arXiv: Biomolecules最新文献_第3页

Predictions of tertiary stuctures of $alpha$-helical membrane proteins by replica-exchange method with consideration of helix deformations 考虑螺旋变形的复制交换法预测α -螺旋膜蛋白的三级结构

arXiv: Biomolecules Pub Date : 2014-09-19 DOI: 10.7566/JPSJ.84.084802

Ryo Urano, H. Kokubo, Y. Okamoto

引用次数: 3

Opsin vs opsin: new materials for biotechnological applications 视蛋白vs视蛋白:生物技术应用的新材料

arXiv: Biomolecules Pub Date : 2014-02-03 DOI: 10.1063/1.4892445

E. Alfinito, L. Reggiani

引用次数: 16

Can pseudocomplementary peptide nucleic acid nucleases (pcPNANs) be a new tool for genetic engineering 伪互补肽核酸核酸酶(pcPNANs)能否成为基因工程的新工具

arXiv: Biomolecules Pub Date : 2014-01-30 DOI: 10.7287/PEERJ.PREPRINTS.229V1

Penghui Shi

{"title":"Can pseudocomplementary peptide nucleic acid nucleases (pcPNANs) be a new tool for genetic engineering","authors":"Penghui Shi","doi":"10.7287/PEERJ.PREPRINTS.229V1","DOIUrl":"https://doi.org/10.7287/PEERJ.PREPRINTS.229V1","url":null,"abstract":"Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) comprise a powerful class of tools that are redefining the boundaries of biological research. Although these technologies have begun to enable targeted genome modifications, there remains a need for new technologies that are scalable, affordable, and easy to engineer. In this paper, we propose a new tool for genetic engineering, the pseudocomplementary peptide nucleic acid nucleases (pcPNANs), which are composed of a pseudocomplementary PNA (pcPNA) specific for a DNA target sequence, a FokI nuclease cleavage domain and a nuclear localization signal. pcPNANs may induce targeted DNA double-strand breaks that activate DNA damage response pathways and enable custom alterations. Their cleavage-site is determined by simple Watson-Crick rule, and thus pcPNANs for aimed cleavage of genomes can be straightforwardly designed and synthesized without any selection procedure. Accordingly, the cleavage-site and site-specificity are freely chosen by changing the sequences and the lengths of pcPNA strands. We believe that the potentiality of pcPNAN as a new tool for genetic engineering will be confirmed in the future.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"98 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84545580","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: 0

Effect of ionic ordering in conductivity experiments of DNA aqueous solutions 离子排序对DNA水溶液电导率实验的影响

arXiv: Biomolecules Pub Date : 2014-01-03 DOI: 10.15407/UJPE59.05.0479

O. O. Liubysh, O. Alekseev, S. Tkachov, S. Perepelytsya

{"title":"Effect of ionic ordering in conductivity experiments of DNA aqueous solutions","authors":"O. O. Liubysh, O. Alekseev, S. Tkachov, S. Perepelytsya","doi":"10.15407/UJPE59.05.0479","DOIUrl":"https://doi.org/10.15407/UJPE59.05.0479","url":null,"abstract":"The effects of ionic ordering in DNA water solutions are studied by conductivity experiments. The conductivity measurements are performed for the solutions of DNA with KCl salt in the temperature range from 28 to 70 C. Salt concentration vary from 0 to 2 M. The conductivity of solutions without DNA but with the same concentration of KCl salt are also performed. The results show that in case of salt free solution of DNA the melting process of the double helix is observed, while in case of DNA solution with added salt the macromolecule denaturation is not featured. For salt concentrations lower than some critical one (0.4 M) the conductivity of DNA solution is higher than the conductivity of KCl water solution without DNA. Starting from the critical concentration the conductivity of KCl solution is higher than the conductivity of DNA solution with added salt. For description of the experimental data phenomenological model is elaborated basing on electrolyte theory. In framework of the developed model a mechanism of counterion ordering is introduced. According to this mechanism under the low salt concentrations electrical conductivity of the system is caused by counterions of DNA ion-hydrate shell. Increasing the amount of salt to the critical concentration counterions condense on DNA polyanion. Further increase of salt concentration leads to the formation of DNA-salt complexes that decreases the conductivity of the system.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82579657","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: 6

Simplified flexibility analysis of proteins 简化蛋白质柔韧性分析

arXiv: Biomolecules Pub Date : 2013-12-19 DOI: 10.1201/b17979-12

Y. Sanejouand

引用次数: 0

Sensing viruses by mechanical tension of DNA in responsive hydrogels 通过反应性水凝胶中DNA的机械张力感应病毒

arXiv: Biomolecules Pub Date : 2013-10-21 DOI: 10.1103/PhysRevX.4.021002

Jaeoh Shin, Andrey G. Cherstvy, R. Metzler

{"title":"Sensing viruses by mechanical tension of DNA in responsive hydrogels","authors":"Jaeoh Shin, Andrey G. Cherstvy, R. Metzler","doi":"10.1103/PhysRevX.4.021002","DOIUrl":"https://doi.org/10.1103/PhysRevX.4.021002","url":null,"abstract":"The rapid worldwide spread of severe viral infections, often involving novel modifications of viruses, poses major challenges to our health care systems. This means that tools that can efficiently and specifically diagnose viruses are much needed. To be relevant for a broad application in local health care centers, such tools should be relatively cheap and easy to use. Here we discuss the biophysical potential for the macroscopic detection of viruses based on the induction of a mechanical stress in a bundle of pre-stretched DNA molecules upon binding of viruses to the DNA. We show that the affinity of the DNA to the charged virus surface induces a local melting of the double-helix into two single-stranded DNA. This process effects a mechanical stress along the DNA chains leading to an overall contraction of the DNA. Our results suggest that when such DNA bundles are incorporated in a supporting matrix such as a responsive hydrogel, the presence of viruses may indeed lead to a significant, macroscopic mechanical deformation of the matrix. We discuss the biophysical basis for this effect and characterize the physical properties of the associated DNA melting transition. In particular, we reveal several scaling relations between the relevant physical parameters of the system. We promote this DNA-based assay for efficient and specific virus screening.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"99 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75284580","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: 29

In silico investigation of lactone and thiolactone inhibitors in bacterial quorum sensing using molecular modeling 用分子模型研究细菌群体感应中的内酯和硫代内酯抑制剂

arXiv: Biomolecules Pub Date : 2013-05-16 DOI: 10.5539/IJC.V5N4P9

Marawan Ahmed, S. Bird, Feng Wang, E. Palombo

引用次数: 18

Dynamics of ion-phosphate lattice of DNA in left-handed double helix form 左双螺旋形式DNA的离子-磷酸盐晶格动力学

arXiv: Biomolecules Pub Date : 2013-04-01 DOI: 10.15407/UJPE58.06.0554

S. Perepelytsya, S. Volkov

引用次数: 5

Stereochemistry of polypeptide conformation in coarse grained analysis 粗粒分析中多肽构象的立体化学

arXiv: Biomolecules Pub Date : 2013-02-08 DOI: 10.1142/9789814449144_0011

Anil Korkut, W. Hendrickson

{"title":"Stereochemistry of polypeptide conformation in coarse grained analysis","authors":"Anil Korkut, W. Hendrickson","doi":"10.1142/9789814449144_0011","DOIUrl":"https://doi.org/10.1142/9789814449144_0011","url":null,"abstract":"The conformations available to polypeptides are determined by the interatomic forces acting on the peptide units, whereby backbone torsion angles are restricted as described by the Ramachandran plot. Although typical proteins are composed predominantly from {alpha}-helices and {beta}-sheets, they nevertheless adopt diverse tertiary structure, each folded as dictated by its unique amino-acid sequence. Despite such uniqueness, however, the functioning of many proteins involves changes between quite different conformations. The study of large-scale conformational changes, particularly in large systems, is facilitated by a coarse-grained representation such as provided by virtually bonded C{alpha} atoms. We have developed a virtual atom molecular mechanics (VAMM) force field to describe conformational dynamics in proteins and a VAMM-based algorithm for computing conformational transition pathways. Here we describe the stereochemical analysis of proteins in this coarse-grained representation, comparing the relevant plots in coarse-grained conformational space to the corresponding Ramachandran plots, having contoured each at levels determined statistically from residues in a large database. The distributions shown for an all-{alpha} protein, two all-{beta} proteins and one {alpha}+{beta} protein serve to relate the coarse-grained distributions to the familiar Ramachandran plot.","PeriodicalId":8447,"journal":{"name":"arXiv: Biomolecules","volume":"40 1","pages":"136-147"},"PeriodicalIF":0.0,"publicationDate":"2013-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80021268","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

Dynamical Aspects of Information in Copolymerization Processes 共聚过程信息的动态方面

arXiv: Biomolecules Pub Date : 2012-11-12 DOI: 10.1007/978-3-319-00395-5_58

P. Gaspard

引用次数: 0