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Related Concept Videos

Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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Related Experiment Video

Updated: Jul 5, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Mathematically complete nucleotide and protein sequence searching using Ssearch.

Alexander J Ropelewski1, Hugh B Nicholas, David W Deerfield

  • 1Pittsburgh Supercomputing Center, Pittsburgh, Pennsylvania, USA.

Current Protocols in Bioinformatics
|April 23, 2008
PubMed
Summary

This study presents a method to predict transmembrane alpha-helical bundle structures. It uses molecular dynamics and amino acid substitutions to identify the correct protein structure.

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Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Related Experiment Videos

Last Updated: Jul 5, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Transmembrane proteins are crucial for cellular functions.
  • Predicting the structure of alpha-helical bundles is essential for understanding protein function.
  • Current methods may lack accuracy for complex structures.

Purpose of the Study:

  • To develop and describe a protocol for predicting the structure of simple transmembrane alpha-helical bundles.
  • To utilize global molecular dynamics search and silent amino acid substitutions for accurate structure prediction.

Main Methods:

  • Global Molecular Dynamics Search (GMDS) to explore configuration space.
  • Analysis of silent amino acid substitutions to validate candidate structures.
  • Repetition of GMDS across homologous proteins to ensure structural persistence.

Main Results:

  • Generation of multiple candidate structures for helical bundles.
  • Identification of the correct structure by its ability to accommodate all silent substitutions.
  • A robust protocol for predicting transmembrane alpha-helical bundle structures.

Conclusions:

  • The described protocol effectively predicts transmembrane alpha-helical bundle structures.
  • Combining GMDS with silent amino acid substitution analysis enhances prediction accuracy.
  • This method provides a reliable approach for structural biologists and bioinformaticians.