Denaturation of HIV-1 protease (PR) monomer by acetic acid: mechanistic and trajectory insights from molecular dynamics simulations and NMR.

abstract：:Solvent properties of aqueous media (dipolarity/polarizability, hydrogen bond donor acidity, and hydrogen bond acceptor basicity) were measured in the coexisting phases of Dextran-PEG aqueous two-phase systems (ATPSs) containing .5 and 2.0 M urea. The differences between the electrostatic and hydrophobic properties of...

journal_title：Journal of biomolecular structure & dynamics

authors： Ferreira LA,Povarova OI,Stepanenko OV,Sulatskaya AI,Madeira PP,Kuznetsova IM,Turoverov KK,Uversky VN,Zaslavsky BY

更新日期：2017-01-01 00:00:00

abstract：:Molecular mechanics and molecular dynamics studies are performed to investigate the conformational preference of cell surface higher gangliosides (GT1A and GT1B) and their interaction with Cholera Toxin. The water mediated hydrogen bonding network exists between sugar residues in gangliosides. An integrated molecular ...

journal_title：Journal of biomolecular structure & dynamics

authors： Sharmila DJ,Veluraja K

更新日期：2006-06-01 00:00:00

abstract：:Histone deacetylase 8 (HDAC8) has emerged as an important therapeutic target due to its involvement in various cancerous and neurodegenerative disease states. Since pan HDAC inhibition has been linked to various side effects, the need of the hour is to develop inhibitors truly selective for one isoform. This work atte...

journal_title：Journal of biomolecular structure & dynamics

authors： Kashyap K,Kakkar R

更新日期：2020-01-01 00:00:00

abstract：:Trying to answer the question posed in the title, we have carried out a detailed theoretical investigation of the biologically important mechanism of the tautomerization of the A·T Watson-Crick DNA base pair, information that is hard to establish experimentally. By combining theoretical investigations at the MP2 and d...

journal_title：Journal of biomolecular structure & dynamics

authors： Brovarets OO,Hovorun DM

更新日期：2014-01-01 00:00:00

abstract：:Adenosine receptors (ARs) belong to family A of GPCRs that are involved in many diseases, including cerebral and cardiac ischemic diseases, immune and inflammatory disorders, etc. Thus, they represent important therapeutic targets to treat these conditions. Computational techniques such as molecular dynamics (MD) simu...

journal_title：Journal of biomolecular structure & dynamics

authors： Martínez-Archundia M,Correa-Basurto J,Montaño S,Rosas-Trigueros JL

更新日期：2019-11-01 00:00:00

abstract：:Fpg protein (formamidopyrimidine or 8-oxoguanine DNA glycosylase) from E. coli catalyzes excision of several damaged purine bases, including 8-oxoguanine and 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine from DNA. In this study the interaction of E. coli Fpg with various specific and nonspecific oligodeoxynucleo...

journal_title：Journal of biomolecular structure & dynamics

authors： Ishchenko AA,Koval VV,Fedorova OS,Douglas KT,Nevinsky GA

更新日期：1999-10-01 00:00:00

abstract：:Low sampling efficiency in conformational space is the well-known problem for conventional molecular dynamics. It greatly increases the difficulty for molecules to find the transition path to native state, and costs amount of CPU time. To accelerate the sampling, in this paper, we re-couple the critical degrees of fre...

journal_title：Journal of biomolecular structure & dynamics

authors： Chen C,Huang Y,Xiao Y

更新日期：2013-01-01 00:00:00

abstract：:An important regulatory domain of NF-[Formula: see text]B Essential Modulator (NEMO) is a ubiquitin-binding zinc finger, with a tetrahedral CYS3HIS1 zinc-coordinating binding site. Two variations of NEMO's zinc finger are implicated in various disease states including ectodermal dysplasia and adult-onset glaucoma. To ...

journal_title：Journal of biomolecular structure & dynamics

authors： Godwin RC,Gmeiner WH,Salsbury FR Jr

更新日期：2018-08-01 00:00:00

abstract：:The solution structure of two double helical nucleic acid fragments, viz, r(CGCGCG) and d(CGCGCG), was probed by means of two-dimensional nuclear Overhauser effect spectroscopy. The two compounds were selected as models for the A-type and B-type double helical conformations, respectively, and it is shown that for each...

journal_title：Journal of biomolecular structure & dynamics

authors： Haasnoot CA,Westerink HP,van der Marel GA,van Boom JH

更新日期：1984-10-01 00:00:00

abstract：:The intrinsic luminescence of different forms of the alfalfa mosaic virus (AMV) strain 425 coat protein has been studied, both statically and time resolved. It was found that the emission of the protein (Mr 24,250), which contains two tryptophans at positions 54 and 190 and four tyrosines, is completely dominated by t...

journal_title：Journal of biomolecular structure & dynamics

authors： Kan JH,Wijnaendts van Resandt RW,Dekkers HP

更新日期：1986-02-01 00:00:00

abstract：:Crystals of the small ribosomal subunit from Thermus thermophilus diffract to 3A and exhibit reasonable isomorphism and moderate resistance to irradiation. A 5A MIR map of this particle shows a similar shape to the part assigned to this particle within the cryo-EM reconstructions of the whole ribosome and contains reg...

journal_title：Journal of biomolecular structure & dynamics

authors： Auerbach T,Pioletti M,Avila H,Anagnostopoulos K,Weinstein S,Franceschi F,Yonath A

更新日期：2000-02-01 00:00:00

abstract：:Breast cancer (BC) is the second most prevalent cancer worldwide. Estrogen receptor beta (ERβ) is an essential protein of breast cells to suppress estrogen-induced uncontrolled proliferation. Thus, small molecules that can modulate and enhance ERβ expression would be an effective agent to suppress BC development. Stud...

journal_title：Journal of biomolecular structure & dynamics

authors： Bhattacharjee A,Hossain MU,Chowdhury ZM,Rahman SMA,Bhuyan ZA,Salimullah M,Keya CA

更新日期：2020-03-11 00:00:00

abstract：:The eIF2α kinase activity of the heme-regulated inhibitor (HRI) is regulated by heme which makes it a unique member of the family of eIF2α kinases. Since heme concentrations create an equilibrium for the kinase to be active/inactive, it becomes important to study the heme binding effects upon the kinase and understand...

journal_title：Journal of biomolecular structure & dynamics

authors： Bhavnani V,Kaviraj S,Panigrahi P,Suresh CG,Yapara S,Pal J

更新日期：2018-08-01 00:00:00

abstract：:This article describes, for the first time, the effect of three different sizes of silver nanoparticles on the binding of curcumin to lysozyme as examined by spectroscopic and zeta potential techniques at physiological conditions. The binding constants of curcumin to lysozyme in the presence of silver nanoparticles we...

journal_title：Journal of biomolecular structure & dynamics

authors： Kamshad M,Jahanshah Talab M,Beigoli S,Sharifirad A,Chamani J

更新日期：2019-05-01 00:00:00

abstract：:Abstract Although the recent structural studies on polymerases have brought new insights on polymerase fidelity, the role of DNA sequence and structure is not well understood. Here, the analysis of the crystal structures of hotspots for polymerase slippage shows that, in the B- form, these sequences share common str...

journal_title：Journal of biomolecular structure & dynamics

authors： Timsit Y

更新日期：2000-01-01 00:00:00

abstract：:In this study, we have theoretically demonstrated the intrinsic ability of the wobble G·T(w)/G*·T*(w)/G·T(w1)/G·T(w2) and Watson-Crick-like G*·T(WC) DNA base mispairs to interconvert into each other via the DPT tautomerization. We have established that among all these transitions, only one single G·T(w) ↔ G*·T(WC) pat...

journal_title：Journal of biomolecular structure & dynamics

authors： Brovarets' OO,Hovorun DM

更新日期：2015-01-01 00:00:00

abstract：:Three dimensional models of NB-ARC domains in five different proteins were constructed based on the recently published crystal structure of the apoptotic protease activating factor 1, of which two are for tomato species, one each for flax, Arabidopsis, and nematode. Standard multiple sequence alignment was performed f...

journal_title：Journal of biomolecular structure & dynamics

authors： Chattopadhyaya R,Pal A

更新日期：2008-02-01 00:00:00

abstract：:Visible and near infrared magnetic circular dichroism (MCD) spectra of heme proteins and enzymes as well as those of a protein-free heme bound to 2-methylimidazole were recorded and compared at 4.2 K in unrelaxed metastable and relaxed equilibrium heme stereochemistry. The relaxed and unrelaxed stereochemistries of a ...

journal_title：Journal of biomolecular structure & dynamics

authors： Sharonov YuA,Pismensky VF,Yarmola EG

更新日期：1989-08-01 00:00:00

abstract：:Our work investigates the interaction of synthesized graphene with the SARS-CoV-2 virus using molecular docking and molecular dynamics (MD) simulation method. The layer dependent inhibitory effect of graphene nanosheets on spike receptor-binding domain of 6LZG, complexed with host receptor i.e. angiotensin-converting ...

journal_title：Journal of biomolecular structure & dynamics

authors： Raval B,Srivastav AK,Gupta SK,Kumar U,Mahapatra SK,Gajjar PN,Banerjee I

更新日期：2020-09-11 00:00:00

abstract：:The so-called CCAAT box is believed to be a major promoter element of higher eukaryotes though it is ill-defined being deduced from very limited sequence data. The comprehensive computer analysis of an unbiased set of 168 promoters presented here removes several of the persisting uncertainties. In particular, it delin...

journal_title：Journal of biomolecular structure & dynamics

authors： Bucher P,Trifonov EN

更新日期：1988-06-01 00:00:00

abstract：:The design and DNA binding activity of beta-structure-forming peptides and netropsin-peptide conjugates are reported. It is found that a pair of peptides-S,S'-bis(Lys-Gly-Val-Cys-Val-NH-NH-Dns)-bridged by an S-S bond binds at least 10 times more strongly to poly(dG).poly(dC) than to poly(dA).poly(dT). This peptide can...

journal_title：Journal of biomolecular structure & dynamics

authors： Nikolaev VA,Grokhovsky SL,Surovaya AN,Leinsoo TA,Sidorova NYu,Zasedatelev AS,Zhuze AL,Strahan GA,Shafer RH,Gursky GV

更新日期：1996-08-01 00:00:00

abstract：:Microtubule affinity regulating kinase 4 (MARK4) plays essential role in the tau-assisted regulation of microtubule dynamics. Over expression of MARK4 causes early phosphorylation of Ser262 of tau protein which is essential for microtubule binding. Hyperphosphorylation of tau protein causes the formation of paired hel...

journal_title：Journal of biomolecular structure & dynamics

authors： Naqvi AAT,Jairajpuri DS,Noman OMA,Hussain A,Islam A,Ahmad F,Alajmi MF,Hassan MI

更新日期：2020-08-01 00:00:00

abstract：:The objective of the present study was to evaluate the effects of propolis, pollen, and caffeic acid phenethyl ester (CAPE) on tyrosine hydroxylase (TH) activity and total RNA levels of Nω-nitro-L-arginine methyl ester (L-NAME) inhibition of nitric oxide synthase in the heart, adrenal medulla, and hypothalamus of hype...

journal_title：Journal of biomolecular structure & dynamics

authors： Ekhteiari Salmas R,Durdagi S,Gulhan MF,Duruyurek M,Abdullah HI,Selamoglu Z

更新日期：2018-02-01 00:00:00

abstract：:We dissect the protein-protein interfaces into water preservation (WP), water hydration (WH) and water dehydration (WD) sites by comparing the water-mediated hydrogen bonds (H-bond) in the bound and unbound states of the interacting subunits. Upon subunit complexation, if a H-bond between an interface water and a prot...

journal_title：Journal of biomolecular structure & dynamics

authors： Mukherjee S,Nithin C,Divakaruni Y,Bahadur RP

更新日期：2019-03-01 00:00:00

abstract：:The selective recognition of the aminoterminal binding pharmacophore Tyr-D-Xaa-Phe of the opioid heptapeptide dermorphin, Tyr-D-Ala-Phe-Gly-Tyr-Pro-Ser-NH2 (DRM)1, and of dermenkephalin, Tyr-D-Met-Phe-His-Leu-Met-Asp-NH2 (DREK), by the mu-opioid receptor and delta-opioid receptor, respectively, depends upon the consti...

journal_title：Journal of biomolecular structure & dynamics

authors： Riand J,Baron D,Nicolas P,Benajiba A,Teng Y,Naim M

更新日期：1999-12-01 00:00:00

abstract：:The knowledge of the relationship between the three-dimensional structure of a protein and its biological and stability is one of the most challenging problem in protein chemistry, since offers the possibility of changing both the specific action of a protein and its stability. In this work, we have approached the pro...

journal_title：Journal of biomolecular structure & dynamics

authors： Pedone EM,Bartolucci S,Rossi M,Saviano M

更新日期：1998-10-01 00:00:00

abstract：:Methylenetetrahydrofolate reductase (MTHFR) protein catalyzes the only biochemical reaction which produces methyltetrahydrofolate, the active form of folic acid essential for several molecular functions. The Ala222Val polymorphism of human MTHFR encodes a thermolabile protein associated with increased risk of neural t...

journal_title：Journal of biomolecular structure & dynamics

authors： Abhinand PA,Shaikh F,Bhakat S,Radadiya A,Bhaskar LV,Shah A,Ragunath PK

更新日期：2016-01-01 00:00:00

abstract：:The potassium channel Kv1.3 is an important pharmacological target and the Kaliotoxin-type toxins (α-KTX-3 family) are its specific blockers. Here, we study the binding process of two kinds of Kaliotoxin-type toxins:BmKTX and its mutant (BmKTX-D33H) toward to Kv1.3 channel using MD simulation and umbrella sampling sim...

journal_title：Journal of biomolecular structure & dynamics

authors： Zheng Q,Na R,Yang L,Yu H,Zhao X,Huang X

更新日期：2020-05-06 00:00:00

abstract：:We have analysed by various approaches the structure of cloned synthetic sequences in supercoiled plasmids. Individual inserts were formed by d(C-G)n blocks interrupted by the presence of A.T pairs positioned either in phase or out of phase of pur-pyr alternation. Based on the thermodynamic analysis we obtained result...

journal_title：Journal of biomolecular structure & dynamics

authors： Vlach J,Sponar J

更新日期：1990-04-01 00:00:00

abstract：:Cystatins are classical competitive inhibitors of C1 family cysteine proteases (papain family). Phytocystatin superfamily shares high sequence homology and typical tertiary structure with conserved glutamine-valine-glycine (Q-X-V-X-G) loop blocking the active site of C1 proteases. Here, we develop a cysteine-bounded c...

journal_title：Journal of biomolecular structure & dynamics

authors： Mishra M,Singh V,Tellis MB,Joshi RS,Pandey KC,Singh S

更新日期：2020-12-09 00:00:00