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Related Concept Videos

Reversible and Irreversible Processes01:14

Reversible and Irreversible Processes

The thermodynamic processes can be classified into reversible and irreversible processes. The processes that can be restored to their initial state are called reversible processes. It is only possible if the process is in quasi-static equilibrium, i.e., it takes place in infinitesimally small steps, and the system remains at equilibrium However, these are ideal processes and do not occur naturally. An ideal system undergoing a reversible process is always in thermodynamic equilibrium within...
Leaky Scanning02:28

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...
Restarting Stalled Replication Forks02:37

Restarting Stalled Replication Forks

DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart, a...
Restarting Stalled Replication Forks02:37

Restarting Stalled Replication Forks

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Mesh Analysis01:20

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Mesh analysis is a valuable method for simplifying circuit analysis using mesh currents as key circuit variables. Unlike nodal analysis, which focuses on determining unknown voltages, mesh analysis applies Kirchhoff's voltage law (KVL) to find unknown currents within a circuit. This method is particularly convenient in reducing the number of simultaneous equations that need to be solved.
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Related Experiment Video

Updated: Jun 12, 2026

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

An analysis of reentrant loops.

Changhui Yan1, Jingru Luo

  • 1Department of Computer Science, North Dakota State University, Fargo, ND 58108-6050, USA. Changhui.Yan@ndsu.edu

The Protein Journal
|June 15, 2010
PubMed
Summary

Reentrant loops in transmembrane proteins have unique hydrophobicity patterns. These patterns, with low hydrophobicity deep in the membrane, stabilize the structure and can be detected using profile hidden Markov models (HMMs).

Area of Science:

  • Structural biology
  • Protein science
  • Bioinformatics

Background:

  • Reentrant loops are key structural motifs in alpha-helical transmembrane proteins.
  • Their unique topology, traversing only halfway through the membrane, remains poorly understood.

Purpose of the Study:

  • To investigate the driving forces behind reentrant loop formation and stabilization.
  • To identify sequence patterns associated with reentrant loops.

Main Methods:

  • Analysis of amino acid hydrophobicity distribution within reentrant loops.
  • Development and application of profile hidden Markov models (HMMs).

Main Results:

  • Reentrant loops exhibit low hydrophobicity at the membrane's deepest point and higher hydrophobicity near surfaces.

Related Experiment Videos

Last Updated: Jun 12, 2026

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

  • This specific hydrophobicity distribution creates detectable sequence patterns.
  • Profile HMMs accurately identify reentrant loops with high sensitivity and specificity.

    • Conclusions:

    • Hydrophobicity distribution is a critical factor stabilizing reentrant loop structure.
    • Profile HMMs provide an effective computational tool for detecting reentrant loops in protein sequences.