journal
MENU ▼
Read by QxMD icon Read
search

Journal of Biomolecular Structure & Dynamics

journal
https://www.readbyqxmd.com/read/28641482/insights-into-eukaryotic-evolution-from-transmembrane-domain-lengths
#1
Aditya Mittal, Snigdha Singh
Biological membranes, comprised of proteins anchored by their trans-membrane domains (TMDs) creating a semi-permeable phase with lipid constituents, serve as "checkposts" for not only intracellular trafficking in eukaryotic cells but also for material transactions of all living cells with external environments. Hydropathy (or hydrophobicity) plots of "bitopic" proteins (i.e. having single alpha-helical TMDs) are routinely utilized in biochemistry texts for predicting their TMDs. The number of amino acids (i...
June 22, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28636842/dna-binding-mode-transition-of-tau-in-the-presence-of-zinc-ions
#2
Kazem Asadollahi, Gholamhosein Riazi, Azra Rabbani Chadegani, Saharnaz Rafiee
No abstract text is available yet for this article.
June 21, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28633570/enantioselective-light-switch-effect-of-%C3%AE-and-%C3%AE-ru-phenanthroline-2-dipyrido-3-2-a-2-3-c-phenazine-2-bound-to-g-quadruplex-dna
#3
Jin Ha Park, Hyun Suk Lee, Myung Duk Jang, Sung Wook Han, Seog K Kim, Young-Ae Lee
The interaction of Δ- and Λ-[Ru(phen)2DPPZ](2+) (DPPZ = dipyrido[3,2-a:2', 3'-c]phenazine, phen = phenanthroline) with a G-quadruplex formed from 5'-G2T2G2TGTG2T2G2-3'(15-mer) was investigated. The well-known enhancement of luminescence intensity (the 'light-switch' effect) was observed for the [Ru(phen)2DPPZ](2+) complexes upon formation of an adduct with the G-quadruplex. The emission intensity of the G-quadruplex-bound Λ-isomer was 3-fold larger than that of the Δ-isomer when bound to the G-quadruplex, which is opposite of the result observed in the case of double stranded DNA (dsDNA); the light switch effect is larger for the dsDNA-bound Δ-isomer...
June 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28633569/thermal-and-chemical-denaturation-of-colocasia-esculenta-tuber-agglutinin-from-%C3%AE-2%C3%AE-2-to-unfolded-state
#4
Himadri Biswas, Rajagopal Chattopadhyaya
The major tuber storage protein of Colocasia esculenta, is a monocot mannose-binding, widely used dietary lectin, containing two polypeptides of 12.0 and 12.4 kDa. By both gel filtration and dynamic light scattering at pH 7.2, the lectin has a α2β2 form of apparent molecular mass of 48.2 kDa and a hydrodynamic radius of 6.1±0.2 nm; however, at pH 3, it migrates as αβ and has a reduced hydrodynamic radius of 4.6±0.3 nm. Our circular dichroism spectroscopy studies show that the lectin retains approximately 100% of its secondary structure between pH 2-8, going down to ~90% for extreme acidic / alkaline conditions...
June 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28633568/the-potential-inhibitory-effect-of-%C3%AE-casein-on-the-aggregation-and-deposition-of-a%C3%AE-1-42-fibrils-in-alzheimer-s-disease-insight-from-in-vitro-and-in-silico-studies
#5
Sedighehsadat Hojati, Arezou Ghahghaei, Milad Lagzian
Aβ1-40 and Aβ1-42 have been shown to be the main components of the amyloid plaques found in the extracellular environment of neurons in Alzheimer's disease. β-Casein, a milk protein, has been shown to display a remarkable chaperone ability in preventing the aggregation of proteins. In this study, the ability of β-casein to suppress the amyloid fibril formation of Aβ1-42 has been examined through in vitro studies and molecular docking simulation. The results demonstrate the inhibitory effect of β-casein on fibril formation in Aβ1-42, in a concentration dependent manner, suggesting that the chaperone binds to the Aβ1-42 and prevents amyloid fibril formation...
June 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28632421/novel-urushiol-derivatives-as-hdac8-inhibitors-rational-design-virtual-screening-molecular-docking-and-molecular-dynamics-studies
#6
Hao Zhou, Chengzhang Wang, Tao Deng, Ran Tao, Wenjun Li
Three series of novel urushiol derivatives were designed by introducing a hydroxamic acid moiety into the tail of an alkyl side chain and substituents with differing electronic properties or steric bulk onto the benzene ring and alkyl side chain. The compounds' binding affinity towards HDAC8 was screened by Glide docking. The highest-scoring compounds were processed further with molecular docking, MD simulations and binding free energy studies to analyze the binding modes and mechanisms. Ten compounds had Glide scores of -8...
June 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28599617/insight-into-the-key-features-for-ligand-binding-in-y1230-mutated-c-met-kinase-domain-by-molecular-dynamics-simulations
#7
Libo Yan, Li Zhang, Yanmin Zhang, Xin Qiao, Jing Pan, Haichun Liu, Shuai Lu, Bingren Xiang, Tao Lu, Haoliang Yuan
c-Met kinase has been considered as an attractive target for developing antitumor agents. The strong interactions between Tyr1230 and the inhibitors emphasized its importance for ligand binding. The clinically related Tyr1230 mutations have made negative impacts on current c-Met kinase inhibitors, especially the exquisitely selective ones, like PF-04217903, while the multi-targeted inhibitors, like Crizotinib, were not affected so much. In this study, the protein-ligand interactions between c-Met kinase domain (wild, Y1230C and Y1230H) and these inhibitors were compared...
June 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28627970/genome-wide-codon-usage-profiling-of-ocular-infective-chlamydia-trachomatis-serovars-and-drug-target-identification
#8
Anupriya Sadhasivam, Umashankar Vetrivel
Chlamydia trachomatis (C.t) is a gram-negative obligate intracellular bacteria and is a major causative of infectious blindness and sexually transmitted diseases. Among the varied serovars of this organism, A, B & C are reported as prominent ocular pathogens. Genomic studies of these strains shall aid in deciphering potential drug targets and genomic influence on pathogenesis. Hence, in this study we performed deep statistical profiling of codon usage in these serovars. The overall base composition analysis reveals that these serovars are over biased to AU than GC...
June 19, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28627969/identification-of-potential-inhibitors-of-fasciola-gigantica-thioredoxin1-computational-screening-molecular-dynamics-simulation-and-binding-free-energy-studies
#9
Rohit Shukla, Harish Shukla, Parismita Kalita, Amit Sonkar, Tripti Pandey, Dev Bukhsh Singh, Awanish Kumar, Timir Tripathi
Fasciola gigantica is the causative organism of fascioliasis and is responsible for major economic losses in livestock production globally. F. gigantica thioredoxin1 (FgTrx1) is an important redox-active enzyme involved in maintaining the redox homeostasis in the cell. To identify a potential anti-fasciolid compound, we conducted a structure-based virtual screening of natural compounds from the ZINC database (n = 1,67,740) against the FgTrx1 structure. The ligands were docked against FgTrx1 and 309 ligands were found to have better docking score...
June 19, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28617661/molecular-dynamics-approach-to-probe-the-antigenicity-of-pagn-an-outer-membrane-protein-of-salmonella-typhi
#10
Nabajyoti Goswami, Md Iftikar Hussain, Probodh Borah
PagN is a highly immunogenic 27-kDa outer membrane adhesin present in Salmonella Typhi. It plays a major role in the pathogenesis of typhoid fever and has emerged as a strong vaccine candidate. In this report, we predict the three dimensional structure of PagN and describe the conformational dynamics associated with its 4 extracellular loops based on two 100-ns molecular dynamics simulations at 300 K and 310 K. The formation and deformation of the secondary structures on these loops were also investigated during the simulations which revealed loops L1 and L2 to be highly flexible, whereas the relative flexibility of loops L3 and L4 was minimal...
June 15, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28617190/experimental-and-theoretical-studies-of-cadmium-ions-absorption-by-a-new-reduced-recombinant-defensin
#11
Karim Mahnam, Samira Foruzandeh, Neda Mirakhorli, Behnaz Saffar
Heavy metal pollutants such as Cd, Hg, Pb, As and Se are considered as both a global problem and a growing threat to the humanity. Being strongly poisonous to the metal-sensitive enzymes and leading to the growth inhibition and death of organisms, these metals have a toxic impact on the plants and animals. Inducing the metal-binding cysteine-rich peptides such as metallothioneins, phytochelatins, and defensins, higher organisms like plants and animals usually react to the heavy metal stress. In this study, a recombinant defensin protein was expressed in bean and its ability in the cadmium absorption was determined...
June 15, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28617091/fragment-based-virtual-screening-approach-and-molecular-dynamics-simulation-studies-for-identification-of-bace1-inhibitor-leads
#12
Prabu Manoharan, Nanda Ghoshal
Traditional structure-based virtual screening method to identify drug-like small molecules for BACE1 is so far unsuccessful. Location of BACE1, poor Blood Brain Barrier permeability and P-glycoprotein (Pgp) susceptibility of the inhibitors make it even more difficult. Fragment-based drug design method is suitable for efficient optimization of initial hit molecules for target like BACE1. We have developed a fragment-based virtual screening approach to identify/optimize the fragment molecules as a starting point...
June 15, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28571517/mechanistic-insights-into-the-activity-of-ptf1-p48-pancreas-transcription-factor-1a-probing-the-interactions-levels-of-ptf1-p48-with-e2a-e47-transcription-factor-e2-alpha-and-id3-inhibitor-of-dna-binding-3
#13
Nishith Saurav Topno, Muthu Kannan, Ramadas Krishna
Ptf1-p48 (Pancreas specific transcription factor 1a) is transcription regulatory protein known for the activation of exocrine specific genes. Downregulation of its expression formulates early stages of pancreatic adenocarcinoma as deduced by its association with oncogenic bHLH (Basic Helix-Loop-Helix) protein ID3 (Inhibitor of DNA binding 3) protein whose overexpression induces cytoplasmic mislocalization of Ptf1-p48. The precise mechanism and/or functional role of Ptf1-p48in promoting pancreatic cancer is vague...
June 15, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28571516/nsaids-as-potential-treatment-option-for-preventing-amyloid-%C3%AE-toxicity-in-alzheimer-s-disease-an-investigation-by-docking-molecular-dynamics-and-dft-studies
#14
Faizul Azam, Nada Hussin Alabdullah, Hadeel Mohammed Ehmedat, Abdullah Ramadan Abulifa, Ismail Taban, Sreedevi Upadhyayula
Aggregation of amyloid beta (Aβ) protein considered as one of contributors in development of Alzheimer's disease (AD). Several investigations have identified the importance of non-steroidal anti-inflammatory drugs (NSAIDs) as Aβ aggregation inhibitors. Here, we have examined the binding interactions of 24 NSAIDs belonging to eight different classes, with Aβ fibrils by exploiting docking and molecular dynamics studies. Minimum energy conformation of the docked NSAIDs were further optimized by density functional theory (DFT) employing Becke's three-parameter hybrid model, Lee-Yang-Parr (B3LYP) correlation functional method...
June 15, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28565938/n-4-hydroxyphenyl-3-4-5-trimethoxybenzamide-derivatives-as-potential-memory-enhancers-synthesis-biological-evaluation-and-molecular-simulation-studies
#15
Poonam Piplani, Manish Sharma, Pakhuri Mehta, Ruchi Malik
The present paper describes the synthesis, biological evaluation and molecular simulation studies of a series of N-(4-hydroxyphenyl)-3,4,5-trimethoxybenzamide derivatives with N,N-dialkylaminoethoxy/propoxy moiety as potential memory enhancers with acetylcholinesterase-inhibiting activity having IC50 in low micromolar range (4.0-16.5 μM). All the compounds showed a good degree of agreement between in vivo and in vitro results as most of these derivatives showed dose-dependent increase in percent retention...
June 15, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28566049/molecular-dynamics-simulations-of-apo-and-holo-forms-of-fatty-acid-binding-protein-5-and-cellular-retinoic-acid-binding-protein-ii-reveal-highly-mobile-protein-retinoic-acid-ligand-and-water-molecules
#16
Nathanael H Hunter, Blair C Bakula, Chrystal D Bruce
Structural and dynamic properties from a series of 300 ns molecular dynamics, MD, simulations of two intracellular lipid binding proteins, iLBPs, (Fatty Acid Binding Protein 5, FABP5, and Cellular Retinoic Acid Binding Protein II, CRABP-II) in both the apo form and when bound with retinoic acid reveal a high degree of protein and ligand flexibility. The ratio of FABP5 to CRABP-II in a cell may determine whether it undergoes natural apoptosis or unrestricted cell growth in the presence of retinoic acid. As a result, FABP5 is a promising target for cancer therapy...
June 14, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28566016/a-computational-study-to-identify-the-key-residues-of-peroxisome-proliferator-activated-receptor-gamma-in-the-interactions-with-its-antagonists
#17
Tayebeh Sharifi, Yousef Ghayeb
Peroxisome proliferator-activated receptors (PPARs) compose a family of nuclear receptors, PPARα, PPARβ, and PPARγ, which mediate the effects of lipidic ligands at the transcriptional level. Among these, the PPARγ has been known to regulate adipocyte differentiation, fatty acid storage and glucose metabolism, and is a target of antidiabetic drugs. In this work, the interactions between PPARγ and its six known antagonists were investigated using computational methods such as molecular docking, molecular dynamics (MD) simulations, and the hybrid quantum mechanics/molecular mechanics (QM/MM)...
June 14, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28608751/molecular-modelling-studies-of-kdr-mutations-in-voltage-gated-sodium-channel-revealed-significant-conformational-variations-contributing-to-insecticide-resistance
#18
Nanda Kumar Yellapu, Jeyakodi Gopal, Gunasekaran Kasinahtan, Jambulingam Purushothaman
Voltage gated sodium channels (VGSC) of mosquito vectors are the primary targets of DDT and other synthetic pyrethroids used in public health programs. The knockdown resistant (kdr) mutations in VGSC are associated with the insecticide resistance especially in Anophelines. The present study is aimed to emphasize and demarcate the impact of three kdr-mutations such as L1014S, L1014F and L1014H on insecticide resistance. The membrane model of sodium transport domain of VGSC (STD-VGSC) was constructed using de novo approach based on domain and trans-membrane predictions...
June 13, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28605995/dna-trinucleotide-gaa-repeats-in-human-genome-hint-for-disease-pathogenesis
#19
Himanshu Narayan Singh, Barbara Scheiber-Mojdehkar, Moganty R Rajeswari
Short DNA triplet repeats are generally considered to 'benign' in nature, however, it can lead to abnormal genetic features by inducing hyper expansion including mutational hotspots, unusual DNA structure etc. Thus, the expanded DNA base triplets in human genome are expected to play crucial role in disease pathogenesis. One such triplet repeat expansion of (GAA) is observed in FXN gene which is well established to cause neurological disease "Friedreich's ataxia". To explore the association of repeats in other genes if any, we performed a systematic search in the entire human genome...
June 12, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28605994/structure-based-screening-and-molecular-dynamics-simulations-offer-novel-natural-compounds-as-potential-inhibitors-of-mycobacterium-tuberculosis-isocitrate-lyase
#20
Rohit Shukla, Harish Shukla, Amit Sonkar, Tripti Pandey, Timir Tripathi
Mycobacterium tuberculosis is the etiological agent of tuberculosis in humans and is responsible for more than two million deaths annually. M. tuberculosis isocitrate lyase (MtbICL) catalyzes the first step in the glyoxylate cycle, plays a pivotal role in the persistence of M. tuberculosis, which acts as a potential target for an anti-tubercular drug. To identify the potential anti-tuberculosis compound, we conducted a structure-based virtual screening of natural compounds from the ZINC database (n = 1,67,748) against the MtbICL structure...
June 12, 2017: Journal of Biomolecular Structure & Dynamics
journal
journal
28750
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"