The 3' terminal colicin fragment of Escherichia coli 16S ribosomal RNA. Conformational details revealed by enzymic and chemical probing.

abstract：:The sequence dependent conformation, flexibility and hydration properties of DNA molecules constitute selectivity determinants in the formation of protein-DNA complexes. TATA boxes in which AT basepairs (bp) have been substituted by IC bp (TITI box) allow for probing these selectivity determinants for the complexation...

journal_title：Journal of biomolecular structure & dynamics

authors： Pastor N,MacKerell AD Jr,Weinstein H

更新日期：1999-02-01 00:00:00

abstract：:The novel method allowing identification of protein structure elements responsible for catalytic activity manifestation is proposed. Structural organization of various hydrolases was studied using the ANIS (ANalysis of Informational Structure) method. ANIS allows to reveal a hierarchy of the ELements of Information St...

journal_title：Journal of biomolecular structure & dynamics

authors： Nekrasov AN,Zinchenko AA

更新日期：2008-04-01 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

authors： Dhal AK,Pani A,Yun SI,Mahapatra RK

更新日期：2020-07-07 00:00:00

abstract：:High-mobility group A1 (HMGA1) is a non-histone chromosomal protein, which is known as 'architectural' transcription factor that facilitates the assembly of 'enhanceosome.' Because of its elevated expression in a number of human malignancies, with barely minimal levels in healthy adults, HMGA1 is considered as potenti...

journal_title：Journal of biomolecular structure & dynamics

authors： Akhter MZ,Rajeswari MR

更新日期：2017-03-01 00:00:00

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 "min...

journal_title：Journal of biomolecular structure & dynamics

authors： Trifonov EN

更新日期：2016-12-01 00:00:00

abstract：:Previous work has shown that edaravone inhibits fibrillogenesis of amyloid-β protein (Aβ). However, the detailed mechanism by which edaravone inhibits the conformational transition of the Aβ42 monomer is not known at the molecular level. Here, explicit-solvent molecular dynamics (MD) simulations were coupled with mole...

journal_title：Journal of biomolecular structure & dynamics

authors： Liu F,Ma Z,Sang J,Lu F

更新日期：2020-05-01 00:00:00

abstract：:The small ubiquitin-like modifier (SUMO) proteins are a kind of proteins that can be attached to a series of proteins. The sumoylation of protein is an important posttranslational modification. Thus, the prediction of the sumoylation site of a given protein is significant. Here we employed a combined method to perform...

journal_title：Journal of biomolecular structure & dynamics

authors： Cai Y,He J,Lu L

更新日期：2011-04-01 00:00:00

abstract：:We performed thermodynamic analysis of temperature-induced unfolding of mesophilic and thermophilic proteins. It was shown that the variability in protein thermostability associated with pH-dependent unfolding or linked to the substitution of amino acid residues on the protein surface is evidence of the governing role...

journal_title：Journal of biomolecular structure & dynamics

authors： Khechinashvili NN,Capital Ka Cyrillicabanov AV,Kondratyev MS,Polozov RV

更新日期：2014-01-01 00:00:00

abstract：:The assembly and maturation of viruses with icosahedral capsids must be coordinated with icosahedral symmetry. The icosahedral symmetry imposes also the restrictions on the cooperative specific interactions between genomic RNA/DNA and coat proteins that should be reflected in quasi-regular segmentation of viral genomi...

journal_title：Journal of biomolecular structure & dynamics

authors： Chechetkin VR,Lobzin VV

更新日期：2019-06-01 00:00:00

abstract：:Transcription factor NAM-B1 has a major role in the process of senescence, which results in higher Fe and Zn concentrations in grains of wild wheat (T. durum; Td). The absence of the wild type NAMB1 in T. aestivum (Ta), one of the cardinal crops essential for more than 1/3rd of the global population, affects Fe and Zn...

journal_title：Journal of biomolecular structure & dynamics

authors： Kaul T,Eswaran M,Ahmad S,Thangaraj A,Jain R,Kaul R,Raman NM,Bharti J

更新日期：2020-08-01 00:00:00

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

authors： Ompraba G,Velmurugan D,Louis PA,Rafi ZA

更新日期：2010-02-01 00:00:00

abstract：:Stress tolerance is one of the most prominent and interesting topics in biology since many macro- and micro-adaptations have evolved in resistant organisms that are worth studying. When it comes to confronting various environmental stressors, the extremophile Artemia is unrivaled in the animal kingdom. In the present ...

journal_title：Journal of biomolecular structure & dynamics

authors： Khodajou-Masouleh H,Shahangian SS,Attar F,H Sajedi R,Rasti B

更新日期：2020-07-31 00:00:00

abstract：:Short and long disordered regions of proteins have different preference for different amino acid residues. Different methods often have to be trained to predict them separately. In this study, we developed a single neural-network-based technique called SPINE-D that makes a three-state prediction first (ordered residue...

journal_title：Journal of biomolecular structure & dynamics

authors： Zhang T,Faraggi E,Xue B,Dunker AK,Uversky VN,Zhou Y

更新日期：2012-01-01 00:00:00

abstract：:Parkinson's disease (PD) is characterized by the loss of dopamine-generating neurons in the substantia nigra and corpus striatum. Current treatments alleviate PD symptoms rather than exerting neuroprotective effect on dopaminergic neurons. New drugs targeting the dopaminergic neurons by specific uptake through the hum...

journal_title：Journal of biomolecular structure & dynamics

authors： Djikic T,Martí Y,Spyrakis F,Lau T,Benedetti P,Davey G,Schloss P,Yelekci K

更新日期：2019-02-01 00:00:00

abstract：:COVID-19 is an infectious pandemic caused by the SARS-CoV-2 virus. The critical components of SARS-CoV-2 are the spike protein (S-protein) and the main protease (Mpro). Mpro is required for the maturation of the various polyproteins involved in replication and transcription. S-protein helps the SARS-CoV-2 to enter the...

journal_title：Journal of biomolecular structure & dynamics

authors： Mondal P,Natesh J,Abdul Salam AA,Thiyagarajan S,Meeran SM

更新日期：2020-11-05 00:00:00

abstract：:Pebrine is a microsporidian disease caused by Nosema bombycis in Bombyx mori (silk worm) which results in brown/black spots. The affected larvae either spin cocoons which are flimsy with low silk content or not spin a cocoon. It has been hypothesised that Serine Protease Inhibitor 106 (SPN106) is responsible for evasi...

journal_title：Journal of biomolecular structure & dynamics

authors： U M S,Karunakar P,Krishnamurthy V

更新日期：2020-10-01 00:00:00

abstract：:The operator-binding domain of the lambda-repressor contains five alpha-helices and an extended N-terminal arm in the crystal structure determined by Pabo and Lewis reported in Nature 298, 443, 1982 (1). The four helices form a "box" enclosing a hydrophobic core with the fifth helix interacting with the equivalent hel...

journal_title：Journal of biomolecular structure & dynamics

authors： Bashford D,Weaver DL,Karplus M

更新日期：1984-03-01 00:00:00

abstract：:Tyrphostin 9 (Tyr 9) is a potent platelet-derived growth factor receptor (PDGFR) inhibitor, which induces apoptosis in various cancer cell types. The binding of Tyr 9 to the major transport protein, human serum albumin (HSA) was investigated using several spectroscopic techniques and molecular docking method. Fluoresc...

journal_title：Journal of biomolecular structure & dynamics

authors： Kandandapani S,Ridzwan NFW,Mohamad SB,Tayyab S

更新日期：2020-09-01 00:00:00

abstract：:Proteins interact with carbohydrates to perform various cellular interactions. Of the many carbohydrate ligands that proteins bind with, mannose constitute an important class, playing important roles in host defense mechanisms. Accurate identification of mannose-interacting residues (MIR) may provide important clues t...

journal_title：Journal of biomolecular structure & dynamics

authors： Pai PP,Mondal S

更新日期：2016-10-01 00:00:00

abstract：:DNaseI digestion studies (Brukner et al, EMBO J 14, 1812-1818 1995) and nucleosomebinding data (Satchwell et al, J. Mol. Biol. 191, 639-659 1986, Goodsell and Dickerson, Nucleic trinucleotides. A detailed comparison of the two models suggests that while both of them represent improvements with respect to dinucleotide ...

journal_title：Journal of biomolecular structure & dynamics

authors： Brukner I,Sánchez R,Suck D,Pongor S

更新日期：1995-10-01 00:00:00

abstract：:The structural and thermodynamic characters of alpha-syn12 peptide in aqueous solution at different pH and temperatures have been investigated through temperature replica exchange molecular dynamics (T-REMD) simulations with GROMOS 43A1 force field. The two independent T-REMD simulations were completed at pH = 7.0 and...

journal_title：Journal of biomolecular structure & dynamics

authors： Cao Z,Liu L,Wang J

更新日期：2010-12-01 00:00:00

abstract：:Previous reports have shown that protein-drug interaction helps to improve the pharmacokinetics of the drugs. Human serum albumin (HSA) is one of the basic components of blood plasma and it serves as a storage and carrier protein. In the present study, the interaction of a new synthesized Pt [iso]2 complex (cis - [Pt(...

journal_title：Journal of biomolecular structure & dynamics

authors： Mohammadgholi A,Leilabadi-Asl A,Divsalar A,Eslami-Moghadam M

更新日期：2020-04-07 00:00:00

abstract：:The effect of two widely used polyphenols, curcumin and EGCG was investigated on the amyloid fibrillogenesis of the well-characterized model protein human lysozyme (HuL), associated with non-neuropathic systemic amyloidosis, towards exploring their efficacy as modulators of HuL amyloid aggregation and toxicity and unr...

journal_title：Journal of biomolecular structure & dynamics

authors： Zaidi FK,Bhat R

更新日期：2020-12-17 00:00:00

abstract：:P21-activated kinase-1 (PAK1) is an enzyme associated with multiple metabolic networks and different types of cancers. Hence, there is a need to study the global network map of PAK1 to understand its role and regulatory mechanisms by means of its significant molecular interactive partners. This will help to explore it...

journal_title：Journal of biomolecular structure & dynamics

authors： Yellapu NK,Pulaganti M,Pakala SB

更新日期：2017-08-01 00:00:00

abstract：:Binding interactions of the phenazinium dye Janus green blue (JGB) with human and bovine serum albumins (BSA - and BSA) have been explored for the first time from multi-spectroscopic and calorimetric measurements aided by in silico calculations. The formation of ground state complexes between JGB and the respective se...

journal_title：Journal of biomolecular structure & dynamics

authors： Saha S,Bhattacharjee S,Chowdhury J

更新日期：2021-01-07 00:00:00

abstract：:It has been shown that the frequency versus size distribution of A and T overlapping and non-overlapping homopolymer tracts of N > 5 in D. discoideum gene flanking and intron regions are significantly greater than in coding regions(1). In the present report, we demonstrate, that a spatial periodicity exists in long A ...

journal_title：Journal of biomolecular structure & dynamics

authors： Marx KA,Hess ST,Blake RD

更新日期：1994-08-01 00:00:00

abstract：:Flavonoids correspond to a major class of polyphenolic phytochemicals with flavone as major parent scaffold. This class of compounds is attributed with very rich nutritional as well as therapeutic values. The present study focuses on a panel of 16 flavonoid molecules that are demonstrated to exhibit various bioactivit...

journal_title：Journal of biomolecular structure & dynamics

authors： Meshram RJ,Bagul KT,Pawnikar SP,Barage SH,Kolte BS,Gacche RN

更新日期：2020-03-01 00:00:00

abstract：:The N-terminal receiver domain of NtrC is the molecular switch in the two-component signal transduction. It is the first protein where structures of both the active (phosphyroylated) and inactive (unphosphyroylated) states are determined experimentally. Phosphorylation of the NtrC at the active site induces large stru...

journal_title：Journal of biomolecular structure & dynamics

authors： Hu X,Wang Y

更新日期：2006-04-01 00:00:00

abstract：:The sharp spurt in positive cases of novel coronavirus-19 (SARS-CoV-2) worldwide has created a big threat to human. In view to expedite new drug leads for COVID-19, Main Proteases (Mpro) of novel Coronavirus (SARS-CoV-2) has emerged as a crucial target for this virus. Nitric oxide (NO) inhibits the replication cycle o...

journal_title：Journal of biomolecular structure & dynamics

authors： Al-Sehemi AG,Pannipara M,Parulekar RS,Patil O,Choudhari PB,Bhatia MS,Zubaidha PK,Tamboli Y

更新日期：2020-07-08 00:00:00

abstract：:In this study, various molecular dynamics simulations were conducted to investigate the effects of ethanol and temperature on the conformational changes of human lysozyme, which may lead insights into amyloidosis. The analyses of some important structural characteristics, such as backbone root-mean-square deviation, s...

journal_title：Journal of biomolecular structure & dynamics

authors： Liu HL,Wu YC,Zhao JH,Fang HW,Ho Y

更新日期：2006-12-01 00:00:00