当前位置： SCI文献检索 > JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS期刊下所有文献 > Molecular dynamics in protein-single stranded DNA complexes. Two distinct nucleoside mobilities, in poly(deoxythymidylic acid)-poly-L-lysine complexes.

Molecular dynamics in protein-single stranded DNA complexes. Two distinct nucleoside mobilities, in poly(deoxythymidylic acid)-poly-L-lysine complexes.

Abstract：

:Stoichiometric amounts of poly-L-lysine were added to site-specifically spin labeled single stranded nucleic acids and the resulting complexes analyzed by electron spin resonance spectroscopy (ESR). The nucleic acids were spin labeled to different extents and with labels of varying tether length. The ESR data are used to determine nucleoside dynamics and some structural features in these complexes. It is concluded that two distinct base mobilities exist in the complexes; one set is characterized by a mean correlation time tau -R = 2 ns, and the other one by a tau -R greater than or equal to 50 ns. A model is proposed which suggests that a poly-L-lys single stranded nucleic acid complex consists of low mobility segments flanked by more mobile bases. An interesting feature of the proposed model is its applicability to explain ESR data of single strand binding protein-spin labeled nucleic acid complexes, which can also be interpreted in terms of two distinct nucleoside mobility states. It is hypothesized that this phenomenon could be of biological significance for the release of protein ligands from a protein-nucleic acid complex.

journal_name

J Biomol Struct Dyn

journal_title

Journal of biomolecular structure & dynamics

authors

Bobst AM,Kao SC,Bobst EV,Pauly GT

doi

10.1080/07391102.1985.10508414

subject

Has Abstract

pub_date

1985-10-01 00:00:00

pages

249-60

issue

2

eissn

0739-1102

issn

1538-0254

journal_volume

3

pub_type

杂志文章

相关文献

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS文献大全
  • Effect of base stacking on the relative thermodynamic stability of oligonucleotide complexes: a spectroscopic study.

    abstract：:Three-strand oligonucleotide complexes are employed to assess the effect of base stacking and base pair mismatch on the relative thermodynamic stabilities of oligonucleotide duplexes. The melting behavior of three-strand oligonucleotide complexes incorporating nicks and gaps as well as internal single base mismatches ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2004.10506995

    authors： Murphy D,Doyle H,Eritja R,Redmond G

    更新日期：2004-10-01 00:00:00

  • Prediction of structural consequences for disease causing variants in C21orf2 protein using computational approaches.

    abstract：:Amyotrophic lateral sclerosis (ALS), a progressive motor-neurone disease, affects individuals usually aged between 50 and 70 years. C21orf2, recently identified as the new ALS susceptibility gene, harbours rare missense mutations that cause this fatal disease. We used bioinformatics and molecular modelling approaches ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2018.1429313

    authors： Iyer S,Acharya KR,Subramanian V

    更新日期：2019-02-01 00:00:00

  • Modeling the correlation functions of conformational motions in proteins.

    abstract：:A first principles calculation of the correlation function for conformational motion (CM) in proteins is carried out within the framework of a microscopic model of a protein as a heterogeneous system. The fragments of the protein are assumed to be identical hard spheres undergoing the CM within their conformational po...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2000.10506563

    authors： Sitnitsky AE

    更新日期：2000-02-01 00:00:00

  • Synthesis and spectroscopic characterizations of hexakis[(1-(4'-oxyphenyl)-3-(substituted-phenyl)prop-2-en-1-one)]cyclotriphosphazenes: their in vitro cytotoxic activity, theoretical analysis and molecular docking studies.

    abstract：:The hexachlorocyclotriphosphaze compound (N3P3Cl6, HCCP) was reacted with excess (E)-(1-(4'-oxyphenyl)-3-(substituted-phenyl)prop-2-en-1-ones (2-11) to produce hexakis[(1-(4-oxyphenyl)-3-(substituted-phenyl)prop-2-en-1-one)]cyclotriphosphazenes (CP 2-11). The structures of products (CP 2-11) were confirmed using eleme...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1846621

    authors： Doğan H,Bahar MR,Çalışkan E,Tekin S,Uslu H,Akman F,Koran K,Sandal S,Görgülü AO

    更新日期：2020-11-19 00:00:00

  • Effects of helix and fingertip mutations on the thermostability of xyn11A investigated by molecular dynamics simulations and enzyme activity assays.

    abstract：:Local conformational changes and global unfolding pathways of wildtype xyn11A recombinant and its mutated structures were studied through a series of atomistic molecular dynamics (MD) simulations, along with enzyme activity assays at three incubation temperatures to investigate the effects of mutations at three differ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2017.1404934

    authors： Sutthibutpong T,Rattanarojpong T,Khunrae P

    更新日期：2018-11-01 00:00:00

  • Cyanobacterial metabolites as promising drug leads against the Mpro and PLpro of SARS-CoV-2: an in silico analysis.

    abstract：:A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) has emerged as the causative agent behind the coronavirus disease 2019 (COVID-19) pandemic. Treatment efforts have been severely impeded due to the lack of specific effective antiviral drugs for the treatment of COVID-associated pathologies. In the pre...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1794972

    authors： Naidoo D,Roy A,Kar P,Mutanda T,Anandraj A

    更新日期：2020-07-21 00:00:00

  • Methylglyoxal modification reduces the sensitivity of hen egg white lysozyme to stress-induced aggregation: Insight into the anti-amyloidogenic property of α-dicarbonyl compound.

    abstract：:The reactive α-oxoaldehyde, methylglyoxal reacts with different proteins to form Advanced Glycation End Products (AGEs) through Maillard reaction. Its level increases significantly in diabetic condition. Here, we have investigated the effect of different concentrations of methylglyoxal (200-400 µM) on the monomeric pr...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1702589

    authors： Banerjee S

    更新日期：2020-11-01 00:00:00

  • Multi-spectroscopic studies of the interaction of new synthesized platin complex with human carrier protein of serum albumin.

    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

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1745690

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

    更新日期：2020-04-07 00:00:00

  • Calculating degree based multiplicative topological indices of Hyaluronic Acid-Paclitaxel conjugates' molecular structure in cancer treatment.

    abstract：:A large number of medical experiments have confirmed that the features of drugs have a close correlation with their molecular structure. Drug properties can be obtained by studying the molecular structure of corresponding drugs. The calculation of the topological index of a drug structure enables scientists to have a ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1800512

    authors： Jahanbani A,Shao Z,Sheikholeslami SM

    更新日期：2020-07-30 00:00:00

  • In silico studies of the inhibition mechanism of dengue with papain.

    abstract：:Dengue virus is becoming a major global disease; the envelope protein is the major target for vaccine development against Dengue. Nowadays, the attention has focused on developing inhibitors based on Papain is a promising target for treating Dengue. In the present work, the theoretical studies of E-protein(Cys74-Glu79...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1742205

    authors： Saranya V,Radhika R,Shankar R,Vijayakumar S

    更新日期：2020-04-06 00:00:00

  • Loading efficacy and binding analysis of retinoids with milk proteins: a short review.

    abstract：:In this review, the loading efficacies of retinoids with milk proteins are investigated. It has been shown that milk proteins β-lactoglobulin, α-, and β-caseins bind retinol and retinoic acid via hydrophobic, hydrophilic, and H-bonding contacts causing minor alterations of protein secondary structure. Hydrophobic cont...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章,评审

    doi：10.1080/07391102.2017.1411833

    authors： Agudelo D,Bourassa P,Bariyanga J,Tajmir-Riahi HA

    更新日期：2018-12-01 00:00:00

  • Unprecedented hydrophobic stabilizations from a reverse wobble T·T mispair in DNA minidumbbell.

    abstract：:Minidumbbell (MDB) is a newly found non-B DNA structure formed by short single-strand sequences. Up to now, three MDBs have been reported to form at neutral pH by sequences containing two repeats of TTTA, CCTG and CTTG. Among them, the thermodynamically less stable TTTA and CCTG MDBs have been proposed to be the struc...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1621211

    authors： Guo P,Lam SL

    更新日期：2020-04-01 00:00:00

  • Carbon and boron nanotubes as a template material for adsorption of 6-Thioguanine chemotherapeutic: a molecular dynamics and density functional approach.

    abstract：:The interaction of 6-Thioguanine molecule, an antitumor drug with carbon nanotube and boron nitride nanotube (BNNT) is investigated using molecular dynamics simulations. Based on the obtained results, the strongest negative van der Waals interaction is found between 6-TG and BNNT among the studied nanotubes, which ind...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1585951

    authors： Hasanzade Z,Raissi H

    更新日期：2020-02-01 00:00:00

  • Novel P,C-orthopalladated complexes containing histidine and phenylalanine amino acids: synthesis, DNA and BSA interactions, in vitro antitumoral activity and molecular docking approach.

    abstract：:Novel [Pd(o-CH2C6H4P(o-tolyl)2)(histidine)] (1) and [Pd(o-CH2C6H4P(o tolyl)2)(phenylalanine)] (2) P,C-orthopalladated complexes have been prepared and characterized by elemental analysis, IR and NMR spectroscopy. To study the stability of the compounds in biological media, the complexes were incubated in Tris buffer d...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1865202

    authors： Hashemi S,Karami K,Saberi Dehkordi Z,Momtazi-Borojeni AA,Esmaeili SA

    更新日期：2020-12-24 00:00:00

  • Novel quinazolin-sulfonamid derivatives: synthesis, characterization, biological evaluation, and molecular docking studies.

    abstract：:In the design of novel drugs, the formation of hybrid molecules via the combination of several pharmacophores can give rise to compounds with interesting biochemical profiles. A series of novel quinazolin-sulfonamid derivatives (9a-m) were synthesized, characterized and evaluated for their in vitro antidiabetic, antic...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1847193

    authors： Sepehri N,Mohammadi-Khanaposhtani M,Asemanipoor N,Hosseini S,Biglar M,Larijani B,Mahdavi M,Hamedifar H,Taslimi P,Sadeghian N,Norizadehtazehkand M,Gulcin I

    更新日期：2020-11-23 00:00:00

  • 7-Azido-actinomycin D: a photoaffinity probe of the sequence specificity of DNA binding by actinomycin D.

    abstract：:Actinomycin D (ActD) is a DNA-binding antitumor antibiotic that appears to act in vivo by inhibiting RNA polymerase. The mechanism of DNA binding of ActD has attracted much attention because of its strong preference for 5'-dGpdC-3' sequences. Binding is thought to involve intercalation of the tricyclic aromatic phenox...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1989.10508509

    authors： Rill RL,Marsch GA,Graves DE

    更新日期：1989-12-01 00:00:00

  • Structural assessment and identification of 11β-hydroxysteroid dehydrogenase type 1 inhibitors.

    abstract：:Communicated by Ramaswamy H. Sarma. ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 信件

    doi：10.1080/07391102.2019.1688193

    authors： Ganjoo A,Tripathi A,Chetti P

    更新日期：2020-10-01 00:00:00

  • Novel coumarin derivatives as potent acetylcholinesterase inhibitors: insight into efficacy, mode and site of inhibition.

    abstract：:The inhibitory efficacy of two substituted coumarin derivatives on the activity of neurodegenerative enzyme acetylcholinesterase (AChE) was assessed in aqueous buffer as well as in the presence of human serum albumin (HSA) and compared against standard cholinergic AD drug, Donepezil (DON). The experimental data reveal...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2018.1465853

    authors： Baruah P,Basumatary G,Yesylevskyy SO,Aguan K,Bez G,Mitra S

    更新日期：2019-04-01 00:00:00

  • A study of the eigenvectors of the vibrational modes in crystalline cytidine via high-pressure Raman spectroscopy.

    abstract：:Raman spectroscopy has been used to study the eigenvectors and eigenvalues of the vibrational modes of crystalline cytidine at 295 K and high pressures by evaluating the logarithmic derivative of the vibrational frequency ω with respect to pressure P: [Formula: see text]. Crystalline samples of molecular materials hav...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2014.915763

    authors： Lee SA,Pinnick DA,Anderson A

    更新日期：2015-01-01 00:00:00

  • Role of Thr199 residue in human β-carbonic anhydrase-II pH-dependent activity elucidated by microsecond simulation analysis.

    abstract：:Carbonic anhydrases catalyze the reversible hydration of carbon dioxide to form bicarbonate, a reaction required for many functions such as carbon assimilation, pH acid-base homeostasis, respiration and photosynthesis via a zinc-hydroxide mechanism for carbon dioxide hydration. In earlier studies, it was revealed that...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1865203

    authors： Yadav PR,Basha SH,Pindi PK

    更新日期：2020-12-24 00:00:00

  • Allowance for spatial dispersion of dielectric permittivity in polyelectrolyte model of DNA.

    abstract：:In order to allow for real dielectric properties of a solvent in calculating of electrostatic characteristics of strongly charged polyions such as DNA in salt solution we consider a simple model of linear dielectric response of a medium. The interactions between charged particles are treated in the framework of self-c...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1991.10507933

    authors： Lukashin AV,Beglov DB,Frank-Kamenetskii MD

    更新日期：1991-12-01 00:00:00

  • Deciphering structural stability and binding mechanisms of potential antagonists with smoothened protein.

    abstract：:Identification of new potential inhibitors against Hedgehog pathway activator protein Smoothened (SMO) is considered to be of higher importance to improvise the future cancer therapeutics. Different SMO inhibitors/drugs (e.g. Cyclopamine, Vismodegib, Taladegib) used till date are found to be associated with several dr...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2017.1372310

    authors： Sinha N,Chowdhury S,Sarkar RR

    更新日期：2018-08-01 00:00:00

  • NMR studies of tris-intercalation: solution structure and interaction of d(CTTCGCGCGAAG) with an acridine trimer.

    abstract：:Tris-intercalation of an acridine trimer into the self-complementary dodecanucleotide d(CTTCGCGCGAAG) has been studied, in solution, by means of 1H and 31P nuclear magnetic resonance. In a first step all the non-exchangeable protons (except H5', H5"), the imino protons and seven of the eleven phosphorus have been assi...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1988.10506498

    authors： Laugaa P,Delepierre M,Dupraz B,Igolen J,Roques BP

    更新日期：1988-12-01 00:00:00

  • Cryo-electron microscopy reveals the membrane insertion mechanism of V. cholerae hemolysin.

    abstract：:Vibrio cholerae hemolysin (HlyA) is a 65 kDa pore-forming toxin which causes lysis of target eukaryotic cells by forming heptameric channels in the plasma membrane. Deletion of the 15 kDa C-terminus β-prism carbohydrate-binding domain generates a 50 kDa truncated variant (HlyA50) with 1000-fold-reduced pore-forming ac...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2013.823564

    authors： Dutta S,Banerjee KK,Ghosh AN

    更新日期：2014-01-01 00:00:00

  • An insight to the dynamics of conserved water molecular triad in IMPDH II (human): recognition of cofactor and substrate to catalytic Arg 322.

    abstract：:Inosine 5' monophosphate dehydrogenase (IMPDH II) is a key enzyme involved in the de novo biosynthesis pathway of purine nucleotides and is also considered to be an excellent target for cancer inhibitor design. The conserve R 322 residue (in human) is thought to play some role in the recognition of inhibitor and cofac...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2009.10507304

    authors： Bairagya HR,Mukhopadhyay BP,Sekar K

    更新日期：2009-10-01 00:00:00

  • Electric birefringence of dilute agarose solutions.

    abstract：:The technique of transient electric birefringence was used to investigate the orientation of agarose solutions in pulsed electric fields. If the agarose was dissolved in deionized water, the sign of the birefringence was positive when the electric field was small, indicating that the agarose molecules were orienting p...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1990.10507830

    authors： Stellwagen NC,Stellwagen D

    更新日期：1990-12-01 00:00:00

  • Molecular dynamics simulation and free energy calculation studies of the binding mechanism of allosteric inhibitors with TrkA kinase.

    abstract：:Tropomyosin receptor kinase A (Trk A) is a receptor tyrosine kinase activated by nerve growth factor (NGF). TrkA plays an important role in pain sensation, which leads to significant interest in the development of small molecule inhibitors of TrkA. However, TrkA and the other two highly homologous isoforms, TrkB and T...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1708798

    authors： Wu X,Li Q,Wan S,Zhang J

    更新日期：2021-01-01 00:00:00

  • Genome packaging within icosahedral capsids and large-scale segmentation in viral genomic sequences.

    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

    pub_type： 杂志文章

    doi：10.1080/07391102.2018.1479660

    authors： Chechetkin VR,Lobzin VV

    更新日期：2019-06-01 00:00:00

  • In silico identification of angiotensin-1 converting enzyme inhibitors using text mining and virtual screening.

    abstract：:Cardiovascular diseases are the world's leading cause of death. Hypertension is an important risk factor for cardiovascular and renal diseases. Angiotensin-converting enzyme (ACE) can be a possible therapeutic target for managing angiotensin I conversion to angiotensin II and ultimately controlling hypertension. Indol...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1827038

    authors： Sahin K

    更新日期：2020-10-05 00:00:00

  • A program to automate the discovery of drugs for West Nile and Dengue virus-programmatic screening of over a billion compounds on PubChem, generation of drug leads and automated in silico modelling.

    abstract：:Our work is composed of a python program for programmatic data mining of PubChem to collect data to implement a machine learning-based AutoQSAR algorithm to generate drug leads for the flaviviruses-Dengue and West Nile. The drug leads generated by the program are fed as programmatic inputs to AutoDock Vina package for...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1856185

    authors： Geoffrey B,Sanker A,Madaj R,Tresanco MSV,Upadhyay M,Gracia J

    更新日期：2020-12-04 00:00:00