Intrinsically disordered proteins最新文献_第7页

Hydrogen skeleton, mobility and protein architecture. 氢骨架，流动性和蛋白质结构。

Intrinsically disordered proteins Pub Date : 2013-04-01 eCollection Date: 2013-01-01 DOI: 10.4161/idp.25767

Kalman Tompa, Monika Bokor, Kyou-Hoon Han, Peter Tompa

{"title":"Hydrogen skeleton, mobility and protein architecture.","authors":"Kalman Tompa, Monika Bokor, Kyou-Hoon Han, Peter Tompa","doi":"10.4161/idp.25767","DOIUrl":"https://doi.org/10.4161/idp.25767","url":null,"abstract":"The mobility of the proton-proton radial vectors is introduced as a quantitative measure for the structural dynamics of organic materials, especially protein molecules. As defined for the entire molecule, the hydrogen mobility (HM) is proposed as an \"order parameter,\" which describes the effect of motional narrowing on inter-proton dipole-dipole interactions. HM satisfies all requirements of an order parameter in the Landau molecular field theory of phase transitions. The wide-line NMR second moments needed to obtain HM are exactly defined and measurable physical quantities, which are not produced by mathematical fitting and do not carry the limitations and restrictions of any model (theoretical formalism). We first demonstrate the usefulness of HM on small organic molecules with data taken form the literature. We outline its link with structural and functional characteristics on a range of proteins: HM provides a model-free parameter based on first principles that can clearly distinguish between globular and intrinsically disordered proteins, and can also provide insight into the behavior of disease-related mutants.","PeriodicalId":90188,"journal":{"name":"Intrinsically disordered proteins","volume":"1 1","pages":"e25767"},"PeriodicalIF":0.0,"publicationDate":"2013-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/idp.25767","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35005140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

The alphabet of intrinsic disorder: I. Act like a Pro: On the abundance and roles of proline residues in intrinsically disordered proteins. 内在紊乱的字母表:1 .像专业人士一样行动:关于内在紊乱蛋白质中脯氨酸残基的丰度和作用。

Intrinsically disordered proteins Pub Date : 2013-04-01 eCollection Date: 2013-01-01 DOI: 10.4161/idp.24360

Francois-Xavier Theillet, Lajos Kalmar, Peter Tompa, Kyou-Hoon Han, Philipp Selenko, A Keith Dunker, Gary W Daughdrill, Vladimir N Uversky

{"title":"The alphabet of intrinsic disorder: I. Act like a Pro: On the abundance and roles of proline residues in intrinsically disordered proteins.","authors":"Francois-Xavier Theillet, Lajos Kalmar, Peter Tompa, Kyou-Hoon Han, Philipp Selenko, A Keith Dunker, Gary W Daughdrill, Vladimir N Uversky","doi":"10.4161/idp.24360","DOIUrl":"https://doi.org/10.4161/idp.24360","url":null,"abstract":"A significant fraction of every proteome is occupied by biologically active proteins that do not form unique three-dimensional structures. These intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) have essential biological functions and are characterized by extensive structural plasticity. Such structural and functional behavior is encoded in the amino acid sequences of IDPs/IDPRs, which are enriched in disorder-promoting residues and depleted in order-promoting residues. In fact, amino acid residues can be arranged according to their disorder-promoting tendency to form an alphabet of intrinsic disorder that defines the structural complexity and diversity of IDPs/IDPRs. This review is the first in a series of publications dedicated to the roles that different amino acid residues play in defining the phenomenon of protein intrinsic disorder. We start with proline because data suggests that of the 20 common amino acid residues, this one is the most disorder-promoting.","PeriodicalId":90188,"journal":{"name":"Intrinsically disordered proteins","volume":"1 1","pages":"e24360"},"PeriodicalIF":0.0,"publicationDate":"2013-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/idp.24360","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35006765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 169

Functional fragments of disorder in outer membrane β barrel proteins. 外膜β桶蛋白功能紊乱片段。

Intrinsically disordered proteins Pub Date : 2013-04-01 eCollection Date: 2013-01-01 DOI: 10.4161/idp.24848

Kavitha Kurup, A Keith Dunker, Sankaran Krishnaswamy

{"title":"Functional fragments of disorder in outer membrane β barrel proteins.","authors":"Kavitha Kurup, A Keith Dunker, Sankaran Krishnaswamy","doi":"10.4161/idp.24848","DOIUrl":"https://doi.org/10.4161/idp.24848","url":null,"abstract":"The traditional view of \"sequence-structure-function\" has been amended by the discovery of intrinsically disordered proteins. Almost 50% of PDB structures are now known to have one or more regions of disorder, which are involved in diverse functions. These regions typically possess low aromatic content and sequence complexity as well as high net charge and flexibility. In this study, we examined the composition and contribution of intrinsic disorder in outer membrane β barrel protein functions. Our systematic analysis to find the dual personality (DP) fragments, which often function by disorder-order transitions, revealed the presence of 61 DP fragments with 234 residues in β barrel trans membrane protein structures. It was found that though the disorder is more prevalent in the periplasmic regions, most of the residues which undergo disorder-order transitions are found in the extracellular regions. For example, the calcium binding sites in BtuB protein are found to undergo disorder to order transition upon binding calcium. The conformational change in the cell receptor binding site of the OpcA protein, which is important in host cell interactions of N. meningitidis, was also found to be due to the disorder-order transitions occurring in the presence of the ligand. The natively disordered nature of DP fragments makes it more appropriate to call them \"functional fragments of disorder.\" The present study provides insight into the roles played by intrinsically disordered regions in outer membrane protein functions.","PeriodicalId":90188,"journal":{"name":"Intrinsically disordered proteins","volume":"1 1","pages":"e24848"},"PeriodicalIF":0.0,"publicationDate":"2013-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/idp.24848","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35006766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

A method to trap transient and weak interacting protein complexes for structural studies. 一种捕获瞬态和弱相互作用蛋白复合物用于结构研究的方法。

Intrinsically disordered proteins Pub Date : 2013-04-01 eCollection Date: 2013-01-01 DOI: 10.4161/idp.25464

Vishnu Priyanka Reddy Chichili, Veerendra Kumar, J Sivaraman

{"title":"A method to trap transient and weak interacting protein complexes for structural studies.","authors":"Vishnu Priyanka Reddy Chichili, Veerendra Kumar, J Sivaraman","doi":"10.4161/idp.25464","DOIUrl":"https://doi.org/10.4161/idp.25464","url":null,"abstract":"Several key biological events adopt a \"hit-and-run\" strategy in their transient interactions between binding partners. In some instances, the disordered nature of one of the binding partners severely hampers the success of co-crystallization, often leading to the crystallization of just one of the partners. Here, we discuss a method to trap weak and transient protein interactions for crystallization. This approach requires the structural details of at least one of the interacting partners and binding knowledge to dock the known minimum binding region (peptide) of the protein onto the other using an optimal-sized linker. Prior to crystallization, the purified linked construct should be verified for its intact folding and stability. Following structure determination, structure-guided functional studies are performed with independent, full-length unlinked proteins to validate the findings of the linked complex. We designed this approach and then validated its efficacy using a 24 amino acid minimum binding region of the intrinsically disordered, neuron-specific substrates, Neurogranin and Neuromodulin, joined via a Gly-linker to their interacting partner, Calmodulin. Moreover, the reported functional studies with independent full-length proteins confirmed the findings of the linked peptide complexes. Based on our studies, and in combination with the supporting literature, we suggest that optimized linkers can provide an environment to mimic the natural interactions between binding partners, and offer a useful strategy for structural studies to trap weak and transient interactions involved in several biological processes.","PeriodicalId":90188,"journal":{"name":"Intrinsically disordered proteins","volume":"1 1","pages":"e25464"},"PeriodicalIF":0.0,"publicationDate":"2013-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/idp.25464","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35005137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

MFDp2: Accurate predictor of disorder in proteins by fusion of disorder probabilities, content and profiles. MFDp2:通过融合无序概率，内容和概况来准确预测蛋白质的无序。

Intrinsically disordered proteins Pub Date : 2013-04-01 eCollection Date: 2013-01-01 DOI: 10.4161/idp.24428

Marcin J Mizianty, Zhenling Peng, Lukasz Kurgan

{"title":"MFDp2: Accurate predictor of disorder in proteins by fusion of disorder probabilities, content and profiles.","authors":"Marcin J Mizianty, Zhenling Peng, Lukasz Kurgan","doi":"10.4161/idp.24428","DOIUrl":"https://doi.org/10.4161/idp.24428","url":null,"abstract":"Intrinsically disordered proteins (IDPs) are either entirely disordered or contain disordered regions in their native state. IDPs were found to be abundant in complex organisms and implicated in numerous cellular processes. Experimental annotation of disorder lags behind the rapidly growing sizes of the protein databases, and thus computational methods are used to close this gap and to investigate the disorder. MFDp2 is a novel content-rich and user-friendly web server for sequence-based prediction of protein disorder that builds upon our residue-level disorder predictor MFDp and chain-level disorder content predictor DisCon. It applies novel post-processing filters and uses sequence alignment to improve predictive quality. Using a new benchmark data set, which has reduced sequence identity to corresponding training data sets, MFDp2 is shown to provide competitive predictive quality when compared with MFDp and a comprehensive set of 13 other state-of-the-art predictors, including publicly available versions of the top predictors from CASP9. Our server obtains the highest Mathews Correlation Coefficient (MCC) and the second best Area Under the receiver operating characteristic Curve (AUC). In addition to the disorder predictions, our server also outputs well-described sequence-derived information that allows profiling the predicted disorder. We conveniently visualize sequence conservation, predicted secondary structure, relative solvent accessibility and alignments to chains with annotated disorder. We allow predictions for multiple proteins at the same time and each prediction can be downloaded as text-based (parsable) file. The web server, which includes help pages and tutorial, is freely available at biomine.ece.ualberta.ca/MFDp2/.","PeriodicalId":90188,"journal":{"name":"Intrinsically disordered proteins","volume":"1 1","pages":"e24428"},"PeriodicalIF":0.0,"publicationDate":"2013-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/idp.24428","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35006764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 52

Designing disorder: Tales of the unexpected tails. 设计混乱:意想不到的尾巴的故事。

Intrinsically disordered proteins Pub Date : 2013-01-01 DOI: 10.4161/idp.26790

David P Minde, Els F Halff, Sander Tans

引用次数: 18

Biophysical characterization of α-synuclein and its controversial structure. α-突触核蛋白的生物物理特性及其有争议的结构。

Intrinsically disordered proteins Pub Date : 2013-01-01 Epub Date: 2013-04-01 DOI: 10.4161/idp.26255

T Reid Alderson, John L Markley

引用次数: 64

Strain phenomenon in protein aggregation: Interplay between sequence and conformation. 蛋白质聚集中的应变现象:序列和构象之间的相互作用。

Intrinsically disordered proteins Pub Date : 2013-01-01 DOI: 10.4161/idp.27130

Leonid Breydo

引用次数: 1

Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator. 结构系统发育的轮廓提取和多重叠加使用静电同余作为鉴别器。

Intrinsically disordered proteins Pub Date : 2013-01-01 DOI: 10.4161/idp.25463

Sandeep Chakraborty, Basuthkar J Rao, Nathan Baker, Bjarni Asgeirsson

{"title":"Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator.","authors":"Sandeep Chakraborty, Basuthkar J Rao, Nathan Baker, Bjarni Asgeirsson","doi":"10.4161/idp.25463","DOIUrl":"https://doi.org/10.4161/idp.25463","url":null,"abstract":"Phylogenetic analysis of proteins using multiple sequence alignment (MSA) assumes an underlying evolutionary relationship in these proteins which occasionally remains undetected due to considerable sequence divergence. Structural alignment programs have been developed to unravel such fuzzy relationships. However, none of these structure based methods have used electrostatic properties to discriminate between spatially equivalent residues. We present a methodology for MSA of a set of related proteins with known structures using electrostatic properties as an additional discriminator (STEEP). STEEP first extracts a profile, then generates a multiple structural superimposition providing a consolidated spatial framework for comparing residues and finally emits the MSA. Residues that are aligned differently by including or excluding electrostatic properties can be targeted by directed evolution experiments to transform the enzymatic properties of one protein into another. We have compared STEEP results to those obtained from a MSA program (ClustalW) and a structural alignment method (MUSTANG) for chymotrypsin serine proteases. Subsequently, we used PhyML to generate phylogenetic trees for the serine and metallo-β-lactamase superfamilies from the STEEP generated MSA, and corroborated the accepted relationships in these superfamilies. We have observed that STEEP acts as a functional classifier when electrostatic congruence is used as a discriminator, and thus identifies potential targets for directed evolution experiments. In summary, STEEP is unique among phylogenetic methods for its ability to use electrostatic congruence to specify mutations that might be the source of the functional divergence in a protein family. Based on our results, we also hypothesize that the active site and its close vicinity contains enough information to infer the correct phylogeny for related proteins.","PeriodicalId":90188,"journal":{"name":"Intrinsically disordered proteins","volume":"1 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/idp.25463","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32787762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Digested disorder: Quarterly intrinsic disorder digest (April-May-June, 2013). 消化紊乱:季度内在紊乱文摘(2013年4月- 5月- 6月)。

Intrinsically disordered proteins Pub Date : 2013-01-01 DOI: 10.4161/idp.27454

Shelly DeForte, Krishna D Reddy, Vladimir N Uversky

引用次数: 5