International Review of Biophysical Chemistry最新文献

{"title":"Structure and Function of Eukaryotic DNA-Binding Proteins in DNA Repair","authors":"S. J. Kind, M. Sanderson","doi":"10.15866/IREBIC.V2I6.1543","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I6.1543","url":null,"abstract":"This article reviews the current status of how structural studies are impacting on our understanding of the mechanism of Eukaryotic repair from a function standpoint. A wide array of different repair mechanisms are covered, namely DNA base excision repair (BER), nucleotide excision repair (NER) and mismatch repair (MMR)","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"156 1","pages":"193-206"},"PeriodicalIF":0.0,"publicationDate":"2011-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75409742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Study of Biomolecular Recognition Using Time-Resolved Optical Spectroscopy","authors":"Tanumoy Mondol, Soma Banerjee, Subrata Batabyal, S. Pal","doi":"10.15866/IREBIC.V2I6.1545","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I6.1545","url":null,"abstract":"Molecular recognition process refers to the weak non-covalent interaction, which takes place selectively and specifically between small ligand molecules with biological macromolecules. Understanding of such recognition in biological and biomimetic milieu is the central attraction for drug designing, which is crucial for the improvement of human healthcare. A thorough knowledge of the structural, dynamical and energetic parameters that dictate such molecular interactions can find immense use in the modulations of the ligand-macromolecule recognition process. In this article, we present our continuous effort to investigate the fundamental physical processes involved in the biomolecular recognition, e.g. efficiency (binding affinity and rigidity of the complex) and role of solvent molecules in the molecular recognition using steady state and predominantly, ultrafast time-resolved fluorescence spectroscopy. In this perspective, we have thoroughly investigated the molecular recognition of small ligand/drug molecules (Rifampicin; Rf, 4-(dicyanomethylene)-2-methyl-6-(p-dimethylaminostyryl)-4H-pyran; DCM, and Nile Blue; NB) by a human transporter protein, Human Serum Albumin (HSA), and also established the nonspecific type of interaction between a ligand molecule (Rf) and a biomimetic system (Sodium Dodecyl Sulfate (SDS) micelle). Simultaneous recognition of an intercalator (Ethidium Bromide, EtBr) and a DNA minor groove binder (Hoeschst 33258, H258) to a dodecamer DNA of specific sequence has also been monitored. Besides, we report an investigation on the recognition of ethidium (Et) cation, a potential mutagen, by synthetic DNA and various cell nuclei in presence of a stimulant drug, caffeine, employing the mentioned spectroscopic techniques along with NMR and fluorescence microscopy. Moreover, we have explored the differential molecular recognition of 8-anilino-1-naphthalenesulfonic acid (ANS) and 2,6-p-toluidinonaphthalene sulfonate (TNS) by bovine pancreatic -chymotrypsin (CHT) upon interaction with genomic DNA. The correlation of the molecular recognition of the DNA and DNA-protein complexes with the hydration dynamics has been further exploited in our studies. In addition, we have developed functional nanoparticles/Quantum dots (QDs) that are covalently linked to biological molecules to detect the molecular interaction phenomenon between biomolecules. It should be noted that QDs have a significant contribution in the field of nano-biotechnology due to its high quantum yield, low photo-bleaching and increased biological application (cell labeling, in vivo imaging, gene delivery, sensing of fluorescence and molecular recognition). In this regard, we have exploited QDs as a potential energy donor/acceptor system and validated Forster resonance energy transfer (FRET) model over nano-surface energy transfer (NSET) technique. Therefore, the ultrafast non-radiative energy migration from tryptophan (Trp214) present in HSA to the HSA bound CdS QD, and fro","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"27 1","pages":"211-237"},"PeriodicalIF":0.0,"publicationDate":"2011-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78583465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of Soy Protein Supplementation on Hepatic Lipid Profile in Rats Fed a Cholesterol-Based Diet","authors":"O. Oluba, F. Bamisaye, A. O. Olusola, A. O. Iyamu, G. Eidangbe","doi":"10.15866/IREBIC.V2I5.1538","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I5.1538","url":null,"abstract":"The effect of soy protein intake on liver lipid homeostasis in cholesterol-fed rats was investigated. One hundred and five albino Wistar rats divided into five groups (n = 21) were fed 20% soy protein without cholesterol (A), 20% soy protein + 5% cholesterol (B), 20% soy protein + 10% cholesterol (C), 0% soy protein + 20% cholesterol (D), and 5% soy protein + 20% cholesterol (E) for six weeks. Liver total cholesterol, esterified cholesterol, low density lipoprotein cholesterol and triglyceride levels were significantly reduced (p<0.05) in soy protein fed rats (B and C) when compared with those fed cholesterol with no or minimal soy protein (D and E) supplement respectively. It could thus be concluded that soy protein supplementation reduces hepatic lipid load in hypercholesterolemic rats","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"13 1","pages":"165-168"},"PeriodicalIF":0.0,"publicationDate":"2011-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81345709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantum Chemical Analysis of Structural and Conformational Properties of Methisazone and Prototropic Tautomerism of Isatin","authors":"O. Bolsunova, O. Brovarets’, D. Hovorun, L. Zaika, A. Potopalsky","doi":"10.15866/IREBIC.V2I5.1537","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I5.1537","url":null,"abstract":"The conformational diversity of methisazone and prototropic molecular tautomerism of isatin were investigated by means of ab initio calculations at the MP2/6-311++G(2df,pd)//DFT B3LYP/6-311++G(d,p) level of theory. A comprehensive conformational, energetical and polar analysis of the methisazone (1-methyl-1H-indole-2,3-dione 3-thiosemicarbazone), a thiosemicarbazone, was provided. We established that flexibility of the thiosemicarbazone group causes conformational diversity of methisazone molecule. Structural, energetical and electron-topological characteristics of specific intramolecular contacts in methisazone conformers were analyzed. In general, two types of H-bonds (NH…O, CH…N), one type of dihydrogen bond (CH…HN) and three types of van der Waals contacts (N…N, N…O, C…O) were detected by performing electron density topological analysis for all 11 conformers of methisazone. A wide range of biological activity of izatizon based on conformational capacity of methisazone molecule, the main constituent part of this drug, was shortly discussed. Five molecular prototropic tautomers of isatin (1H-indole-2,3-dione) – one diketo and four enol tautomeric forms - were indicated. All five isomers have relative Gibbs free energies within a wide range of ~40 kcal∙mol−1 at physiological temperature. The possible biochemical role of tautomeric forms of isatin was briefly discussed","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"16 1","pages":"159-164"},"PeriodicalIF":0.0,"publicationDate":"2011-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80582244","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Self-Assembly of Amyloid Beta Peptide Over Dialkoxy Disulfide Functionalized Nano Gold Colloidal Particles","authors":"K. Yokoyama, Amy Tran, R. Priefer","doi":"10.15866/IREBIC.V2I5.1540","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I5.1540","url":null,"abstract":"Aiming to more stably produce an oligomer form of amyloid beta (i.e., a key intermediate of fibrillogenesis which eventually leads to Alzheimer’s disease), the surface of gold colloids were functionalized with nitro-, phenyl-, chloro-, and methoxy-dibenzyloxy disulfide, and molecular interactions were investigated in a dimethyl sulfoxide environment. The transition of color change was observed at pHo as the pH value was lowered externally. As evidence of disulfide being adsorbed on the colloidal surface, the pHo values were dependent of each substituent of the dibenzyloxy disulfide compounds. The trend of pHo exhibited a parabolic relationship as a function of F-value (Swain-Lupton Field constant). Functionalization of gold colloidal surface with methoxy-dibenzyloxy disulfide achieved larger amplitude in repetitive peak shift between pH 4 and 10 implying a formation of an oligomer under the reversible process","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"11 1","pages":"174-183"},"PeriodicalIF":0.0,"publicationDate":"2011-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82429766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mapping surface heterogeneity: the AFM-based approach","authors":"James R. Smith, T. Nevell, J. Tsibouklis","doi":"10.15866/IREBIC.V2I5.1541","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I5.1541","url":null,"abstract":"In this short review, the use of maps is presented charting the surface distribution of the forces of adhesion, indentation and friction, as obtained with the atomic force microscope for the study of surface homogeneity. Phase-separated polymer blends are chosen as examples to demonstrate the complementarity of the method with the more usual topographical imaging approach. Consequent to recent advances towards the determination of surface energy at the sub-micrometre scale, the mapping of this property is now a realistic possibility","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"40 1","pages":"184-190"},"PeriodicalIF":0.0,"publicationDate":"2011-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74199351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Disease –Age- Correlated Oxidative Status of Patients with Hypertensive and Diabetic Co-Morbidity in Central Hospital, Benin City, Nigeria","authors":"O. A. Iyamu, J. Anionye, E. Onyeneke, O. Oluba, Omon M. Oyakhire, O. Aigbe","doi":"10.15866/IREBIC.V2I5.1539","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I5.1539","url":null,"abstract":"The study was designed to compare oxidative status of sufferers of a co-morbidity of hypertension and diabetes mellitus who have clinical evidence of sustained well controlled blood sugar and blood pressure with that of apparently healthy controls and to see if the variation of this oxidative status with progression (age) of the co-morbidity differ from the observations in previous studies with sufferers of solitary hypertension or diabetes. Blood samples were collected from  co-morbidity sufferers (n = 42; 17 males and 25 females ) and 42 apparently healthy volunteers for the determination of plasma levels of two endogenous antioxidant enzymes  (superoxide dismutase, SOD, and catalase, CAT) as well as markers of oxidative damage (malondialdehyde, MDA, and erythrocyte osmotic fragility, EOF). Results obtained showed that the blood levels of both SOD and CAT decreased significantly (P<0.001) as age of co-morbidity increases. Also levels of blood MDA and EOF increased with age of co-morbidity (P<0.001). The variation of these indices with disease age was more statistically significant than that observed in earlier studies with solitary diabetes or hypertension. This study shows that oxidative damage is worse in sufferers of hypertensive and diabetic co-morbidity than in sufferers of solitary diabetes or hypertension","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"19 1","pages":"169-173"},"PeriodicalIF":0.0,"publicationDate":"2011-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78063221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differential Binding Mode of a Phenanthroline-Based Metal Complex to a DNA or RNA Telomeric Sequence","authors":"C. Musetti, S. Bianco, A. Krapcho, M. Palumbo, C. Sissi","doi":"10.15866/IREBIC.V2I4.1529","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I4.1529","url":null,"abstract":"RNA G-quadruplexes have been recently proposed as physiologically relevant structures in cellular processes which suggests they represent attractive novel drug targets. Up-to-date, limited information of their interactions with small molecules is available. In particular, no systematic comparative analysis of the DNA vs RNA recognition processes has been performed. Here, we investigated the RNA G-quadruplex binding properties of a phenanthroline-based metal complex, (P115)Ni(II), known to efficiently recognize the DNA telomeric sequence. We showed that one ligand molecule can be sandwiched between two RNA G-quadruplex units. Conversely, this binding mode is not occurring using the DNA counterpart as the target sequence","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"45 1","pages":"156-158"},"PeriodicalIF":0.0,"publicationDate":"2011-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89940419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of Protein Binding on DNA G-Quadruplex Structures","authors":"S. Nagatoishi, D. Miyoshi, N. Sugimoto","doi":"10.15866/IREBIC.V2I4.1524","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I4.1524","url":null,"abstract":"The non-canonical G-quadruplex is a unique DNA structure that has received widespread attention because of its potential functions not only in vitro but also in vivo. The G-quadruplex is stabilized by formation of Hoogsteen hydrogen bonds in guanine quartets and involves cation coordination and dehydration. Although a number of proteins have been identified that specifically stabilize and destabilize G-quadruplexes, the effect of the protein binding remains unclear. Here, we review the behaviors of proteins binding to G-quadruplexes. We also discuss analyses of the thermodynamic and binding properties of G-quadruplexes in the complexes formed by histones and thrombins. These studies have helped us to understand the essential features of interaction between G-quadruplexes and proteins","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"18 1","pages":"129-134"},"PeriodicalIF":0.0,"publicationDate":"2011-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89440216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hit identification of anthraquinone based molecules as c-myc G-quadruplex inducers/stabilizers via in silico structural similarity approach","authors":"V. P. Ma, W. Lam, Dik‐Lung Ma, C. Leung","doi":"10.15866/IREBIC.V2I4.1521","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I4.1521","url":null,"abstract":"Natural products in Traditional Chinese Medicine (TCM) such as anthraquinone derivatives have a wide variety of pharmacological properties as well as proven record of high efficacy. Previously, our group reported an anthraquinone derivative Fonsecin B as c-myc G-quadruplex stabilizer. We herein report two bioactive anthraquinones with modifiable hydroxyl groups abundant in Chinese Medicine Rheum Palmatum L. (also known as Da Huang) as c-myc G-quadruplex stabilizer, identified by in silico structural similarity approach. Interaction of the anthraquinones with c-myc G-quadruplex was investigated by PCR Stop Assay","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"72 1","pages":"108-111"},"PeriodicalIF":0.0,"publicationDate":"2011-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74375987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}