scholarly journals The breakthrough in protein structure prediction

2021 ◽  
Vol 478 (10) ◽  
pp. 1885-1890
Author(s):  
Andrei N. Lupas ◽  
Joana Pereira ◽  
Vikram Alva ◽  
Felipe Merino ◽  
Murray Coles ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Life Sciences ◽  
Three Dimensional ◽  
Critical Assessment ◽  
Amino Acid Sequences ◽  
Prediction Problem ◽  
Linear Chains ◽  
Single Protein ◽  
Artificial Intelligence Laboratory ◽  
The Relationship

Proteins are the essential agents of all living systems. Even though they are synthesized as linear chains of amino acids, they must assume specific three-dimensional structures in order to manifest their biological activity. These structures are fully specified in their amino acid sequences — and therefore in the nucleotide sequences of their genes. However, the relationship between sequence and structure, known as the protein folding problem, has remained elusive for half a century, despite sustained efforts. To measure progress on this problem, a series of doubly blind, biennial experiments called CASP (critical assessment of structure prediction) were established in 1994. We were part of the assessment team for the most recent CASP experiment, CASP14, where we witnessed an astonishing breakthrough by DeepMind, the leading artificial intelligence laboratory of Alphabet Inc. The models filed by DeepMind's structure prediction team using the program AlphaFold2 were often essentially indistinguishable from experimental structures, leading to a consensus in the community that the structure prediction problem for single protein chains has been solved. Here, we will review the path to CASP14, outline the method employed by AlphaFold2 to the extent revealed, and discuss the implications of this breakthrough for the life sciences.

Structure and function of voltage-dependent sodium channels: comparison of brain II and cardiac isoforms

1996 ◽  
Vol 76 (3) ◽  
pp. 887-926 ◽  
Author(s):  
H. A. Fozzard ◽  
D. A. Hanck
Keyword(s):  
Amino Acid ◽  
Three Dimensional ◽  
Point Mutations ◽  
Amino Acid Sequences ◽  
Na Channel ◽  
Na Channels ◽  
Voltage Dependent ◽  
And Function ◽  
Relationship Of ◽  
The Relationship

Cardiac and nerve Na channels have broadly similar functional properties and amino acid sequences, but they demonstrate specific differences in gating, permeation, ionic block, modulation, and pharmacology. Resolution of three-dimensional structures of Na channels is unlikely in the near future, but a number of amino acid sequences from a variety of species and isoforms are known so that channel differences can be exploited to gain insight into the relationship of structure to function. The combination of molecular biology to create chimeras and channels with point mutations and high-resolution electrophysiological techniques to study function encourage the idea that predictions of structure from function are possible. With the goal of understanding the special properties of the cardiac Na channel, this review examines the structural (sequence) similarities between the cardiac and nerve channels and considers what is known about the relationship of structure to function for voltage-dependent Na channels in general and for the cardiac Na channels in particular.

CooPPS: A SYSTEM FOR THE COOPERATIVE PREDICTION OF PROTEIN STRUCTURES

2004 ◽  
Vol 02 (03) ◽  
pp. 471-495 ◽  
Author(s):  
LUIGI PALOPOLI ◽  
GIORGIO TERRACINA
Keyword(s):  
Structure Prediction ◽  
Protein Structures ◽  
Three Dimensional ◽  
Quality Parameters ◽  
Dimensional Structure ◽  
Prediction Problem ◽  
Common Reference ◽  
Prediction Tools ◽  
Definition Of

Predicting the three-dimensional structure of proteins is a difficult task. In the last few years several approaches have been proposed for performing this task taking into account different protein chemical and physical properties. As a result, a growing number of protein structure prediction tools is becoming available, some of them specialized to work on either some aspects of the predictions or on some categories of proteins; however, they are still not sufficiently accurate and reliable for predicting all kinds of proteins. In this context, it is useful to jointly apply different prediction tools and combine their results in order to improve the quality of the predictions. However, several problems have to be solved in order to make this a viable possibility. In this paper a framework and a tool is proposed which allows: (i) definition of a common reference applicative domain for different prediction tools; (ii) characterization of prediction tools through evaluating some quality parameters; (iii) characterization of the performances of a team of predictors jointly applied over a prediction problem; (iv) the singling out of the best team for a prediction problem; and (v) the integration of predictor results in the team in order to obtain a unique prediction. A system implementing the various steps of the proposed framework (CooPPS) has been developed and several experiments for testing the effectiveness of the proposed approach have been carried out.

scholarly journals Sequence Analysis and Structure Prediction of Malaysia SARS-CoV-2 Strain’s Structural and Accessory Proteins

2021 ◽  
Vol 12 (3) ◽  
pp. 3259-3304
Keyword(s):  
Structure Prediction ◽  
Active Sites ◽  
Homo Sapiens ◽  
Functional Characterization ◽  
Protein Structures ◽  
Three Dimensional ◽  
Experimental Models ◽  
Amino Acid Sequences ◽  
Accessory Proteins ◽  
Evolutionary Analysis

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that transmitted from animal to human became a life-threatening pandemic in 2020. Scientists are currently testing several drugs to eradicate the COVID-19 outbreak. However, there is no 100 % effective drug or vaccine against SARS-CoV-2 has been discovered so far. In this study, we explored the structure prediction and functional analysis of 75 Malaysia SARS-CoV-2 strain’s structural and accessory proteins without the presence of experimental models. Physiochemical analysis, secondary structure analysis, structure prediction, functional characterization, active site identification, and evolutionary analysis based on the amino acid sequences retrieved from National Centre for Biotechnology Information (NCBI). Three-dimensional (3-D) protein structures were built using the Swiss model. The quality of protein models was verified by ERRAT, PROCHECK, and Verify 3D tools. Active prediction analysis revealed the high potential active sites of proteins where the anti-viral drug or vaccine may bind and inhibit the viral activities. Molecular phylogenetic analysis of ORF10, ORF8, and ORF6 proteins from five different species was analyzed. The results from this analysis proved that Homo sapiens SARS-CoV-2 had high genetic similarity with the bat coronavirus. These analyses may help in designing structure-based anti-viral drugs or to develop potential vaccines for SARS-CoV-2.

scholarly journals Proteins sequence analysis of Contagious Caprine Pleuropneumonia

2017 ◽  
Vol 33 (3) ◽  
pp. 309-319
Author(s):  
Ayuba Dauda ◽  
Abdulmojeed Yakubu ◽  
Ihe Dim ◽  
Deeve Gwaza
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Chemical Properties ◽  
Alpha Helix ◽  
Amino Acid Sequences ◽  
Contagious Bovine Pleuropneumonia ◽  
Isoleucine Leucine ◽  
Grand Average

A total of twenty (20) contagious bovine pleuropneumonia (CCPP) proteins were retrieved from the GenBank (www.ncbi.nlm.nih.gov). The proteins sequences were used to investigate the molecular identity of various CCPP proteins. The physico-chemical properties of CCPP proteins were performed using protparam tool. Isoelectric point (pI), molecular weight (MW), extinction coefficient (EC); instability index (II), aliphatic index (AI) and grand average of hydropathicity (GRAVY) were computed. The study revealed that the pI of CCPP proteins were acidic and basic in nature. The EC and II of CCPP proteins indicate better stability which is an indication of resistant to mutation and thermally stable. The GRAVY of CCPP proteins revealed some are positive while some are negative. The positive value indicates solubility (hydrophilic) in water while negative is not soluble (hydrophobic) in water. The amino acid composition of CCPP proteins indicates that they are rich in isoleucine, leucine and lysine. The three dimensional structures (3D) of the CCPP proteins were determine using Phyre2 server. The amino acid sequences of CCPP proteins were subjected to secondary structure prediction using ExPASy?s SOPMA tool. The proteins are more of alpha helix structure. The genetic information eminating from this study may bring insight into mutagenesis and pharmacogenetic. <br><br><font color="red"><b> This article has been retracted. Link to the retraction <u><a href="http://dx.doi.org/10.2298/BAH1803369E">10.2298/BAH1803369E</a><u></b></font>

Is the growth rate of Protein Data Bank sufficient to solve the protein structure prediction problem using template-based modeling?

2015 ◽  
Vol 11 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Michal Brylinski
Keyword(s):  
Protein Structure ◽  
Protein Data Bank ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Structural Information ◽  
Three Dimensional ◽  
Data Bank ◽  
Prediction Problem ◽  
Three Dimensional Models ◽  
Protein Structure Prediction Problem

AbstractThe Protein Data Bank (PDB) undergoes an exponential expansion in terms of the number of macromolecular structures deposited every year. A pivotal question is how this rapid growth of structural information improves the quality of three-dimensional models constructed by contemporary bioinformatics approaches. To address this problem, we performed a retrospective analysis of the structural coverage of a representative set of proteins using remote homology detected by COMPASS and HHpred. We show that the number of proteins whose structures can be confidently predicted increased during a 9-year period between 2005 and 2014 on account of the PDB growth alone. Nevertheless, this encouraging trend slowed down noticeably around the year 2008 and has yielded insignificant improvements ever since. At the current pace, it is unlikely that the protein structure prediction problem will be solved in the near future using existing template-based modeling techniques. Therefore, further advances in experimental structure determination, qualitatively better approaches in fold recognition, and more accurate template-free structure prediction methods are desperately needed.

scholarly journals Group-1 Grass Pollen Allergens with Near-Identical Sequences Identified in Species of Subtropical Grasses Commonly Found in Southeast Asia

Medicina ◽  
2019 ◽  
Vol 55 (5) ◽  
pp. 193 ◽  
Author(s):  
Sirirat Aud-in ◽  
Koravit Somkid ◽  
Wisuwat Songnuan
Keyword(s):  
Southeast Asia ◽  
Grass Pollen ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
Grass Species ◽  
Pollen Allergens ◽  
Allergenic Protein ◽  
The Relationship ◽  
Group 1

Background and objectives: Group-1 grass allergens or beta-expansins (EXPBs) are major allergens from pollen of all grass species. Previous studies showed that they are highly conserved (64–85%) in Pooideae species, which are found mostly in the temperate regions. However, the information about group-1 allergens from common grass species in subtropical areas is still lacking. This study aimed to assess the sequence diversity of group-1 grass pollen allergens in subtropical areas, especially in Southeast Asia. Materials and Methods: Group-1 allergens were cloned from pollen of eight grass species using a single set of primers. Sequences were analyzed and IgE and IgG4 binding regions were compared to the previously reported epitopes in homologous EXPBs. The phylogenetic analysis was used to assess the relationship between sequences of these species and previously characterized EXPBs. Moreover, three-dimensional structure of the EXPB was modeled based on homology to Zea m 1. Results: Sequences from eight grass species were nearly identical. It is conceivable that the primers used for cDNA amplification detected the same isoform in different species. In fact, the deduced amino acid sequences shared 97.79–100% identity with each other and 15/819 polymorphic nucleotide positions were identified. The predicted structure showed that the IgE and IgG4 epitopes and polymorphic residues were located in both domains 1 and 2. The dendrogram presents clustering of class A EXPBs into four groups corresponding to the grass subfamilies. Conclusions: This study identified the allergens with near-identical sequences from different grass species. This isoform could be the major cross-reacting allergenic protein from commonly found grass species.

Thathir Quality Scholarship Program For Students At University level

2018 ◽  
Vol 2 (3) ◽  
pp. 206-219
Author(s):  
Louay Qais Abdullah ◽  
Duraid Faris Khayoun
Keyword(s):  
College Students ◽  
Life Sciences ◽  
Economic Feasibility ◽  
First Year ◽  
Grant Program ◽  
Scholarship Program ◽  
University Level ◽  
Faculty Of Education ◽  
The University ◽  
The Relationship

The study focused basically on measuring the relationship between the material cost of the students benefits program and the benefits which are earned by it, which was distributed on college students in the initial stages (matinee) and to show the extent of the benefits accruing from the grant program compared to the material burdens which matched and the extent of success or failure of the experience and its effect from o scientific and side on the Iraqi student through these tough economic circumstances experienced by the country in general, and also trying to find ways of proposed increase or expansion of distribution in the future in the event of proven economic feasibility from the program. An data has been taking from the data fro the Department of Financial Affairs and the Department of Studies and Planning at the University of Diyala with taking an data representing an actual and minimized pattern and questionnaires to a sample of students from the Department of Life Sciences in the Faculty of Education of the University of Diyala on the level of success and failure of students in the first year of the grant and the year before for the purpose of distribution comparison. The importance of the study to measure the extent of interest earned in comparision whit the material which is expenseon the program of grant (grant of students) to assist the competent authorities to continue or not in the program of student grants for the coming years.

Sea Urchins and Circuses: The Modernist Natural Histories of Jean Painlevé and Alexander Calder

2018 ◽  
Vol 13 (2) ◽  
pp. 187-211
Author(s):  
Patricia E. Chu
Keyword(s):  
New Media ◽  
Sea Urchins ◽  
Life Sciences ◽  
Three Dimensional ◽  
Machine Age ◽  
Avant Garde ◽  
History Of ◽  
And Performance ◽  
The One ◽  
Natural Historian

The Paris avant-garde milieu from which both Cirque Calder/Calder's Circus and Painlevé’s early films emerged was a cultural intersection of art and the twentieth-century life sciences. In turning to the style of current scientific journals, the Paris surrealists can be understood as engaging the (life) sciences not simply as a provider of normative categories of materiality to be dismissed, but as a companion in apprehending the “reality” of a world beneath the surface just as real as the one visible to the naked eye. I will focus in this essay on two modernist practices in new media in the context of the history of the life sciences: Jean Painlevé’s (1902–1989) science films and Alexander Calder's (1898–1976) work in three-dimensional moving art and performance—the Circus. In analyzing Painlevé’s work, I discuss it as exemplary of a moment when life sciences and avant-garde technical methods and philosophies created each other rather than being classified as separate categories of epistemological work. In moving from Painlevé’s films to Alexander Calder's Circus, Painlevé’s cinematography remains at the forefront; I use his film of one of Calder's performances of the Circus, a collaboration the men had taken two decades to complete. Painlevé’s depiction allows us to see the elements of Calder's work that mark it as akin to Painlevé’s own interest in a modern experimental organicism as central to the so-called machine-age. Calder's work can be understood as similarly developing an avant-garde practice along the line between the bestiary of the natural historian and the bestiary of the modern life scientist.

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