Pub Date : 2012-10-29DOI: 10.1364/LTST.2012.STH2A.2
Rohit Singh, D. George, A. Markelz
We introduce Modulated Orientation Sensitive Terahertz Spectroscopy (MOSTS) that can both increase contrast between adjacent modes and remove the broad band librational background to allow mode identification for large macro molecules such as proteins.
{"title":"Uncovering hidden macromolecular dynamics with Modulated Orientation Sensitive Terahertz Spectroscopy","authors":"Rohit Singh, D. George, A. Markelz","doi":"10.1364/LTST.2012.STH2A.2","DOIUrl":"https://doi.org/10.1364/LTST.2012.STH2A.2","url":null,"abstract":"We introduce Modulated Orientation Sensitive Terahertz Spectroscopy (MOSTS) that can both increase contrast between adjacent modes and remove the broad band librational background to allow mode identification for large macro molecules such as proteins.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"208 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2012-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76430315","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}
HIV integrase is a 32 kDa protein produced from the C-terminal portion of the Pol gene product, and is an attractive target for new anti-HIV drugs. Integrase is an enzyme produced by a retrovirus (such as HIV) that enables its genetic material to be integrated into the DNA of the infected cell. Raltegravir and Elvitegravir are two important drugs against integrase.
{"title":"Docking Studies on HIV Integrase Inhibitors Based On Potential Ligand Binding Sites","authors":"Subhomoi Borkotoky","doi":"10.5121/ijbb.2012.2303","DOIUrl":"https://doi.org/10.5121/ijbb.2012.2303","url":null,"abstract":"HIV integrase is a 32 kDa protein produced from the C-terminal portion of the Pol gene product, and is an attractive target for new anti-HIV drugs. Integrase is an enzyme produced by a retrovirus (such as HIV) that enables its genetic material to be integrated into the DNA of the infected cell. Raltegravir and Elvitegravir are two important drugs against integrase.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2012-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79268478","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}
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.
{"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":"1 1","pages":""},"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}
Pub Date : 2012-03-12DOI: 10.5176/2251-2489_BICB06
Baby Jerald, Gopalakrishnan Nair, E. Rajasekaran
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.
{"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":"169 1","pages":""},"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}
The damping effect to the DNA bubble is investigated within the Peyrard-Bishop model. In the continuum limit, the dynamics of the bubble of DNA is described by the damped nonlinear Schrodinger equation and studied by means of variational method. It is shown that the propagation of solitary wave pattern is not vanishing in a non-viscous system. Inversely, the solitary wave vanishes soon as the viscous force is introduced.
{"title":"Dynamics of DNA Bubble in Viscous Medium","authors":"A. Sulaiman, F. P. Zen, H. Alatas, L. T. Handoko","doi":"10.1063/1.4730745","DOIUrl":"https://doi.org/10.1063/1.4730745","url":null,"abstract":"The damping effect to the DNA bubble is investigated within the Peyrard-Bishop model. In the continuum limit, the dynamics of the bubble of DNA is described by the damped nonlinear Schrodinger equation and studied by means of variational method. It is shown that the propagation of solitary wave pattern is not vanishing in a non-viscous system. Inversely, the solitary wave vanishes soon as the viscous force is introduced.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2012-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74248575","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}
Three, interrelated biologically-relevant examples of biased random walks are presented: (1) A model for DNA melting, modelled as DNA unzipping, which provides a way to illustrate the role of the Boltzmann factor in a venue well-known to biology and pre-medical students; (2) the activity of helicase motor proteins in unzipping double-stranded DNA, for example, at the replication fork, which is an example of a Brownian ratchet; (3) force generation by actin polymerization, which is another Brownian ratchet, and for which the force and actin-concentration dependence of the velocity of actin polymerization is determined.
{"title":"The Boltzmann factor, DNA melting, and Brownian ratchets: Topics in an introductory physics sequence for biology and premedical students","authors":"S. Mochrie","doi":"10.1119/1.3638908","DOIUrl":"https://doi.org/10.1119/1.3638908","url":null,"abstract":"Three, interrelated biologically-relevant examples of biased random walks are presented: (1) A model for DNA melting, modelled as DNA unzipping, which provides a way to illustrate the role of the Boltzmann factor in a venue well-known to biology and pre-medical students; (2) the activity of helicase motor proteins in unzipping double-stranded DNA, for example, at the replication fork, which is an example of a Brownian ratchet; (3) force generation by actin polymerization, which is another Brownian ratchet, and for which the force and actin-concentration dependence of the velocity of actin polymerization is determined.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"197 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2011-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73137124","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}
Pub Date : 2011-05-04DOI: 10.1142/S0218339013500174
Amparo Ba'illo, Laura Mart'inez-Munoz, M. Mellado
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.
共振能量转移方法被广泛用于评估活细胞中蛋白质相互作用和蛋白质构象变化。荧光共振能量转移(FRET)测量能量转移作为受体:供体比例的函数，产生FRET饱和曲线。通过Michaelis-Menten动力学对这些曲线进行建模，可以通过两个参数进行表征，这两个参数用于评估两种蛋白质之间的表观亲和力，并在不同的实验条件下比较这种亲和力。为了减少采样变异性的影响，在相同的生物条件下，生成了饱和度曲线的多个统计样本。在这里，我们研究了三个程序来确定统计样本是否在一个集合是同质的，在某种意义上说，他们是从相同的回归模型中提取的。从假设检验的观点来看，我们考虑了一个F检验和一个基于自举重采样的过程。第三种方法从模型选择的角度分析问题，采用了赤池信息准则(Akaike information criterion, AIC)。虽然我们只考虑Michaelis-Menten模型，但所有的统计过程都适用于任何其他非线性回归模型。我们通过蒙特卡罗研究和活细胞中CXCR4二聚体复合物的FRET饱和曲线分析比较了均匀性测试方法的性能，CXCR4是G蛋白偶联受体家族的七跨膜受体。我们发现，F检验、bootstrap过程和模型选择方法通常会得出类似的结论，尽管AIC在样本量较小时给出了最好的结果，而F检验和bootstrap方法更适合于大样本。在实际应用中，三种方法易于同时使用，且具有一致性，便于得出样品均匀性结论。
{"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":"8 1","pages":""},"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}
Pub Date : 2011-03-15DOI: 10.1007/978-3-642-25740-7_4
Kyle A. Beauchamp, Parin Sripakdeevong, Rhiju Das
{"title":"Why Can’t We Predict RNA Structure At Atomic Resolution?","authors":"Kyle A. Beauchamp, Parin Sripakdeevong, Rhiju Das","doi":"10.1007/978-3-642-25740-7_4","DOIUrl":"https://doi.org/10.1007/978-3-642-25740-7_4","url":null,"abstract":"","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"563 1","pages":"43-65"},"PeriodicalIF":0.0,"publicationDate":"2011-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77606247","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}
Pub Date : 2010-09-09DOI: 10.1002/9781118158715.CH2
B. Eisenberg
. Ions in water are the liquid of life. Life occurs almost entirely in ‘salt water’. Life began in salty oceans. Animals kept that salt water within them when they moved out of the ocean to drier surroundings. The plasma and blood that surrounds all cells are electrolytes more or less resembling sea water. The plasma inside cells is an electrolyte solution that more or less resembles the sea water in which life began. Water itself (without ions) is lethal to animal cells and damaging for most proteins. Water must contain the right ions in the right amounts if it is to sustain life. Physical chemistry is the language of electrolyte solutions and so physical chemistry, and biology, particularly physiology, have been intertwined since physical chemistry was developed some one hundred fifty years ago. Physiology, of course, was studied by the Greeks some millennia earlier, but the biological role of electrolyte solutionscould not be understood until ions were discovered by chemists some 2,000 years later.
{"title":"Crowded Charges in Ion Channels","authors":"B. Eisenberg","doi":"10.1002/9781118158715.CH2","DOIUrl":"https://doi.org/10.1002/9781118158715.CH2","url":null,"abstract":". Ions in water are the liquid of life. Life occurs almost entirely in ‘salt water’. Life began in salty oceans. Animals kept that salt water within them when they moved out of the ocean to drier surroundings. The plasma and blood that surrounds all cells are electrolytes more or less resembling sea water. The plasma inside cells is an electrolyte solution that more or less resembles the sea water in which life began. Water itself (without ions) is lethal to animal cells and damaging for most proteins. Water must contain the right ions in the right amounts if it is to sustain life. Physical chemistry is the language of electrolyte solutions and so physical chemistry, and biology, particularly physiology, have been intertwined since physical chemistry was developed some one hundred fifty years ago. Physiology, of course, was studied by the Greeks some millennia earlier, but the biological role of electrolyte solutionscould not be understood until ions were discovered by chemists some 2,000 years later.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"56 1","pages":"77-223"},"PeriodicalIF":0.0,"publicationDate":"2010-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83900043","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}
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