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Related Concept Videos

Multi-pass Transmembrane Proteins and β-barrels01:09

Multi-pass Transmembrane Proteins and β-barrels

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In multi-pass transmembrane proteins, the polypeptide chain crosses the membrane more than once. The transmembrane polypeptide chain either forms an α-helix or β-strand structure. α-Helix containing multi-pass transmembrane proteins are ubiquitous, whereas β-strand containing ones are mainly found in gram-negative bacteria, mitochondria, and chloroplasts.
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Structure of Porins01:21

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Mitochondria, chloroplasts, and gram-negative bacteria have transmembrane, beta-barrel proteins called porins to mediate the free diffusion of ions and metabolites across the membrane. Mitochondrial porin precursors contain conserved amino acid sequences called beta signals at their C-terminal. Beta signals have a  motif of PoXGXXHyXHy (Po-Polar, X-Any amino acid, G-Glycine, Hy-LargeHydrophobic), which are crucial for precursor recognition to initiate precursor assembly. Beta-barrel...
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Integral membrane proteins are proteins adhered to the lipid bilayer of a cell organelle or membrane. They can be of two types: transmembrane integral proteins that span the lipid bilayer and monotopic proteins that are attached to either side of the membrane but do not pass through it.
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Integral membrane proteins are tightly associated with the cell membrane and play a crucial role in cell communication, signaling, adhesion, and transport of the molecules. Some integral membrane proteins are present only in the membrane monolayer. For example, the enzyme fatty acid amide hydrolase is present in the cytoplasmic side of the membrane monolayer. In contrast, another type of integral membrane protein, also known as a transmembrane protein, spans across the membrane. Transmembrane...
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The living membranes are flexible due to their fluid mosaic nature; however, their bending into different shapes is an active process regulated by specific lipids and proteins. The membrane bending can be transient as seen in vesicles or stable for a long time as in microvilli. Cells regulate the size, location, and duration of the membrane curvature.
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The rough ER membrane synthesizes, assembles, and embeds transmembrane proteins in diverse topologies. These proteins function as transporters or channels and can remain in the ER membrane or are sent to the Golgi complex, lysosome, and cell membrane.
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Structural Determinants of Transmembrane β-Barrels.

Themis Lazaridis1

  • 1Department of Chemistry, City College of New York/CUNY, 138th Street & Convent Avenue, New York, New York 10031.

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|December 8, 2015
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Summary

Predicting beta-barrel membrane protein structures is difficult. This study introduces an improved implicit membrane model (IMM1-pore) and analyzes residue interactions, aiding in understanding and predicting these crucial protein folds.

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Area of Science:

  • Structural biology
  • Computational biophysics
  • Membrane protein research

Background:

  • Recognizing beta-barrel membrane proteins from sequence is challenging.
  • Understanding physical determinants of transmembrane beta-barrel structure is crucial for accurate prediction.
  • Existing models require enhancement for proteins with internal aqueous pores.

Purpose of the Study:

  • To extend the IMM1 implicit membrane model to accommodate membrane proteins with internal aqueous pores (IMM1-pore).
  • To evaluate the IMM1-pore model's ability to generate stable trajectories and discriminate correct folds for beta-barrel proteins.
  • To investigate the sequence-structure relationship and energy contributions for transmembrane beta-barrel folding using OmpA and retinol binding protein.

Main Methods:

  • Extension of the IMM1 implicit membrane model to create the IMM1-pore model.
  • Molecular dynamics simulations of three beta-barrel membrane proteins using IMM1-pore.
  • Fold recognition and energy evaluation by threading sequences onto known structures (OmpA and retinol binding protein).
  • Decomposition of energy contributions by residue to identify stability drivers.

Main Results:

  • The IMM1-pore model produced stable molecular dynamics trajectories for beta-barrel proteins.
  • The model demonstrated the ability to discriminate correct folds for 10- and 12-stranded transmembrane beta-barrels.
  • Energy analysis revealed that interior polar residue interactions stabilize OmpA, while exterior polar/charged residues and less favorable interior interactions hinder retinol binding protein folding.
  • The energy function successfully distinguished native structures from decoys.

Conclusions:

  • The enhanced IMM1-pore model is effective for simulating and predicting beta-barrel membrane protein structures.
  • Specific residue interactions, particularly interior polar contacts, are key determinants of beta-barrel stability.
  • These findings provide insights for designing improved scoring functions for beta-barrel protein structure prediction and fold recognition.