Abstract:
:Our earlier study on the nucleosomes containing TBP binding sites (TATA boxes) indicated that generally the same sequence, which harbors the TATA box, encodes simultaneously an alternative rotational setting of the box, so that the TATA element is either exposed (position "minor groove out") or hidden in position "minor groove in". The sequence elements (dinucleotides) residing on the inner surface of DNA in contact with histone octamers are identified by calculating YR tracks in the promoter regions of the genes - periodically reappearing YR elements, at distances of 10-11 bases from one another. Non-YR elements of the YR tracks are also verified by nucleosome mapping procedure based on alternation of runs of purines with runs of pyrimidines. The tracks observed in yeast promoter regions are found to split into two, passing further downstream either through the TATA element or 4-6 bases toward the tail of the box. The points of splitting which play the role of TATA switches are located in close vicinity or within the transcription factor binding sites. This suggests the regulatory function of transcription factors changing the YR tracks by over- or under-twisting DNA induced by their binding.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Trifonov ENdoi
10.1080/07391102.2015.1134348subject
Has Abstractpub_date
2016-12-01 00:00:00pages
2741-2747issue
12eissn
0739-1102issn
1538-0254journal_volume
34pub_type
杂志文章abstract::Phospholipase A(2) belongs to a super family of enzymes that is massively over expressed in a variety of severe inflammatory diseases, which degrades membrane phospholipids. It has also been reported that this activity leads to loss of tissue, organ integrity and function. This enzyme is an important target for anti-i...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2010.10507333
更新日期:2010-02-01 00:00:00
abstract::Indoleamine-2,3-dioxygenase 1 (IDO1) is an extrahepatic, heme-containing and tryptophan-catalyzing enzyme responsible for causing blockade of T-cell proliferation and differentiation by depleting tryptophan level in cancerous cells. Therefore, inhibition of IDO1 may be a useful strategy for immunotherapy against cance...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1615000
更新日期:2020-04-01 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
pub_type: 杂志文章
doi:10.1080/07391102.1999.10508376
更新日期:1999-12-01 00:00:00
abstract::Non-homologous end joining (NHEJ) is a major DNA double strand breaks (DSBs) repair pathway that maintains genome integrity. However, this pathway may reduce radiotherapy efficacy by repairing DSBs on cancer cells. This research reported a computer-aided drug design (CADD) method to identify novel inhibitors from trad...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2011.10508616
更新日期:2011-06-01 00:00:00
abstract::A protein with the reversed direction of its polypeptide chain, retro-SHH, was analyzed by several spectroscopic techniques including circular dichroism and high-resolution NMR to understand its solution structure and structural consequences of interaction with the micelles formed by the zwitterionic detergent dodecyl...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2012.762724
更新日期:2014-01-01 00:00:00
abstract::Repeat regions are low-complexity regions in the human genome that largely code for intrinsic disorder in proteins. Expansions outside the normal thresholds in repeat regions are likely to be pathogenic, leading to the so-called repeat expansion diseases. There have been numerous studies on the most common group of re...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2021.1871957
更新日期:2021-01-18 00:00:00
abstract::Within the five classes (α, β, γ, δ, and ζ) of carbonic anhydrases (CAs) the first two, containing mammal and plant representatives, are the most studied among all CAs. In this study, we have focused our investigation on the beta-class carbonic anhydrase of Methanobacterium thermoautotrophicum. We investigated both th...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2015.1025100
更新日期:2016-01-01 00:00:00
abstract::Time Correlated Single Photon Counting (TCSPC) was used for the first time to analyze the effect/changes in the mode of intercalation of ethidium bromide (EtBr) and acridine orange (AO) to calf thymus DNA brought about due to interaction of naturally occurring methylxanthines such as theophylline (X1), theobromine (X2...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2003.10506884
更新日期:2003-04-01 00:00:00
abstract::A useful property of DMSO solvent has been exploited to reveal a new catalytic route for cytidine amino proton exchange, relevant to exchange in the macromolecular state, but hidden in aqueous solution. Additional exchange mechanisms in aqueous monomeric cytidine (and adenosine) are obscured by the formation of a fast...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1986.10506359
更新日期:1986-12-01 00:00:00
abstract::This work is devoted to the careful QM/QTAIM analysis of the evolution of the basic physico-chemical parameters along the intrinsic reaction coordinate (IRC) of the biologically important 2AP·T(WC)↔2AP·T*(w) and 2AP·C*(WC)↔2AP·C(w) Watson-Crick(WC)↔wobble(w) tautomeric transformations obtained at each point of the IRC...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2017.1331864
更新日期:2018-05-01 00:00:00
abstract::α-helices are the most common form of secondary structure found in proteins. In order to study controlled protein folding, as well as manipulate the interface of helical peptides with targets in protein-protein interactions, many techniques have been developed to induce and stabilize α-helical structure in short synth...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2014.897260
更新日期:2015-01-01 00:00:00
abstract::Interaction between a cationic porphyrin and its ferric derivative with oligo(dA.dT)15 and oligo(dG.dC)15 was studied by UV-vis spectroscopy, resonance light scattering (RLS), and circular dichroism (CD) at different ionic strengths; molecular docking and molecular dynamics simulation were also used for completion. Fo...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2014.963674
更新日期:2015-01-01 00:00:00
abstract::A new molecular mechanism of trinucleotide expansion diseases is suggested. The mechanism involves the formation of double-helical RNA hairpins by transcripts carrying (CNG)(n) sequences, which are processed via the RNAi pathway with subsequent RNA silencing of genes containing (CNG)(n) sequences. Depletion of protein...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2005.10531230
更新日期:2005-12-01 00:00:00
abstract::Eukaryotic translation initiation factors (eIFs) are the group of regulatory proteins that are involved in the initiation of translation events. Among them, eIF4A1, a member of the DEAD-box RNA helicase family, participates in a wide spectrum of activities which include, RNA splicing, ribosome biogenesis, and RNA degr...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1751295
更新日期:2020-05-05 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
pub_type: 杂志文章
doi:10.1080/07391102.2017.1288660
更新日期:2018-02-01 00:00:00
abstract::Enumerating procedure for symbol sequences is proposed. Relationship between Hamming distance for symbol sequences and Euclidean distance for corresponding enumerations is established, and more universal Hamming-transformed Euclidean measure is constructed. A distribution function of amino acid substitutions and some ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1997.10508187
更新日期:1997-10-01 00:00:00
abstract::We report here two new small-size peptides acting as modulators of the β-site APP cleaving enzyme 1 (BACE1) exosite. Ac-YPYFDPL-NH2 and Ac-YPYDIPL-NH2 displayed a moderate but significant inhibitory effect on BACE1. These peptides were obtained from a molecular modeling study. By combining MD simulations with ab initi...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2016.1145143
更新日期:2017-02-01 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
pub_type: 杂志文章
doi:10.1080/07391102.2018.1564700
更新日期:2019-11-01 00:00:00
abstract::Kisspeptins are neuropeptide that has emerged as an essential gatekeeper for reproduction and onset of puberty in higher vertebrates including fish. In present study, structural analysis, molecular docking and molecular dynamics simulations of kisspeptin receptor (kiss2r) were carried out, which is a G-protein-coupled...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1633407
更新日期:2020-05-01 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
pub_type: 杂志文章
doi:10.1080/07391102.1996.10508927
更新日期:1996-08-01 00:00:00
abstract::The results of Raman and Infrared (IR) spectroscopic investigations on the vibrational modes of dimethyl phosphorothioate (DMPS) anion, [(CH3O)2(POS)]-, are reported. Ab initio calculations of the vibrational modes, the IR and Raman spectra and the interatomic force constants of DMPS were performed. A normal mode calc...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1997.10508149
更新日期:1997-02-01 00:00:00
abstract::In the present work, we propose to design drugs that target the enzyme dihydrofolate redutase (DHFR) as a means of a novel drug therapy against plague. Potential inhibitors of DHFR from Yersinia pestis (YpDHFR) were selected by virtual screening and subjected to docking, molecular dynamics (MD) simulations, and Poisso...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2015.1110832
更新日期:2016-10-01 00:00:00
abstract::The interactions of the drugs 2,7-bis[(diethylamino)-ethoxy]-fluoren-9-one dihydrochloride (Tilorone), 2,7-bis[(dipropylamino)-acetamido]-fluoren-9-one dihydrochloride (FA-2), 2'-(4-hydroxyphenyl)-5-(4-methyl-1-piperazinyl)-2,5'-bi-1H-benzimidazole trihydrochloride (Hoechst 33258), and hematoporphyrin IX derivative (H...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1998.10508239
更新日期:1998-10-01 00:00:00
abstract::MAP/microtubule affinity-regulating kinase 4 (MARK4) is a member of adenosine monophosphate-activated protein kinases, directly associated with cancer and neurodegenerative diseases. Here, we have cloned, expressed, and purified two variants of MARK4 [the kinase domain (MARK4-F2), and kinase domain along with 59 N-ter...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2015.1074942
更新日期:2016-06-01 00:00:00
abstract::Poly(dA-dT).poly(dA-dT) can adopt the B- and D- forms in the fibrous state. Theoretical energy calculations and fiber diffraction analyses suggest that there can be three structural models of poly(dA-dT).poly(dA-dT) in each of these two forms viz right and left-handed Watson Crick models and left-handed Hoogsteen--a t...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1983.10507450
更新日期:1983-10-01 00:00:00
abstract::Calcium Dependent Protein Kinases are found in the Apicomplexan, algae, and plants; however, they are not reported in vertebrates and are regarded as excellent drug targets for pharmaceutical interventions. Calcium Dependent Protein Kinases of Cryptosporidium are probably involved in the regulation of invasion and egr...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1790036
更新日期:2020-07-07 00:00:00
abstract::We have developed an iterative hybrid algorithm (HA) to predict the 3D structure of peptides starting from their amino acid sequence. The HA is made of a modified genetic algorithm (GA) coupled to a local optimizer. Each HA iteration is carried out in two phases. In the first phase several GA runs are performed upon t...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2003.10506906
更新日期:2003-08-01 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
pub_type: 杂志文章
doi:10.1080/07391102.2020.1760135
更新日期:2020-05-06 00:00:00
abstract::Diabetes is very much known as a wide-spread disorder all around the world with serious complications for the diabetic patient. In order to reduce these complications, inhibition the activity of aldose reductase (AR) and cyclooxygenase-2 (COX-2) enzymes is a proposed pathway. Within this work potency of curcumin (CUR)...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1800513
更新日期:2020-07-31 00:00:00
abstract::Room temperature mid-infrared experiments between 500 and 1800 cm(-1) have been performed on crystalline deoxyadenosine as a function of pressure up to about 10 GPa. Discontinuities observed near 2 and 4 GPa indicate that two separate phase transitions occur at these pressures. Changes in the spectra suggest that both...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2007.10507147
更新日期:2007-06-01 00:00:00