scholarly journals A Graph-Directed Approach for Creation of a Homology Modeling Library: Application to Venom Structure Prediction

2019 ◽  
Author(s):  
Rachael A Mansbach ◽  
Srirupa Chakraborty ◽  
Timothy Travers ◽  
S. Gnanakaran
Keyword(s):  
Homology Modeling ◽  
Structure Prediction ◽  
Three Dimensional ◽  
Threat Assessment ◽  
Drug Candidates ◽  
The Family ◽  
Template Library ◽  
Therapeutic Leads ◽  
Candidate Identification

Many toxins are short, cysteine-rich peptides that are of great interest as novel therapeutic leads and of great concern as lethal biological agents due to their high affinity and specificity for various receptors involved in neuromuscular transmission. To perform initial candidate identification for design of a drug impacting a particular receptor or for threat assessment as a harmful toxin, one requires a set of candidate structures of reasonable accuracy with potential for interaction with the target receptor. In this article, we introduce a graph-based algorithm for identifying good extant template structures from a library of evolutionarily-related cysteine-containing sequences for structural determination of target sequences by homology modeling. We employ this approach to study the conotoxins, a set of toxin peptides produced by the family of aquatic cone snails. Currently, of the approximately six thousand known conotoxin sequences, only about three percent have experimentally characterized three-dimensional structures, leading to a serious bottleneck in identifying potential drug candidates. We demonstrate that the conotoxin template library generated by our approach may be employed to perform homology modeling and greatly increase the number of characterized conotoxin structures. We also show how our approach can guide experimental design by identifying and ranking sequences for structural characterization in a similar manner. Overall, we present and validate an approach for venom structure modeling and employ it to expand the library of extant conotoxin structures by almost 300% through homology modeling employing the template library determined in our approach.

scholarly journals Characterisation of a Novel A-Superfamily Conotoxin

Biomedicines ◽  
2020 ◽  
Vol 8 (5) ◽  
pp. 128
Author(s):  
David T. Wilson ◽  
Paramjit S. Bansal ◽  
David A. Carter ◽  
Irina Vetter ◽  
Annette Nicke ◽  
...  
Keyword(s):  
Nicotinic Acetylcholine Receptor ◽  
Disulfide Bonds ◽  
Three Dimensional ◽  
Structural Type ◽  
Dimensional Structure ◽  
Na Channels ◽  
Nicotinic Acetylcholine ◽  
Therapeutic Leads ◽  
Helical Region

Conopeptides belonging to the A-superfamily from the venomous molluscs, Conus, are typically α-conotoxins. The α-conotoxins are of interest as therapeutic leads and pharmacological tools due to their selectivity and potency at nicotinic acetylcholine receptor (nAChR) subtypes. Structurally, the α-conotoxins have a consensus fold containing two conserved disulfide bonds that define the two-loop framework and brace a helical region. Here we report on a novel α-conotoxin Pl168, identified from the transcriptome of Conus planorbis, which has an unusual 4/8 loop framework. Unexpectedly, NMR determination of its three-dimensional structure reveals a new structural type of A-superfamily conotoxins with a different disulfide-stabilized fold, despite containing the conserved cysteine framework and disulfide connectivity of classical α-conotoxins. The peptide did not demonstrate activity on a range of nAChRs, or Ca2+ and Na+ channels suggesting that it might represent a new pharmacological class of conotoxins.

On Potential Energy Models for EA-based Ab Initio Protein Structure Prediction

2010 ◽  
Vol 18 (2) ◽  
pp. 255-275 ◽  
Author(s):  
Milan Mijajlovic ◽  
Mark J. Biggs ◽  
Dusan P. Djurdjevic
Keyword(s):  
Protein Structure ◽  
Potential Energy ◽  
Ab Initio ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Three Dimensional ◽  
Free Energy Surface ◽  
Energy Models ◽  
Parameter Values

Ab initio protein structure prediction involves determination of the three-dimensional (3D) conformation of proteins on the basis of their amino acid sequence, a potential energy (PE) model that captures the physics of the interatomic interactions, and a method to search for and identify the global minimum in the PE (or free energy) surface such as an evolutionary algorithm (EA). Many PE models have been proposed over the past three decades and more. There is currently no understanding of how the behavior of an EA is affected by the PE model used. The study reported here shows that the EA behavior can be profoundly affected: the EA performance obtained when using the ECEPP PE model is significantly worse than that obtained when using the Amber, OPLS, and CVFF PE models, and the optimal EA control parameter values for the ECEPP model also differ significantly from those associated with the other models.

scholarly journals RNA 3D Structure Prediction Using Coarse-Grained Models

2021 ◽  
Vol 8 ◽  
Author(s):  
Jun Li ◽  
Shi-Jie Chen
Keyword(s):  
Structure Prediction ◽  
3D Structure ◽  
Three Dimensional ◽  
Coarse Grained ◽  
Biological Functions ◽  
3D Structures ◽  
Rna Molecules ◽  
Atomic Structures ◽  
Long Time

The three-dimensional (3D) structures of Ribonucleic acid (RNA) molecules are essential to understanding their various and important biological functions. However, experimental determination of the atomic structures is laborious and technically difficult. The large gap between the number of sequences and the experimentally determined structures enables the thriving development of computational approaches to modeling RNAs. However, computational methods based on all-atom simulations are intractable for large RNA systems, which demand long time simulations. Facing such a challenge, many coarse-grained (CG) models have been developed. Here, we provide a review of CG models for modeling RNA 3D structures, compare the performance of the different models, and offer insights into potential future developments.

A DIFFERENT LOOK AT THE QUALITY OF MODELED THREE-DIMENSIONAL PROTEIN STRUCTURES

2008 ◽  
Vol 06 (02) ◽  
pp. 335-345 ◽  
Author(s):  
ALEKSANDAR POLEKSIC ◽  
MARK FIENUP ◽  
JOSEPH F. DANZER ◽  
DEREK A. DEBE
Keyword(s):  
Drug Design ◽  
Homology Modeling ◽  
Binding Site ◽  
Small Molecule ◽  
Binding Sites ◽  
Structure Prediction ◽  
Protein Structures ◽  
Three Dimensional ◽  
Automated Method

Measuring the accuracy of protein three-dimensional structures is one of the most important problems in protein structure prediction. For structure-based drug design, the accuracy of the binding site is far more important than the accuracy of any other region of the protein. We have developed an automated method for assessing the quality of a protein model by focusing on the set of residues in the small molecule binding site. Small molecule binding sites typically involve multiple regions of the protein coming together in space, and their accuracy has been observed to be sensitive to even small alignment errors. In addition, ligand binding sites contain the critical information required for drug design, making their accuracy particularly important. We analyzed the accuracy of the binding sites on two sets of protein models: the predictions submitted by the top-performing CASP7 groups, and the models generated by four widely used homology modeling packages. The results of our CASP7 analysis significantly differ from the previous findings, implying that the binding site measure does not correlate with the traditional model quality measures used in the structure prediction benchmarks. For the modeling programs, the resolution of binding sites is extremely sensitive to the degree of sequence homology between the query and the template, even when the most accurate alignments are used in the homology modeling process.

scholarly journals Three dimensional cross-modal image inference: label-free methods for subcellular structure prediction

2017 ◽  
Author(s):  
Chek Ounkomol ◽  
Daniel A. Fernandes ◽  
Sharmishtaa Seshamani ◽  
Mary M. Maleckar ◽  
Forrest Collman ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Live Cell Imaging ◽  
Cell Imaging ◽  
Fluorescent Dyes ◽  
Three Dimensional ◽  
Live Cells ◽  
Label Free ◽  
State Changes ◽  
Microscopy Images

AbstractFluorescence microscopy has enabled imaging of key subcellular structures in living cells; however, the use of fluorescent dyes and proteins is often expensive, time-consuming, and damaging to cells. Here, we present a tool for the prediction of fluorescently labeled structures in live cells solely from 3D brightfield microscopy images. We show the utility of this approach in predicting several structures of interest from the same static 3D brightfield image, and show that the same tool can prospectively be used to predict the spatiotemporal position of these structures from a bright-field time series. This approach could also be useful in a variety of application areas, such as cross-modal image registration, quantification of live cell imaging, and determination of cell state changes.

scholarly journals Study of the Langat virus RNA-dependent RNA polymerase through homology modeling

2021 ◽  
Vol 26 (1) ◽  
pp. e944
Author(s):  
Kalliopi Io Diakou ◽  
Thanasis Mitsis ◽  
Katerina Pierouli ◽  
Eleni Papakonstantinou ◽  
Vasileios Megalooikonomou ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Homology Modeling ◽  
Three Dimensional ◽  
Close Relative ◽  
Three Dimensional Model ◽  
Rna Dependent Rna Polymerase ◽  
Modeling Process ◽  
Virus Rna ◽  
The Family ◽  
Langat Virus

Langat virus is a member of the Flaviviridae family and a close relative of a group of important tick-borne viruses that cause human encephalitis. RNA-dependent RNA polymerase is a significant component of the replication mechanism of the Flaviviridae viral family. In the present work, a three-dimensional model of the Langat virus RNA-dependent RNA polymerase was designed through homology modeling. The experimentally determined structure of the RNA-dependent RNA polymerase of Dengue virus type II, another member of the same viral family, was employed as template for the homology modeling process. The resulting model underwent a series of optimisations and its quality was verified using the Verify3D algorithm. Important functional characteristics of the family of viral RNA-dependent RNA polymerases were identified in the generated model, thus affirming the potential for its use in the possible design of anti-viral agents for Langat virus.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Role of the family focused technologies in the clinical course of pregnancy at women of high obstetric risk

2016 ◽  
pp. 64-66
Author(s):  
S.Yu. Vdovichenko ◽  
Keyword(s):  
Comparison Group ◽  
Traditional Approach ◽  
Married Couple ◽  
Premature Births ◽  
Individual Support ◽  
The Family ◽  
Risk Patients ◽  
Individual Preparation

The objective: to show a role of the family focused technologies in depression of frequency of pathology of pregnancy at women of high obstetric risk. Patients and methods. For determination of efficiency of prophylaxis of pathology of pregnancy on the basis of use of the family focused technologies complex clinical-psychological and laboratory and tool examination of 300 women with factors of obstetric risk which were divided into two groups was conducted. In the main group – 182 women with motivation on partner labors to which provided training on system of individual preparation of married couple to labors. The comparison group consisted of 118 women who were not in prenatal training and had individual support in childbirth, with the traditional approach to pain management. Results. Use of the family focused technologies during pregnancy allows to reduce significantly the frequency of the main complications of pregnancy, especially not incubation and premature births. Conclusion. In our opinion, the technique is simple, available and can widely be used in practical health care at women with high obstetric risk. Key words: obstetric risk, the family focused technologies, prophylaxis.

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