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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
Structure of a Gene01:30

Structure of a Gene

A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
Prokaryotic Gene Structure and Organization01:28

Prokaryotic Gene Structure and Organization

Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...

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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

A structure filter for the Eukaryotic Linear Motif Resource.

Allegra Via1, Cathryn M Gould, Christine Gemünd

  • 1Center for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy. allegra.via@uniroma1.it

BMC Bioinformatics
|October 27, 2009
PubMed
Summary
This summary is machine-generated.

Predicting functional linear motifs in proteins is challenging. This study introduces a new method using protein structures to better assess motif accessibility and context, improving the reliability of functional motif prediction.

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07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Protein bioinformatics
  • Molecular biology
  • Structural biology

Background:

  • Proteins are modular, composed of globular domains and disordered segments.
  • Linear motifs are short, functional sequence modules found in disordered regions and exposed loops of globular domains.
  • Predicting functional linear motifs requires distinguishing true positives from random occurrences, using attributes like taxonomy, cellular compartment, conservation, and accessibility.

Purpose of the Study:

  • To develop a novel method for assessing the functional potential of linear motifs.
  • To improve the confidence in predicting linear motif function by considering structural context.
  • To provide a tool that aids researchers in prioritizing motif candidates for experimental validation.

Main Methods:

  • Developed a method to map putative linear motifs onto protein structures, utilizing high-quality SCOP domain structures.
  • Scored candidate motifs based on solvent accessibility and secondary structural context derived from 3D protein structures.
  • Calibrated scores using experimentally verified motif instances and random matches to establish confidence levels.

Main Results:

  • The new method significantly improves the classification of functional motifs.
  • Achieved a 3-fold enrichment for functional motifs classified as high confidence.
  • Demonstrated a 2.5-fold enrichment for random motifs classified as low confidence.
  • Implemented as a pipeline with a graphical interface via the ELM resource and a Web Service.

Conclusions:

  • Bioinformatic tools for linear motif prediction have limitations, necessitating experimental validation.
  • The ELM structure filter assists users in evaluating motifs within globular regions.
  • This tool helps researchers efficiently allocate resources for experimental testing of promising motif candidates.