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Related Concept Videos

Protein Organization01:13

Protein Organization

Overview
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
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Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
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Translocation of Proteins into the Mitochondria

Mitochondrial precursors are translocated to the internal subcompartments via independent mechanisms involving distinct protein machineries called translocases.
Sorting of outer membrane proteins:
Mitochondrial outer membrane proteins are of two types: the transmembrane, beta-barrel porins, and the membrane-anchored, alpha-helical proteins. Beta-barrel porin precursors are translocated by the TOM complex and inserted into the outer mitochondrial membrane by the SAM complex. In contrast,...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Related Experiment Video

Updated: Jul 26, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins.

C Bystroff1, V Thorsson, D Baker

  • 1Department of Biology, Rensselaer Polytechnic Institute, Troy, NY 12180-3590, USA.

Journal of Molecular Biology
|August 5, 2000
PubMed
Summary

A new protein sequence model, HMMSTR, captures local structure motifs across protein families. This branched hidden Markov model improves secondary structure and torsion angle predictions.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Structural Biology

Background:

  • Traditional hidden Markov models (HMMs) often model individual protein families linearly.
  • Capturing recurrent local sequence-structure motifs across diverse protein families remains a challenge.

Purpose of the Study:

  • To introduce HMMSTR, a novel, highly branched hidden Markov model for general protein sequence analysis.
  • To leverage the I-sites library of sequence-structure motifs for improved protein modeling.

Main Methods:

  • Developed HMMSTR with a branched topology, extending the I-sites library.
  • Incorporated motif adjacencies from protein databases and a compact representation for overlapping motifs.
  • Reduced model parameters significantly through efficient motif representation.

Main Results:

  • HMMSTR assigns higher probability to coding sequences compared to dipeptide models.
  • Achieved 74.3% accuracy in secondary structure prediction.
  • Outperformed previous methods in predicting backbone torsion angles and structural context of beta strands and turns.

Conclusions:

  • HMMSTR effectively models general protein sequences by capturing cross-family local structural features.
  • The model demonstrates significant improvements in predicting key structural properties.
  • HMMSTR shows potential utility for tertiary structure prediction.