arXiv: Biomolecules最新文献_第4页

Uncovering hidden macromolecular dynamics with Modulated Orientation Sensitive Terahertz Spectroscopy 利用调制取向敏感太赫兹光谱学揭示隐藏的大分子动力学

arXiv: Biomolecules Pub Date : 2012-10-29 DOI: 10.1364/LTST.2012.STH2A.2

Rohit Singh, D. George, A. Markelz

引用次数: 1

Docking Studies on HIV Integrase Inhibitors Based On Potential Ligand Binding Sites 基于潜在配体结合位点的HIV整合酶抑制剂对接研究

arXiv: Biomolecules Pub Date : 2012-10-11 DOI: 10.5121/ijbb.2012.2303

Subhomoi Borkotoky

引用次数: 3

A Proposal on Quantum Histone Modification in Gene Expression 基因表达中量子组蛋白修饰的研究进展

arXiv: Biomolecules Pub Date : 2012-06-11 DOI: 10.1063/1.4756456

L. Luo

{"title":"A Proposal on Quantum Histone Modification in Gene Expression","authors":"L. Luo","doi":"10.1063/1.4756456","DOIUrl":"https://doi.org/10.1063/1.4756456","url":null,"abstract":"A quantum mechanical model on histone modification is proposed. Along with the methyl / acetate or other groups bound to the modified residues the torsion angles of the nearby histone chain are supposed to participate in the quantum transition cooperatively. The transition rate W is calculated based on the non-radiative quantum transition theory in adiabatic approximation. By using W's the reaction equations can be written for histone modification and the histone modification level can be calculable from the equations, which is decided by not only the atomic group bound to the modified residue, but also the nearby histone chain. The theory can explain the mechanism for the correlation between a pair of chromatin markers observed in histone modification. The temperature dependence and the coherence-length dependence of histone modification are deduced. Several points for checking the proposed theory and the quantum nature of histone modification are suggested as follows: 1, The relationship between lnW and 1/T is same as usual protein folding. The non-Arhenius temperature dependence of the histone modification level is predicted. 2, The variation of histone modification level through point mutation of some residues on the chain is predicted since the mutation may change the coherence-length of the system. 3, Multi-site modification obeys the quantum superposition law and the comparison between multi-site transition and single modification transition gives an additional clue to the testing of the quantum nature of histone modification.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88806341","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}

引用次数: 7

Ion Channels, Natural Nanovalves 离子通道，天然纳米阀

arXiv: Biomolecules Pub Date : 2012-06-06 DOI: 10.1007/978-1-4419-6996-5_12

B. Eisenberg

引用次数: 2

Evaluation of the Structural disorder of the protein FMR1 with Carbon Composition 用碳组成评价FMR1蛋白的结构紊乱

arXiv: Biomolecules Pub Date : 2012-03-12 DOI: 10.5176/2251-2489_BICB06

Baby Jerald, Gopalakrishnan Nair, E. Rajasekaran

{"title":"Evaluation of the Structural disorder of the protein FMR1 with Carbon Composition","authors":"Baby Jerald, Gopalakrishnan Nair, E. Rajasekaran","doi":"10.5176/2251-2489_BICB06","DOIUrl":"https://doi.org/10.5176/2251-2489_BICB06","url":null,"abstract":"Ever since the disorder of proteins is the main cause for many diseases. As compared with other disorders, the major reason that causes disease is of structural inability of many proteins. The potentially imminent availability of recent datasets helps one to discover the protein disorders, however in majority of cases, the stability of proteins depend on the carbon content. Addressing this distinct feature, it is possible to hit upon the carbon distribution along the sequence and can easily recognize the stable nature of protein. There are certain reported mental disorders which fall in to this category. Regardless, such kind of disorder prone protein FMR1p (Fragile X mental retardation 1 protein) is identified as the main cause for the disease Fragile X syndrome. This paper deals with the identification of defects in the FMR1 protein sequence considering the carbon contents along the sequence. This attempt is to evaluate the stability of proteins, accordingly the protein disorders in order to improvise the certain Biological functions of proteins to prevent disease. The transition of the disorder to order protein involves careful considerations and can be achieved by detecting the unstable region that lacks hydrophobicity. This work focuses the low carbon content in the FMR1 protein so as to attain the stable status in future to reduce the morbidity rate caused by Fragile X syndrome for the society.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74775281","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}

引用次数: 1

Dynamics of DNA Bubble in Viscous Medium 粘性介质中DNA气泡动力学

arXiv: Biomolecules Pub Date : 2012-01-03 DOI: 10.1063/1.4730745

A. Sulaiman, F. P. Zen, H. Alatas, L. T. Handoko

引用次数: 2

The Boltzmann factor, DNA melting, and Brownian ratchets: Topics in an introductory physics sequence for biology and premedical students 玻尔兹曼因子，DNA融化，和布朗棘轮:主题在入门物理序列生物学和医学预科学生

arXiv: Biomolecules Pub Date : 2011-05-19 DOI: 10.1119/1.3638908

S. Mochrie

引用次数: 7

Homogeneity tests for Michaelis-Menten curves with application to fluorescence resonance energy transfer data Michaelis-Menten曲线的均匀性检验及其在荧光共振能量转移数据中的应用

arXiv: Biomolecules Pub Date : 2011-05-04 DOI: 10.1142/S0218339013500174

Amparo Ba'illo, Laura Mart'inez-Munoz, M. Mellado

{"title":"Homogeneity tests for Michaelis-Menten curves with application to fluorescence resonance energy transfer data","authors":"Amparo Ba'illo, Laura Mart'inez-Munoz, M. Mellado","doi":"10.1142/S0218339013500174","DOIUrl":"https://doi.org/10.1142/S0218339013500174","url":null,"abstract":"Resonance energy transfer methods are in wide use for evaluating protein-protein interactions and protein conformational changes in living cells. Fluorescence resonance energy transfer (FRET) measures energy transfer as a function of the acceptor:donor ratio, generating FRET saturation curves. Modeling these curves by Michaelis-Menten kinetics allows characterization by two parameters, which serve to evaluate apparent affinity between two proteins and to compare this affinity in different experimental conditions. To reduce the effect of sampling variability, several statistical samples of the saturation curve are generated in the same biological conditions. Here we study three procedures to determine whether statistical samples in a collection are homogeneous, in the sense that they are extracted from the same regression model. From the hypothesis testing viewpoint, we considered an F test and a procedure based on bootstrap resampling. The third method analyzed the problem from the model selection viewpoint, and used the Akaike information criterion (AIC). Although we only considered the Michaelis-Menten model, all statistical procedures would be applicable to any other nonlinear regression model. We compared the performance of the homogeneity testing methods in a Monte Carlo study and through analysis in living cells of FRET saturation curves for dimeric complexes of CXCR4, a seven-transmembrane receptor of the G protein-coupled receptor family. We show that the F test, the bootstrap procedure and the model selection method lead in general to similar conclusions, although AIC gave the best results when sample sizes were small, whereas the F test and the bootstrap method were more appropriate for large samples. In practice, all three methods are easy to use simultaneously and show consistency, facilitating conclusions on sample homogeneity.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76181265","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}

引用次数: 5

Why Can’t We Predict RNA Structure At Atomic Resolution? 为什么我们不能在原子分辨率上预测RNA结构?

arXiv: Biomolecules Pub Date : 2011-03-15 DOI: 10.1007/978-3-642-25740-7_4

Kyle A. Beauchamp, Parin Sripakdeevong, Rhiju Das

引用次数: 15

Crowded Charges in Ion Channels 离子通道中的拥挤电荷

arXiv: Biomolecules Pub Date : 2010-09-09 DOI: 10.1002/9781118158715.CH2

B. Eisenberg

引用次数: 80