scholarly journals Protein Helical Structures: Defining Handedness and Localization Features

Symmetry ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 879
Author(s):  
Alla E. Sidorova ◽  
Ekaterina V. Malyshko ◽  
Aleksey O. Lutsenko ◽  
Denis K. Shpigun ◽  
Olga E. Bagrova
Keyword(s):  
Quantitative Analysis ◽  
Protein Structures ◽  
Coiled Coil ◽  
Molecular Machines ◽  
Reference Points ◽  
Helical Structures ◽  
Mixed Product ◽  
Coil Axis ◽  
Protein Classes ◽  
Polypeptide Chains

The quantitative evaluation of the chirality of macromolecule structures remains one of the exciting issues in biophysics. In this paper, we propose methods for quantitative analysis of the chirality of protein helical and superhelical structures. The analysis of the chirality sign of the protein helical structures (α-helices and -helices) is based on determining the mixed product of every three consecutive vectors between neighboring reference points—α-carbons atoms. The method for evaluating the chirality sign of coiled-coil structures is based on determining the direction and value of the angle between the coiled-coil axis and the α-helices axes. The chirality sign of the coiled coil is calculated by averaging the value of the cosine of the corresponding angle for all helices forming the superhelix. Chirality maps of helical and superhelical protein structures are presented. Furthermore, we propose an analysis of the distributions of helical and superhelical structures in polypeptide chains of several protein classes. The features common to all studied classes and typical for each protein class are revealed. The data obtained, in all likelihood, can reflect considerations about molecular machines as chiral formations.

scholarly journals Rapid molecular replacement of coiled-coil and transmembrane proteins with AMPLE

2014 ◽  
Vol 70 (a1) ◽  
pp. C347-C347
Author(s):  
Jens Thomas ◽  
Ronan Keegan ◽  
Jaclyn Bibby ◽  
Martyn Winn ◽  
Olga Mayans ◽  
...  
Keyword(s):  
Ab Initio ◽  
Protein Structures ◽  
Coiled Coil ◽  
Molecular Replacement ◽  
Helical Structures ◽  
Desktop Computer ◽  
Search Models ◽  
Nmr Structures ◽  
Structure Solution ◽  
Helical Geometry

Molecular Replacement (MR) is an increasingly popular route to protein structure solution. AMPLE[1] is a software pipeline that uses either cheaply obtained ab inito protein models, or NMR structures to extend the scope of MR, allowing it to solve entirely novel protein structures in a completely automated pipeline on a standard desktop computer. AMPLE employs a cluster-and-truncate approach, combined with multiple modes of side chain treatment, to analyse the candidate models and extract the consensual features most likely to solve the structure. The search models generated in this way are screened by MrBump using Phaser and Molrep and correct solutions are detected using main chain tracing and phase modification with Shelxe. AMPLE proved capable of processing rapidly obtained ab initio structure predictions into successful search models and more recently proved effective in assembling NMR structures for MR[2]. Coiled-coil proteins are a distinct class of protein fold whose structure solution by MR is not typically straightforward. We show here that AMPLE can quickly and routinely solve most coiled-coil structures using ab initio predictions from Rosetta. The predictions are generally not globally accurate, but by encompassing different degrees of truncation of clustered models, AMPLE succeeds by sampling across a range of search models. These sometimes succeed through capturing locally well-modelled conformations, but often simply contain small helical units. Remarkably, the latter regularly succeed despite out-of-register placement and poor MR statistics. We demonstrate that single structures derived from successful ensembles perform less well, and comparable ideal helices solve few targets. Thus, both modelling of distortions from ideal helical geometry and the ensemble nature of the search models contribute to success. AMPLE is a framework applicable to any set of input structures in which variability is correlated with inaccuracy. We also present preliminary data demonstrating structure solution of transmembrane helical structures using Rosetta modelling. We finally consider future sources of starting models which offer the hope that MR with AMPLE, in the absence of close homology between a known structure and the target, may soon be possible with larger proteins.

scholarly journals ARCIMBOLDOon coiled coils

2018 ◽  
Vol 74 (3) ◽  
pp. 194-204 ◽  
Author(s):  
Iracema Caballero ◽  
Massimo Sammito ◽  
Claudia Millán ◽  
Andrey Lebedev ◽  
Nicolas Soler ◽  
...  
Keyword(s):  
Coiled Coil ◽  
Coiled Coils ◽  
Translational Symmetry ◽  
Command Line ◽  
Phase Problem ◽  
Final Solution ◽  
Resolution Limit ◽  
Helical Structures ◽  
Small Model ◽  
Test Pool

ARCIMBOLDOsolves the phase problem by combining the location of small model fragments usingPhaserwith density modification and autotracing usingSHELXE. Mainly helical structures constitute favourable cases, which can be solved using polyalanine helical fragments as search models. Nevertheless, the solution of coiled-coil structures is often complicated by their anisotropic diffraction and apparent translational noncrystallographic symmetry. Long, straight helices have internal translational symmetry and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors. This situation has to be differentiated from the translational symmetry relating different monomers.ARCIMBOLDO_LITEhas been run on single workstations on a test pool of 150 coiled-coil structures with 15–635 amino acids per asymmetric unit and with diffraction data resolutions of between 0.9 and 3.0 Å. The results have been used to identify and address specific issues when solving this class of structures usingARCIMBOLDO. Features fromPhaserv.2.7 onwards are essential to correct anisotropy and produce translation solutions that will pass the packing filters. As the resolution becomes worse than 2.3 Å, the helix direction may be reversed in the placed fragments. Differentiation between true solutions and pseudo-solutions, in which helix fragments were correctly positioned but in a reverse orientation, was found to be problematic at resolutions worse than 2.3 Å. Therefore, after every new fragment-placement round, complete or sparse combinations of helices in alternative directions are generated and evaluated. The final solution is once again probed by helix reversal, refinement and extension. To conclude, density modification andSHELXEautotracing incorporating helical constraints is also exploited to extend the resolution limit in the case of coiled coils and to enhance the identification of correct solutions. This study resulted in a specialized mode withinARCIMBOLDOfor the solution of coiled-coil structures, which overrides the resolution limit and can be invoked from the command line (keyword coiled_coil) orARCIMBOLDO_LITEtask interface inCCP4i.

scholarly journals The geolect of Plungė in terms of regressive assimilation of vowels I, U

2020 ◽  
pp. 1-19
Author(s):  
Simona Vyniautaitė
Keyword(s):  
Cluster Analysis ◽  
Quantitative Analysis ◽  
Reference Points ◽  
Research Model ◽  
Limb Reduction ◽  
Audio Recordings ◽  
Main Variable ◽  
Variable Feature ◽  
Dual Core ◽  
Main Distinguishing Feature

Based on dialectometric methods, the article discusses the geolect of Plungė in terms of regressive assimilation of vowels i, u. The study material consists of about 9 hours of audio recordings, 57 sentences, recited by nine presenters of younger, middle and older generations. 6 words were chosen in which regressive assimilation of vowels can take place, i. e., the words with vowels i, u in accented, unaccented and shifted accent positions. Quantitative analysis of the material (sentences read by the presenters) was performed with the tools of the computer program Gabmap. Pseudo maps of networks, reference points, cluster analysis, as well as differential dialectal features were analyzed. The analysis performed using dialectometry methods shows that differences in limb reduction, word stem, consonant softening become apparent, but in many cases regressive assimilation of vowels i, u becomes the main variable feature. The operation/inaction of the regressive assimilation of vowels i, u is greatly influenced by accent. When vowels are accented, presenters of all generations pronounce them without regressive vowel assimilation. When the vowel i is unaccented, it is assimilated, and the vowel u is spelled narrowly by only a third of the presenters. Dual behavior exists in cases where vowels receive a shifted accent. The pronunciation of both vowels is approximate. Maintaining the main distinguishing feature of the residents of Plungė from the dialect of the residents of Telšiai, although inconsistent, would allow predicting that the linguistic dialect peculiarity of this area could compete with the language code of Telšiai – based on the Samogitian regiolect – or whether the regiolect itself would be / become dual-core (more detailed research based on a multi-faceted research model is needed to confirm this statement). The effect of regressive assimilation in the Plungė dialect, in the geolectic zone in general, can be both a proof of resemblance to the northern Samogitian Telšiai residents and a sign of a decrease in the importance of assimilation as a distinctive feature of the dialects.

scholarly journals FrustratometeR: an R-package to compute Local frustration in protein structures, point mutants and MD simulations

2020 ◽  
Author(s):  
Atilio O. Rausch ◽  
Maria I. Freiberger ◽  
Cesar O. Leonetti ◽  
Diego M. Luna ◽  
Leandro G. Radusky ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Large Scale ◽  
Protein Structures ◽  
Md Simulations ◽  
R Package ◽  
Protein Protein Interactions ◽  
Large Scale Analysis ◽  
Functional Aspects ◽  
Catalytic Sites ◽  
Polypeptide Chains

Once folded natural protein molecules have few energetic conflicts within their polypeptide chains. Many protein structures do however contain regions where energetic conflicts remain after folding, i.e. they have highly frustrated regions. These regions, kept in place over evolutionary and physiological timescales, are related to several functional aspects of natural proteins such as protein-protein interactions, small ligand recognition, catalytic sites and allostery. Here we present FrustratometeR, an R package that easily computes local energetic frustration on a personal computer or a cluster. This package facilitates large scale analysis of local frustration, point mutants and MD trajectories, allowing straightforward integration of local frustration analysis in to pipelines for protein structural analysis.Availability and implementation: https://github.com/proteinphysiologylab/frustratometeR

Mechanics of Interactions of Helices in Proteins

2006 ◽  
Vol 326-328 ◽  
pp. 823-826
Author(s):  
Li Li Xin ◽  
Gregory S. Chirikjian
Keyword(s):  
Rigid Body ◽  
Protein Structures ◽  
Body Motion ◽  
Data Sets ◽  
Line Contact ◽  
Helical Structures ◽  
First Case ◽  
Rigid Rods ◽  
On Line ◽  
Two Parameters

This paper concerns a mechanics of interactions of helical structures in proteins. Helices are the most important secondary structures of proteins and contribute the formation of a more complex 3-D structure, and so the analysis of interactions of helices is quite critical. We examine 1290 protein structures that have 2.0 Å or better resolutions and less than 20 percent of their sequences in common. Interactions between helices are represented by two parameters: the distance and angle. Assuming that helices are slender rigid rods with finite length, we define three different mechanisms of interactions: (1) line-on-line contact; (2) endpoint-to-line contact; and (3) endpointto- endpoint contact. In this paper, interactions for the first case are expressed with the 3-D relative rigid-body motion (position and orientation) and the unique volume element for correctly integrating over rigid-body motions are determined using six parameters. The results are extremely useful for the correct analysis of interactions in terms of distance and angle without the statistical biases inherent in the three data sets.

Using Side-Chain Aromatic Proton Chemical Shifts for a Quantitative Analysis of Protein Structures

2011 ◽  
Vol 50 (41) ◽  
pp. 9620-9623 ◽  
Author(s):  
Aleksandr B. Sahakyan ◽  
Wim F. Vranken ◽  
Andrea Cavalli ◽  
Michele Vendruscolo
Keyword(s):  
Quantitative Analysis ◽  
Chemical Shifts ◽  
Protein Structures ◽  
Aromatic Proton ◽  
Side Chain ◽  
Proton Chemical Shifts

MRPC (Missing Regions in Polypeptide Chains): a knowledgebase

2019 ◽  
Vol 52 (6) ◽  
pp. 1422-1426
Author(s):  
Rajendran Santhosh ◽  
Namrata Bankoti ◽  
Adgonda Malgonnavar Padmashri ◽  
Daliah Michael ◽  
Jeyaraman Jeyakanthan ◽  
...  
Keyword(s):  
Protein Structures ◽  
Three Dimensional ◽  
Protein Molecule ◽  
Data Bank ◽  
Protein Crystal ◽  
Dimensional Structure ◽  
Protein Structure Analysis ◽  
Three Dimensional Structure ◽  
X Ray Crystallography ◽  
Polypeptide Chains

Missing regions in protein crystal structures are those regions that cannot be resolved, mainly owing to poor electron density (if the three-dimensional structure was solved using X-ray crystallography). These missing regions are known to have high B factors and could represent loops with a possibility of being part of an active site of the protein molecule. Thus, they are likely to provide valuable information and play a crucial role in the design of inhibitors and drugs and in protein structure analysis. In view of this, an online database, Missing Regions in Polypeptide Chains (MRPC), has been developed which provides information about the missing regions in protein structures available in the Protein Data Bank. In addition, the new database has an option for users to obtain the above data for non-homologous protein structures (25 and 90%). A user-friendly graphical interface with various options has been incorporated, with a provision to view the three-dimensional structure of the protein along with the missing regions using JSmol. The MRPC database is updated regularly (currently once every three months) and can be accessed freely at the URL http://cluster.physics.iisc.ac.in/mrpc.

Design and Modeling of a Peptide Based NanoTweezer

2006 ◽  
Author(s):  
Gaurav Sharma ◽  
Kaushal Rege ◽  
Constantinos Mavroidis ◽  
Martin L. Yarmush
Keyword(s):  
Molecular Dynamics ◽  
Coiled Coil ◽  
Computational Results ◽  
Actuation Mechanism ◽  
Electrostatic Charges ◽  
Environmentally Responsive ◽  
Force Profile ◽  
Potential Applications ◽  
Polypeptide Chains ◽  
Molecular Dynamics Results

The design hypothesis, architectures, and preliminary computational results of a peptide based nanoTweezer are presented in this paper. We engineered the α-helical coiled coil portion of the yeast transcriptional activator peptide called GCN4 to obtain an environmentally-responsive nanoTweezer. The dimeric coiled coil peptide consists of two identical ~4.5 nm long and ~3 nm wide polypeptide chains. The actuation mechanism depends on the modifying electrostatic charges along the peptide by varying the pH of the solution resulting in the reversible movement of helices and therefore, creating the motion of the tweezer. Preliminary molecular dynamics results indicated that pH changes led to a reversible deflection of 1–2 nm with the nanoTweezer. The force profile of the nanoTweezer motion and some potential applications are also discussed.

scholarly journals Quantitative analysis of APP axonal transport in neurons: role of JIP1 in enhanced APP anterograde transport

2014 ◽  
Vol 25 (22) ◽  
pp. 3569-3580 ◽  
Author(s):  
Kyoko Chiba ◽  
Masahiko Araseki ◽  
Keisuke Nozawa ◽  
Keiko Furukori ◽  
Yoichi Araki ◽  
...  
Keyword(s):  
Quantitative Analysis ◽  
Axonal Transport ◽  
High Frequency ◽  
Coiled Coil ◽  
Tetratricopeptide Repeat ◽  
The Novel ◽  
Anterograde Transport ◽  
Interacting Protein ◽  
A Site

Alzheimer's β-amyloid precursor protein (APP) associates with kinesin-1 via JNK-interacting protein 1 (JIP1); however, the role of JIP1 in APP transport by kinesin-1 in neurons remains unclear. We performed a quantitative analysis to understand the role of JIP1 in APP axonal transport. In JIP1-deficient neurons, we find that both the fast velocity (∼2.7 μm/s) and high frequency (66%) of anterograde transport of APP cargo are impaired to a reduced velocity (∼1.83 μm/s) and a lower frequency (45%). We identified two novel elements linked to JIP1 function, located in the central region of JIP1b, that interact with the coiled-coil domain of kinesin light chain 1 (KLC1), in addition to the conventional interaction of the JIP1b 11–amino acid C-terminal (C11) region with the tetratricopeptide repeat of KLC1. High frequency of APP anterograde transport is dependent on one of the novel elements in JIP1b. Fast velocity of APP cargo transport requires the C11 domain, which is regulated by the second novel region of JIP1b. Furthermore, efficient APP axonal transport is not influenced by phosphorylation of APP at Thr-668, a site known to be phosphorylated by JNK. Our quantitative analysis indicates that enhanced fast-velocity and efficient high-frequency APP anterograde transport observed in neurons are mediated by novel roles of JIP1b.

Address of the President Sir Alan Hodgkin, O. M. at the Anniversary Meeting, 1 December 1975

1976 ◽  
Vol 192 (1109) ◽  
pp. 371-391
Keyword(s):  
Molecular Biology ◽  
Coiled Coil ◽  
Helical Structure ◽  
X Ray Diffraction ◽  
Helical Structures ◽  
X Ray ◽  
Double Helical Structure ◽  
Leading Role ◽  
Replication Scheme ◽  
Related Proteins

The Copley Medal is awarded to Dr F. H. C. Crick, F. R. S. In 1953 Crick and Watson proposed the double-helical model for DNA, in which the bases are arranged in complementary pairs so that the molecule is capable of self-replication and is thus the essential carrier of genetic information in living cells. This proposal was based on an inspired interpretation of the results of X-ray diffraction analysis of DNA carried out by Wilkins, Franklin and their collaborators, and on the chemical analyses of Chargaff and others. The replication scheme inherent in the double-helical structure of DNA made it possible for the first time to discuss the mechanism of heredity in molecular terms; it has been the most fruitful concept in the whole of biology during the past 25 years, and has been the basis for the explosive development of molecular biology. Besides his part in this dramatic discovery, Crick played a very important part in increasing our understanding of the way in which the genetic message is carried on DNA (the ‘coding’ problem), and of the mechanisms by which it is translated into specific sequences of amino acids in the proteins synthesized by the cell. He has also continued to play a leading rôle in many other aspects of molecular biology, and has made important contributions to X-ray studies of crystalline proteins, fibrous proteins and viruses. These include the theory of diffraction from helical structures, the coiled-coil model of α-keratin and related proteins, the structure of collagen, and the theoretical basis of the construction of ‘spherical’ viruses. More recently, Crick has had an important influence on work in the fields of development and of chromosome structure.

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