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Tail-anchoring of Proteins in the ER Membrane01:45

Tail-anchoring of Proteins in the ER Membrane

Tail-anchored, or TA, proteins are estimated to make up to 3-5% of membrane proteins found in the eukaryotic cell. Such proteins have a single transmembrane domain located approximately 30 amino acid residues upstream from the C-terminal end. As a result, the signal recognition particle (SRP) cannot guide a TA protein to the ER membrane for cotranslational insertion. Hence, they are integrated into the ER membrane post-translationally using their C-terminal end as the anchor. TA proteins...
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Drug Binding to Blood Components

When drugs enter systemic circulation, they interact with various components of the blood, including proteins such as human serum albumin (HSA), α1-acid glycoprotein (AAG), lipoproteins, globulins, and red blood cells (RBCs).
HSA is the most abundant plasma protein and is vital in drug binding. It contains distinct drug-binding sites, with different drugs exhibiting affinity for specific sites. There are three main drug-binding domains for HSA: sites I, II, and III. These domains are further...
Lipids as Anchors01:32

Lipids as Anchors

In the plasma membrane, the lipids forming the bilayer can also act as an anchor to tether proteins to the membrane. The three main types of lipid anchors found in eukaryotes are – prenyl groups, fatty acyl groups, and glycosylphosphatidylinositol or GPI groups. Prenyl and fatty acyl groups act as anchors on the cytosolic surface of the membrane, whereas GPI anchors proteins on the extracellular side.
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Receptor-mediated Endocytosis

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Receptor-mediated Endocytosis01:20

Receptor-mediated Endocytosis

Receptor-mediated endocytosis is when bulk amounts of specific molecules are imported into a cell after binding to cell surface receptors. The molecules bound to these receptors are taken into the cell through inward folding of the cell surface membrane, which is eventually pinched off into a vesicle within the cell. Structural proteins, such as clathrin, coat the budding vesicle.
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Metal-Ligand Bonds02:51

Metal-Ligand Bonds

The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
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Related Experiment Video

Updated: Jun 24, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Docking to heme proteins.

Ute F Röhrig1, Aurélien Grosdidier, Vincent Zoete

  • 1Ludwig Institute for Cancer Research, Ltd., Lausanne, Switzerland.

Journal of Computational Chemistry
|March 17, 2009
PubMed
Summary

We improved metalloprotein docking by introducing Morse-like metal binding potentials (MMBP). This enhanced our EADock algorithm

Area of Science:

  • Computational chemistry
  • Drug discovery
  • Structural biology

Background:

  • In silico screening is crucial for drug design but struggles with metalloprotein targets.
  • Metalloprotein interactions are challenging to parameterize in docking algorithms.
  • Existing methods like EADock, based on CHARMM force fields, show limitations with metalloproteins.

Purpose of the Study:

  • To improve the accuracy of docking algorithms for metalloproteins, specifically heme proteins.
  • To develop and validate a new method for accurately modeling iron-ligand interactions in docking.
  • To assess the general applicability and potential bias of the new method in cross-docking studies.

Main Methods:

  • Implemented Morse-like metal binding potentials (MMBP) into the EADock docking algorithm.

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Measurement of Heme Synthesis Levels in Mammalian Cells
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Measurement of Heme Synthesis Levels in Mammalian Cells

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Measurement of Heme Synthesis Levels in Mammalian Cells
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  • Fitted MMBP parameters using density functional theory calculations.
  • Validated the enhanced algorithm on heme protein complexes and a set of non-iron binders.

    • Main Results:

    • The standard docking protocol achieved only a 28% success rate for heme proteins.
    • Introducing MMBP increased the success rate to 62% for heme protein complexes.
    • MMBP did not introduce bias in docking non-iron binding proteins, indicating reliability.

    Conclusions:

    • MMBP significantly improves the accuracy of docking for iron-containing metalloproteins.
    • The developed method enhances the utility of in silico screening for metalloprotein drug targets.
    • The MMBP approach is robust and suitable for cross-docking studies without introducing bias.