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Journal of Biomolecular Structure & Dynamics

Nurbubu T Moldogazieva, Konstantin V Shaitan, Mikhail Yu Antonov, Innokenty M Mokhosoev, Olga V Levtsova, Аlexander A Terentiev
Short linear motifs (SLiMs) have been recognized to perform diverse functions in a variety of regulatory proteins through the involvement in protein-protein interactions, signal transduction, cell cycle regulation, protein secretion, etc. However, detailed molecular mechanisms underlying their functions including roles of definite amino acid residues remain obscure. In our previous studies, we demonstrated that conformational dynamics of amino acid residues in oligopeptides derived from regulatory proteins such as alpha-fetoprotein (AFP), carcino-embryonic antigen (CEA) and pregnancy specific β1-glycoproteins (PSGs) contributes greatly to their biological activities...
April 27, 2017: Journal of Biomolecular Structure & Dynamics
Felipe Rodrigues de Souza, Danielle Rodrigues Garcia, Teobaldo Cuya Guizado, Kamil Kuca, Ricardo Bicca de Alencastro, Tanos Celmar Costa França
Tabun is one of the most dangerous the nerve agent because it has deleterious effects like inhibition of the essential enzymes acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). Some oximes, such HI6 as 2-PAM are nucleophiles that capable to reactivate inhibited human AChE under some conditions. Zwitterionic and cationic species have the best chance of productive action on inhibited AChE. However uncharged oximes can give important interaction information. In order to investigate the interaction and behavior of cationic and uncharged oximes, we performed molecular docking simulations and molecular dynamics and calculated binding energies of complexes of these compounds with human AChE...
April 26, 2017: Journal of Biomolecular Structure & Dynamics
Sumith Yesudasan, Xianqiao Wang, Rodney D Averett
We developed a new mechanical model for determining the compression and shear mechanical behavior of four different hemoglobin structures. Previous studies on hemoglobin structures have focused primarily on overall mechanical behavior; however, this study investigates the mechanical behavior of hemoglobin, a major constituent of red blood cells (RBCs), using steered molecular dynamics (SMD) simulations to obtain anisotropic mechanical behavior under compression and shear loading conditions. Four different configurations of hemoglobin molecules were considered: deoxyhemoglobin (deoxyHb), oxyhemoglobin (HbO2), carboxyhemoglobin (HbCO), and glycated hemoglobin (HbA1C)...
April 25, 2017: Journal of Biomolecular Structure & Dynamics
Yoonjung Kim, Myeongsang Lee, Hyunsung Choi, Inchul Baek, Jae In Kim, Sungsoo Na
Silk materials are receiving significant attention as base materials for various functional nanomaterials and nanodevices, due to its exceptionally high mechanical properties, biocompatibility, and degradable characteristics. Although crystalline silk regions are composed of various repetitive motifs with differing amino acid sequences, how the effect of humidity works differently on each of the motifs and their structural characteristics remains unclear. We report molecular dynamics (MD) simulations on various silkworm fibroins composed of major motifs (i...
April 25, 2017: Journal of Biomolecular Structure & Dynamics
Daniela Nadvorny, José Lamartine Soares-Sobrinho, Monica F de La Roca Soares, Antônio José Ribeiro, Francisco Veiga, Gustavo M Seabra
No abstract text is available yet for this article.
April 24, 2017: Journal of Biomolecular Structure & Dynamics
R Radhika, R Shankar, S Vijayakumar, P Kolandaivel
The theoretical studies on DNA with the anticancer drug 6-Mercaptopurine (6-MP) are investigated using theoretical methods to shed light on drug designing. Among the DNA base pairs considered, 6-MP is stacked with GC with the highest interaction energy of -46.19 kcal/mol. Structural parameters revealed that structure of the DNA base pairs is deviated from the planarity of the equilibrium position due to the formation of hydrogen bonds and stacking interactions with 6-MP. These deviations are verified through the systematic comparison between X-H bond contraction and elongation and the associated blue shift and red shift values by both NBO analysis and vibrational analysis...
April 24, 2017: Journal of Biomolecular Structure & Dynamics
Sareh Zareian-Jahromi, Hassan Mansouri-Torshizi
Two new Palladium(II) isomeric complexes, [Pd(Gly)(Leu)](I) and [Pd(Gly)(Ile)](II), where Gly is glycine, and Leu and Ile are isomeric amino acids (leucine and isoleucine), have been synthesized and characterized by elemental analysis, molar conductivity measurements, FT-IR, (1)H NMR and UV-Vis. The complexes have been tested for their In vitro cytotoxicity against cancer cell line K562 and their binding properties to calf thymus DNA (CT-DNA) and human serum albumin (HSA) have also been investigated by multispectroscopic techniques...
April 23, 2017: Journal of Biomolecular Structure & Dynamics
Selin Seda Timur, Gözde Yalçın, Özge Çevik, Cenk Andaç, R Neslihan Gürsoy
Recent studies in tumor homing peptides have shown the specificity of LyP-1 (CGNKRTRGC) to tumor lymphatics. In this present work, we evaluated the possible interactions between cyclic LyP-1 and its receptor, p32, with molecular dynamics and docking studies in order to lead the design of novel LyP-1 derivatives, which could bind to p32 more effectively and perform enhanced antitumor effect. The total binding enthalpy energies have been obtained by MM-PBSA thermodynamic computations and the favorability of p32...
April 21, 2017: Journal of Biomolecular Structure & Dynamics
Tabassum Hossain, Achintya Saha, Arup Mukherjee
The acetylcholinesterase enzyme (AChE) plays an important role in central and peripheral nervous systems. Acetylcholine (ACh) acts through the regulation of AChE activity, which can play a key role in accelerating senile amyloid β-peptide (Aβ) plaque deposition. Therefore, inhibition of the AChE enzyme can be used as a key principle to prevent ACh depletion. The present study has been emphasized to explore both ligand- and structure-based 3D QSAR, HQSAR, pharmacophore, molecular docking and simulation studies on a set of structurally diverse inhibitors to optimize prime structural features responsible for selective binding to AChE, and vis-à-vis inhibiting enzyme activity...
April 18, 2017: Journal of Biomolecular Structure & Dynamics
Shuyun Bi, Huifeng Zhou, Jun Wu, Yu Wang
No abstract text is available yet for this article.
April 16, 2017: Journal of Biomolecular Structure & Dynamics
Hamed S Hayatshahi, Christina Bergonzo, Thomas E Cheatham
The interactions in the tertiary structure of a ribosomal RNA fragment in the GTPase Associating Center (GAC) have been experimentally studied, but the roles of the bound and diffuse cations in its folding pathway have not yet been fully elucidated. Melting experiments have shown that the temperature of the first of the two distinguishable transitions in the unfolding pathway of the GAC RNA can be regulated by altering the magnesium concentration, yet the physical interpretation of such ion-dependent effects on folding have not been clearly understood in spite of the availability of crystal structures that depict many GAC RNA-ion interactions...
April 13, 2017: Journal of Biomolecular Structure & Dynamics
Meng Gao, Fei Yang, Lei Zhang, Zhengding Su, Yongqi Huang
βγ-Crystallins are a superfamily of proteins containing crystallin-type Greek key motifs. Some βγ-crystallin domains have been shown to bind Ca(2+). Hahellin is a newly identified intrinsically disordered βγ-crystallin domain from Hahella chejuensis. It folds into a typical βγ-crystallin structure upon Ca(2+) binding and acts as a Ca(2+)-regulated conformational switch. Besides Hahellin, another two putative βγ-crystallins from Caulobacter crescentus and Yersinia pestis are shown to be partially disordered in their apo-form and undergo large conformational changes upon Ca(2+) binding, although whether they acquire a βγ-crystallin fold is not known...
April 13, 2017: Journal of Biomolecular Structure & Dynamics
(no author information available yet)
No abstract text is available yet for this article.
April 12, 2017: Journal of Biomolecular Structure & Dynamics
Mohsin Vahid Khan, Mohd Ishtikhar, Mohammad Khursheed Siddiqui, Masihuz Zaman, Tajalli Ilm Chandel, Nabeela Majid, Mohd Rehan Ajmal, Ali Saber Abdelhameed, Yasser E Shahein, Rizwan Hasan Khan
The aggregation phenomenon (amyloid and amorphous) is associated with several pathological complications in human, such as Alzheimer's, Parkinson's, Huntington, Cataract diseases and Diabetes mellitus type 2. In the present study we are offering evidence and breaking the general belief with regard to the polyphenols action as protein aggregate inhibitors. Herein we confirm that tannic acid (TA) is not only an amyloid inducer, but also it switches one type of conformation, ultimately morphology, into another...
April 11, 2017: Journal of Biomolecular Structure & Dynamics
Manasa Kongot, Neha Maurya, Neeraj Dohare, Mehraj Ud Din Parray, Jitendra Kumar Maurya, Amit Kumar, Rajan Patel
No abstract text is available yet for this article.
April 11, 2017: Journal of Biomolecular Structure & Dynamics
Subramanian Vidhyasankar, Nallasamy Dharmaraj, Ponmalai Kolandaivel
The Carbon nano tubes (CNT) are potential candidate for many biomedical applications especially in targeted drug delivery for cancer diseases. However the use of CNT has limitations due to its insolubility in aqueous media. The self-assembly of cyclic peptide encased on the CNT has enhanced its dispersion in aqueous medium which extend their applications as anti-bacterial and drug delivery agents. To understand this process, an attempt has been made to investigate the dynamics and stability of trimer cyclic peptide encasing with CNT using classical molecular dynamics...
April 11, 2017: Journal of Biomolecular Structure & Dynamics
Privita Verma, Monalisa Tiwari, Vishvanath Tiwari
Emergence of multi-drug resistant strains of Acinetobacter baumannii has caused significant health problems and is responsible for high morbidity and mortality. Overexpression of AdeABC efflux system is one of the major mechanisms. In this study, we have focused on overcoming the drug resistance by identifying inhibitors that can effectively bind and inhibit integral membrane protein, AdeB of this efflux pump. We performed homology modeling to generate structure of AdeB using MODELLER v9.16 followed by model refinement using 3D-Refine tool and validated using PSVS, ProsaWeb, ERRAT etc...
April 10, 2017: Journal of Biomolecular Structure & Dynamics
Manoj Kumar Mahapatra, Krishnendu Bera, Durg Vijay Singh, Rajnish Kumar, Manoj Kumar
Protein tyrosine phosphatase 1B (PTP1B) has been identified as negative regulator of insulin and leptin signalling pathway, hence it can be considered as a new therapeutic target of intervention for the treatment of type2 diabetes. Inhibition of this molecular target takes care of both diabetes and obesity, i.e., diabestiy. In order to get more information on identification and optimisation of lead, pharmacophore modelling, atom-based 3D QSAR, docking and molecular dynamics studies were carried out on a set of ligands containing thiazolidine scaffold...
April 10, 2017: Journal of Biomolecular Structure & Dynamics
Martina Devi, R H Duncan Lyngdoh
Alanine is encoded by the four codons of the GC box (GCA, GCG, GCU, and GCC). Known alanine anticodons include the UGC, IGC, and VGC triplets (I = inosine; V = uridine-5-oxyacetic acid). The energy-minimized structures of all possible codon-anticodon combinations involving all the alanine codons GCA, GCG, GCU, and GCC with the alanine anticodons UGC, IGC, and VGC are studied using the AMBER software. Fifteen H-bonded duplex structures arising out of these combinations are studied here, all having Watson-Crick-type base pairs at the first and second codon positions, and a variety of base pairing possibilities at the third (or wobble) position...
April 10, 2017: Journal of Biomolecular Structure & Dynamics
Shaun T Mutter, Robert J Deeth, Matthew Turner, James A Platts
Ligand field molecular mechanics (LFMM) parameters have been benchmarked for copper (II) bound to the amyloid-β1-16 peptide fragment. Several density functional theory (DFT) optimised small test models, representative of different possible copper coordination modes, have been used to test the accuracy of the LFMM copper bond lengths and angles, resulting in errors typically less than 0.1 Å and 5°. Ligand field molecular dynamics (LFMD) simulations have been carried out on the copper bound amyloid-β1-16 peptide and snapshots extracted from the subsequent trajectory...
March 31, 2017: Journal of Biomolecular Structure & Dynamics
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