplexes of various size and composition by superprecise calorimetry has revised several long-held beliefs concerning the forces responsible for the formation of the double helix. It was established that: 1) the enthalpy and the entropy of duplex unfolding are temperature dependent, increasing with temperature rise and having the same heat capacity increment for CG and AT pairs; 2) the enthalpy of AT melting is greater than that of the CG pair, so the stabilizing effect of the CG pair in comparison with AT results not from its larger enthalpic contribution (as expected from its extra hydrogen bond), but from the larger entropic contribution of the AT pair that results from its ability to fix ordered water in the minor groove and release it upon duplex unfolding; 3) the translation entropy, resulting from the appearance of a new kinetic unit on duplex dissociation, determines the dependence of duplex stability on its length and its concentration (it is an order-of-magnitude smaller than predicted from the statistical mechanics of gases and is fully expressed by the stoichiometric correction term); 4) changes in duplex stability on reshuffling the sequence (the "nearest-neighbor effect") result from the immobilized water molecules fixed by AT pairs in the minor groove; and 5) the evaluated thermodynamic components permit a quantitative expression of DNA duplex stability...
January 9, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29319890/two-novel-unstable-hemoglobin-variants-due-to-in-frame-deletions-of-key-amino-acids-in-the-%C3%AE-globin-chain
#8
Karen Gabriela Scheps, Marcia Anahí Hasenahuer, Gustavo Parisi, Héctor M Targovnik, Eliana García, Ernesto Samuel Veber, Renée Crisp, Graciela Elena, Viviana Varela, María Silvina Fornasari
Hemoglobinopathies are the most common autosomal recessive disorders and are mostly inherited in a recessive manner. However, certain mutations can affect the globin chain stability, leading to dominant forms of thalassemia. The aim of this work was the molecular and structural characterization of two heterozygous in-frame deletions, leading to β-globin variants in pediatric patients in Argentina. The HBB gene of the probands and their parents was sequenced, and other markers of globin chain imbalance were analyzed...
January 10, 2018: European Journal of Haematology
https://www.readbyqxmd.com/read/29316396/hybrid-particle-field-model-for-conformational-dynamics-of-peptide-chains
#9
Sigbjørn Løland Bore, Giuseppe Milano, Michele Cascella
We propose the first model of a polypeptide chain based on a hybrid-particle field approach. The intramolecular potential is built on a two-bead coarse grain mapping for each amino acid. We employ a combined potential for the bending and the torsional degrees of freedom that ensures the stabilization of secondary structure elements in the conformational space of the polypeptide. The electrostatic dipoles associated to the peptide bonds of the main-chain are reconstructed by a topological procedure. The intermolecular interactions comprising both the solute and the explicit solvent are treated by a density functional-based mean-field potential...
January 9, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29307800/effect-of-ultra-high-pressure-on-molecular-structure-and-properties-of-bullfrog-skin-collagen
#10
Jie Nan, Meilian Zou, Haibo Wang, Chengzhi Xu, Juntao Zhang, Benmei Wei, Lang He, Yuling Xu
Ultra-high pressure technology has attracted a great deal of attention in recent years, and has been widely used in food science, medicine, and other fields. This study aimed to determine the effect of ultra-high pressure on the structure and properties of collagen. Native collagen extracted from bullfrog skin was processed under different ultra-high pressure treatment conditions (300, 400, and 500MPa). Then systematic analysis of the molecular structures and properties of the samples after ultra-high pressure treatment were performed...
January 4, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29298880/the-catalytic-inactivation-of-the-n-half-of-human-hexokinase-2-and-structural-and-biochemical-characterization-of-its-mitochondrial-conformation
#11
Mir Hussain Nawaz, Juliana C Ferreira, Lyudmila Nedyalkova, Haizhong Zhu, César Carrasco-López, Serdal Kirmizialtin, Wael M Rabeh
The high proliferation rate of tumor cells demands high energy and metabolites that are sustained by a high glycolytic flux known as the "Warburg effect". The activation and further metabolism of glucose is initiated by hexokinase, a focal point of metabolic regulation. The human hexokinase 2 (HK2) is overexpressed in all aggressive tumors and predominantly found on the mitochondria, where interactions through its N-terminus initiates and maintains tumorigenesis. Here, we report the structure of HK2 in complex with glucose and glucose 6-phosphate...
January 3, 2018: Bioscience Reports
https://www.readbyqxmd.com/read/29296672/prediction-of-new-stabilizing-mutations-based-on-mechanistic-insights-from-markov-state-models
#12
Maxwell I Zimmerman, Kathryn M Hart, Carrie A Sibbald, Thomas E Frederick, John R Jimah, Catherine R Knoverek, Niraj H Tolia, Gregory R Bowman
Protein stabilization is fundamental to enzyme function and evolution, yet understanding the determinants of a protein's stability remains a challenge. This is largely due to a shortage of atomically detailed models for the ensemble of relevant protein conformations and their relative populations. For example, the M182T substitution in TEM β-lactamase, an enzyme that confers antibiotic resistance to bacteria, is stabilizing but the precise mechanism remains unclear. Here, we employ Markov state models (MSMs) to uncover how M182T shifts the distribution of different structures that TEM adopts...
December 27, 2017: ACS Central Science
https://www.readbyqxmd.com/read/29287471/conformation-stability-in-vitro-digestibility-and-allergenicity-of-tropomyosin-from-shrimp-exopalaemon-modestus-as-affected-by-high-intensity-ultrasound
#13
Ziye Zhang, Xiaofeng Zhang, Wei Chen, Peng Zhou
The effects of high intensity ultrasound (HIU) modification (power: 100-800 W, 15 min) on the conformation stability, in vitro digestibility and allergenicity of tropomyosin (TM) from Exopalaemon modestus were investigated. HIU treatment oxidized the Cys, Met and Lys in TM and degraded TM to generate protein fragments by HIU-induced free radicals. The α-helix content decreased, while β-sheet, β-turn and random coil increased. The immunoblotting and ELISA data suggested HIU treatment reduced the allergenicity and contributed to higher digestibility of TM...
April 15, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29285400/structural-insight-into-the-ragulator-complex-which-anchors-mtorc1-to-the-lysosomal-membrane
#14
Zongkai Mu, Lei Wang, Wei Deng, Jiawei Wang, Geng Wu
The mechanistic target of rapamycin (mTOR) signal-transduction pathway plays a key role in regulating many aspects of metabolic processes. The central player of the mTOR signaling pathway, mTOR complex 1 (mTORC1), is recruited by the pentameric Ragulator complex and the heterodimeric Rag GTPase complex to the lysosomal membrane and thereafter activated. Here, we determined the crystal structure of the human Ragulator complex, which shows that Lamtor1 possesses a belt-like shape and wraps the other four subunits around...
2017: Cell Discovery
https://www.readbyqxmd.com/read/29285328/a-new-spiral-dental-implant-a-tool-for-oral-rehabilitation-of-difficult-cases
#15
I Balan, R Calcaterra, D Lauritano, E Grecchi, F Carinci
Spiral dental implant (SDI) is an implant with a conical internal helix that confers the characteristic of self-drilling, self-tapping, and self-bone condensing. These proprieties offer better control during insertion of SDI giving a high primary stabilization, even in poor quality bone. A shorter diameter of SDI results in reduced drilling during insertion and consequently less trauma and minimal bone loss. To address the research purpose, the investigators designed a retrospective cohort study. The study population was composed of 25 patients, 11 males and 14 females that have been treated by Dr...
July 2017: Oral & Implantology
https://www.readbyqxmd.com/read/29285240/molecular-basis-for-the-dna-damage-induction-and-anticancer-activity-of-asymmetrically-substituted-anthrapyridazone-pdz-7
#16
Majus Misiak, Mateusz Heldt, Marlena Szeligowska, Stefania Mazzini, Leonardo Scaglioni, Grzegorz J Grabe, Marcin Serocki, Jan Lica, Marta Switalska, Joanna Wietrzyk, Giovanni L Beretta, Paola Perego, Dominik Zietkowski, Maciej Baginski, Edward Borowski, Andrzej Skladanowski
Anthrapyridazones, imino analogues of anthraquinone, constitute a family of compounds with remarkable anti-cancer activity. To date, over 20 derivatives were studied, of which most displayed nanomolar cytotoxicity towards broad spectrum of cancer cells, including breast, prostate and leukemic ones. BS-154, the most potent derivative, had IC50 values close to 1 nM, however, it was toxic in animal studies. Here, we characterize another anthrapyridazone, PDZ-7, which retains high cytotoxicity while being well tolerated in mice...
December 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/29280735/decoding-the-centromeric-nucleosome-through-cenp-n
#17
Satyakrishna Pentakota, Keda Zhou, Charlotte Smith, Stefano Maffini, Arsen Petrovic, Garry P Morgan, John R Weir, Ingrid R Vetter, Andrea Musacchio, Karolin Luger
Centromere protein (CENP) A, a histone H3 variant, is a key epigenetic determinant of chromosome domains known as centromeres. Centromeres nucleate kinetochores, multi-subunit complexes that capture spindle microtubules to promote chromosome segregation during mitosis. Two kinetochore proteins, CENP-C and CENP-N, recognize CENP-A in the context of a rare CENP-A nucleosome. Here, we reveal the structural basis for the exquisite selectivity of CENP-N for centromeres. CENP-N uses charge and space complementarity to decode the L1 loop that is unique to CENP-A...
December 27, 2017: ELife
https://www.readbyqxmd.com/read/29279008/comparative-analysis-of-thermal-unfolding-simulations-of-rna-recognition-motifs-rrms-of-tar-dna-binding-protein-43-tdp-43
#18
Amresh Prakash, Vijay Kumar, Naveen Kumar Meena, Md Imtaiyaz Hassan, Andrew M Lynn
TAR DNA-binding protein 43 (TDP-43) inclusions have been found in Amyotrophic lateral sclerosis (ALS) and several other neurodegenerative diseases. Many studies suggest the involvement of RNA recognition motifs (RRMs) in TDP-43 proteinopathy. To elucidate the structural stability and the unfolding dynamics of RRMs, we have carried out atomistic molecular dynamics simulations at two different temperatures (300 K and 500 K). The simulations results indicate that there are distinct structural differences in the unfolding pathway between the two domains and RRM1 unfolds faster than RRM2 in accordance with the lower thermal stability found experimentally...
December 26, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29277994/the-choreography-of-the-reductase-and-p450bm3-domains-towards-electron-transfer-is-instigated-by-the-substrate
#19
Kshatresh Dutta Dubey, Sason Shaik
The driving force for the electron transfer (ET) step in the catalytic cycle of cytochrome P450BM3, is investigated using three sets of 1 µs molecular dynamic simulations for the resting state of P450 in complex with the flavin (FMN) in the reductase domain. These sets involve: (i) substrate-free (SF), (ii) substrate (N-palmitoyl glycine, i.e NPG)-bound (SB), and (iii) SB with the semiquinone radical-anion (SQ-) of FMN. Starting from the X-ray structure of the SF heme domain, we observe that the α1 helix (of the reductase) and the C helix (of the heme) undergo reorientation to a parallel orientation, which is the thermochemically stable form...
December 26, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29277568/effect-of-dc-%C3%A2-d-m5c-substitutions-on-the-folding-of-intramolecular-triplexes-with-mixed-tat-and-c-gc-base-triplets
#20
Carolyn E Carr, Rajkumar Ganugula, Ronald Shikiya, Ana Maria Soto, Luis A Marky
Oligonucleotide-directed triple helix formation has been recognized as a potential tool for targeting genes with high specificity. Cystosine methylation in the 5' position is both ubiquitous and a stable regulatory modification, which could potentially stabilize triple helix formation. In this work, we have used a combination of calorimetric and spectroscopic techniques to study the intramolecular unfolding of four triplexes and two duplexes. We used the following triplex control sequence, named Control Tri, d(AGAGAC5TCTCTC5TCTCT), where C5 are loops of five cytosines...
December 22, 2017: Biochimie
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