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Journal of Biomolecular Structure & Dynamics

Gurpreet Kaur, Varsha Dogra, Rajeev Kumar, Sandeep Kumar, Kashmir Singh
The present work aims at the fabrication of iron oxide nanocolloids using biocompatible microemulsion and their cytotoxic, genotoxic effect on Vitis vinifera plant has been evaluated. The three-iron based metallosurfactant complexes were synthesized. Nanosuspensions (Ns) were prepared using microemulsion technique and for the purpose, the microemulsion was prepared using oleic acid, butanol, tween 80 and as synthesized iron metallosurfactant. In this technique, no additional capping agent and/or reducing agent was added...
February 16, 2018: Journal of Biomolecular Structure & Dynamics
Fan Zhao, Wei Jin, Lin Ma, Jian-Ye Zhang, Jin-Long Wang, Jing-Hai Zhang, Yong-Bo Song
Voltage-gated sodium (Na v ) channels play a pivotal role for the changes in membrane potential and belong to large membrane proteins that compose four voltage sensor domains (VSD1-4). In this study we describe the binding mode and selectivity of one of the aryl sulfonamide sodium channel inhibitors, PF-04856264, for the VSD4s in Na v 1.4, Na v 1.5 and Na v 1.7, respectively, through molecular dynamics simulation and enhanced post-dynamics analyses. Our results show that there are three binding site regions (BSR1-3) in the combination of the ligand and receptors, of which BSR1 and BSR3 contribute to the selectivity and affinity of the ligand to the receptor...
February 15, 2018: Journal of Biomolecular Structure & Dynamics
Yudibeth Sixto-López, Martiniano Bello, José Correa-Basurto
Histone deacetylases (HDACs) are a family of proteins whose main function is the removal of acetyl groups from lysine residues located on histone and non-histone substrates, which regulates gene transcription and other activities in cells. HDAC1 dysfunction has been implicated in cancer development and progression; thus, its inhibition has emerged as a new therapeutic strategy. Two additional metal binding sites (Site 1 and Site 2) in HDACs have been described that are primarily occupied by potassium ions, suggesting a possible structural role that affects HDAC activity...
February 15, 2018: Journal of Biomolecular Structure & Dynamics
Rakesh Kumar, Ranjana Maurya, Shweta Saran
Prostate cancer (PC) is one of the leading cancers in men, raising a serious health issue worldwide. Due to lack of suitable biomarker, their inhibitors and the platform for testing those inhibitors result in poor prognosis of PC. AMPK (AMP-activated protein kinase) is a highly conserved protein kinase found in eukaryotes that is involved in growth and development, and also acts as a therapeutic target for PC. The aim of the present study is to identify novel potent inhibitors of AMPK and propose a simple cellular model system for understanding its biology...
February 15, 2018: Journal of Biomolecular Structure & Dynamics
Hamid Tanzadehpanah, Hanie Mahaki, Neda Hosseinpour Moghadam, Sadegh Salehzadeh, Omid Rajabi, Rezvan Najafi, Razieh Amini, Massoud Saidijam
This study was carried out to evaluate the binding interaction of gefitinib (GEF) with human serum albumin (HSA) and calf thymus DNA (ct-DNA) using fluorescence, UV-visible, zeta potential measurements and molecular docking methods in order to understand its pharmacokinetic mechanism. By increasing the temperature, a steady decrease in Stern-Volmer quenching constants was observed for HSA binding properties; this indicates a static type of fluorescence quenching. Negative values were calculated for Gibbs free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) changes, indicating that the reaction is spontaneous and enthalpy-driven...
February 15, 2018: Journal of Biomolecular Structure & Dynamics
Ikrormi Rungsung, Amutha Ramaswamy
The Liver kinase B1 (LKB1) is encoded by LKB1 gene. Several pathogenic mutations of LKB1 causing Peutz-Jeghers syndrome (PJS) and also cancers in breast, gastric, pancreas and colon have been reported. The present study is focused to analyze the effects on the structural dynamics of LKB1 caused by the 4 pathogenic missense mutations (L67P, L182P, G242V and R297S), which are reported to reduce the catalytic activity. In this study, the structural changes of LKB1 in apo- and in heterotrimeric complex (LKB1-STRADα-MO25α) form with wild and mutated LKB1 are investigated using all atomistic molecular dynamic simulation...
February 15, 2018: Journal of Biomolecular Structure & Dynamics
Rui Wang, Srivathsan V Ranganathan, Phensinee Haruehanroengra, Song Mao, Matteo Scalabrin, Daniele Fabris, Alan Chen, Hehua Liu, Abdalla E A Hassan, Jianhua Gan, Jia Sheng
The facile construction of metal-DNA complexes by using 'Click' reactions is reported here. A series of 2'-propargyl-modified DNA oligonucleotides were initially synthesized as structure scaffolds and were then modified through 'Click' reaction to incorporate a bipyridine ligand equipped with an azido group. These metal chelating ligands can be placed in the DNA context in site-specific fashion to provide versatile templates for binding various metal ions, which are exchangeable by using a simple EDTA washing-and-filtration step...
February 15, 2018: Journal of Biomolecular Structure & Dynamics
Sivashanmugam Muthukumaran, K N Sulochana, V Umashankar
Ornithine Decarboxylase (ODC) is an enzyme that initiates polyamine synthesis in human. Polyamines play key roles in cell-cell adhesion, cell motility and Cell cycle regulation. Higher synthesis of polyamines also occurs in rapidly proliferating cancer cells are mediated by ODC. As per earlier studies, Di-Flouro Methyl Orninthine (DFMO) is a proven efficient inhibitor ODC targeting the catalytic activity, however, its usage is limited due to side effects. Targeting ODC is considered as a potential therapeutic modality in the treatment of cancer...
February 13, 2018: Journal of Biomolecular Structure & Dynamics
Esmaeil Behmard, Ali Najafi, Ali Ahmadi
Antibiotic resistance is a threatening challenge for global health, as the expansion of resistance to current antibiotics has made serious therapeutic problems. Genome mutations are key evolutionary mechanisms conferring antibiotic resistance in bacterial pathogens. For example, penicillin and cephalosporins resistance is mostly mediated by mutations in penicillin binding proteins to change the affinity of the drug. Accordingly, threonine point mutations were reported to develop antibiotic resistance in various bacterial infections including pneumococcal infections...
February 11, 2018: Journal of Biomolecular Structure & Dynamics
P Raghuraman, C Sudandiradoss
Singleton Merton syndrome, a critical and rare multifactorial disorder that is closely linked to R516Q mutation in MDA5 protein associated with an enhanced interferon response in the affected individual. In the present study, we provide conclusive key evidence on R516Q mutation and their connectivity towards sequence-structural basis dysfunction of MDA5 protein. Among the various mutations, we found R516Q is the most pathogenic mutation based on mutational signature Q-A-[RE]-G-R-[GA]-R-A-[ED]-[DE]-S-[ST]-Y-[TSAV]-L-V designed from our work...
February 11, 2018: Journal of Biomolecular Structure & Dynamics
Upasana Sridharan, Preethi Ragunathan, Barbara Spellerberg, Karthe Ponnuraj
Metal binding receptors are one of the extracellular components of ATP-binding cassette transporters that are essential for regulation of metal homeostasis in bacteria. Laminin binding adhesin (Lmb) of Streptococcus agalactiae falls under this class of solute binding proteins. It binds to zinc with a high affinity. Crystal structure of Lmb solved previously by our group reveals that the zinc is tetrahedrally coordinated by three histidines and a glutamate at the interdomain cleft. Lmb contains a long disordered loop close to the metal binding site whose precise function is unknown...
February 8, 2018: Journal of Biomolecular Structure & Dynamics
Adriano Mollica, Gokhan Zengin, Serdar Durdagi, Ramin Ekhteiari Salmas, Giorgia Macedonio, Azzurra Stefanucci, Marilisa Pia Dimmito, Ettore Novellino
Human α-glucosidase is an enzyme involved in the catalytic cleavage of the glucoside bond and involved in numerous functionalities of the organism, as well as in the insurgence of diabetes mellitus 2 and obesity. Thus, developing chemicals that inhibit this enzyme is a promising approach for the treatment of several pathologies. Small peptides such as di- and tri-peptides may be in natural organism as well as in the GI tract in high concentration, coming from the digestive process of meat, wheat and milk proteins...
February 8, 2018: Journal of Biomolecular Structure & Dynamics
Vishnu Kant, Saravanan Vijayakumar, Ganesh Chandra Sahoo, Shailendra S Chaudhery, Pradeep Das
OASS is a specific enzyme that helps Leishmania parasite to survive the oxidative stress condition in human macrophages. SAT C-terminal peptides in several organisms, including Leishmania, were reported to inhibit or reduce the activity of OASS. Small peptide and small molecules mimicking the SAT C-terminal residues are designed and tested for the inhibition of OASS in different organisms. Hence, in this study, all the possible tetra-peptide combinations were designed and screened based on the docking ability with Leishmania donovani OASS (Ld-OASS)...
February 7, 2018: Journal of Biomolecular Structure & Dynamics
Hossein Farrokhpour, Alireza Mansouri, Ahmad Reza Rajabi, Alireza Najafi Chermahini
In this work, the transport behaviors of the enantiomers of lactic acid (LA) in two cyclic peptide nanotubes (CPNTs) with different diameters were studied using steered molecular dynamic (SMD) simulation to investigate the effect of the diameter of CPNT on the discrimination of the enantiomers of LA. For this purpose, two cyclic peptides with two different sizes ([Ala-D-Ala-L]5 and [Ala-D-Ala-L]4) were used for constructing two CPNTs so that each CPNT was composed of eight cyclic peptide units. The docking calculations were performed to obtain the appropriate position of each enantiomer at the lumen of each CPNT...
February 2, 2018: Journal of Biomolecular Structure & Dynamics
Hajar Molaee, Mehdi Sahihi, Majid Moghadam, Valiollah Mirkhani, Shahram Tangestaninejad, Iraj Mohammadpoor-Baltork, Hadi Amiri Rudbari
No abstract text is available yet for this article.
February 2, 2018: Journal of Biomolecular Structure & Dynamics
Md Ataul Islam, Tahir S Pillay
In this study we searched for potential β-site amyloid precursor protein cleaving enzyme1 (BACE1) inhibitors using pharmacoinformatics. A large dataset containing 7155 known BACE1 inhibitors was evaluated for pharmacophore model generation. The final model (R = 0.950, RMSD = 1.094, Q2 = 0.901, se = 0.332, [Formula: see text] = 0.901, [Formula: see text] = 0.756, sp = 0.468, [Formula: see text] = 0.667) was revealed with the importance of spatial arrangement of hydrogen bond acceptor and donor, hydrophobicity and aromatic ring features...
February 1, 2018: Journal of Biomolecular Structure & Dynamics
Larisa V Kordyukova, Eleonora V Shtykova, Lyudmila A Baratova, Dmitri I Svergun, Oleg V Batishchev
Influenza A virus, a member of the Orthomyxoviridae family of enveloped viruses, is one of the human and animal top killers, and its structure and components are therefore extensively studied during the last decades. The most abundant component, M1 matrix protein, forms a matrix layer (scaffold) under the viral lipid envelope, and the functional roles as well as structural peculiarities of the M1 protein are still under heavy debate. Despite multiple attempts of crystallization, no high resolution structure is available for the full length M1 of Influenza A virus...
February 1, 2018: Journal of Biomolecular Structure & Dynamics
Rabeeh Khorram, Heidar Raissi, Ali Morsali, Mahnaz Shahabi
In the present study, it is attempted to scrutinize the properties of the Maghemite nanoparticle as a Carmustine drug delivery system by means of the density functional theory calculations regarding their geometries, adsorption energies, vibrational frequencies, and topological features of the electron density. Based on the density functional theory results, it is found that the interaction between Carmustine drug molecule and Maghemite nanoparticle is weak; so that, the adsorption of the Carmustine drug is typically physisorption...
January 30, 2018: Journal of Biomolecular Structure & Dynamics
Thomas A Collier, Anthony Nash, Helen L Birch, Nora H de Leeuw
Type I collagen is an essential extracellular protein that plays an important structural role in tissues that require high tensile strength. However, owing to the molecule's size, to date no experimental structural data are available for the Homo sapiens species. Therefore, there is a real need to develop a reliable homology model and a method to study the packing of the collagen molecules within the fibril. Through the use of the homology model and implementation of a novel simulation technique, we have ascertained the orientations of the collagen molecules within a fibril, which is currently below the resolution limit of experimental techniques...
January 30, 2018: Journal of Biomolecular Structure & Dynamics
Lingyun Wang, Joanne E Murphy-Ullrich, Yuhua Song
Cell surface calreticulin (CRT) binding to thrombospondin-1 (TSP1), regulates cell adhesion, migration, anoikis resistance, and collagen production. Due to the essential role of membrane microdomains in CRT-mediated focal adhesion disassembly, we previously studied the effect of raft-like bilayers on TSP1-CRT interactions with all-atom molecular dynamics (AAMD) simulations. However, the simulated systems of protein on the surface of the bilayer(s) in the explicit solvent are too large for long time scale AAMD simulations due to computational expense...
January 30, 2018: Journal of Biomolecular Structure & Dynamics
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