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Related Concept Videos

Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

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Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
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Directing Proteins to the Rough Endoplasmic Reticulum01:34

Directing Proteins to the Rough Endoplasmic Reticulum

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The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...
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Post-translational Translocation of Proteins to the RER01:27

Post-translational Translocation of Proteins to the RER

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A sizable fraction of proteins destined for ER are first synthesized in the cell cytosol and then transported across the ER membrane–a process called post-translational translocation. Similar to cotranslationally translocated proteins, these proteins also use the Sec translocon complex to enter the ER lumen.
Targeting proteins to the ER
Hsp40 and Hsp70 chaperone molecules bind the translated proteins in the cytosol to prevent their folding. The chaperone binding helps to keep the signal...
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Cotranslational Protein Translocation01:20

Cotranslational Protein Translocation

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Translocation of proteins across membranes is an ancient process that occurs even in bacteria and archaebacteria. In fact, the components of the translocation machinery are still conserved between prokaryotes and eukaryotes.
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...
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Termination of Translation01:44

Termination of Translation

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The large ribosomal subunit has several important structures essential to translation. These include the peptidyl transferase center (PTC) - which is the site where the peptide bond is formed - and a large, internal, water-filled tube through which the nascent polypeptide moves. This latter structure is called the Peptide Exit Tunnel, and it begins at the PTC and spans the body of the large ribosomal subunit. During translation, as the nascent polypeptide chain is synthesized, it passes through...
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Improving Translational Accuracy02:07

Improving Translational Accuracy

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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Residue Interactions Guide Translational Diffusion of Proteins.

Elham Fazelpour1, Jennifer M Haseleu1,2, Christopher J Fennell1

  • 1Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States.

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This study introduces a novel method to predict molecular diffusion coefficients by analyzing protein structures. This approach accurately estimates diffusion for various biomolecules, outperforming mass-based predictions.

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Area of Science:

  • Computational chemistry
  • Biophysics
  • Molecular dynamics

Background:

  • Calculating diffusion coefficients is complex due to molecular interactions and environmental factors.
  • Accurate diffusion prediction is crucial for understanding molecular transport in biological systems.

Purpose of the Study:

  • To develop a new computational method for estimating translational diffusion coefficients of biomolecular structures.
  • To improve the accuracy and efficiency of diffusion coefficient predictions compared to existing methods.

Main Methods:

  • A novel approach was developed by assembling protein structures from component residues.
  • The method links local chemical properties of solvent-exposed patches to hydrodynamic radius contributions.
  • Predictions were made following solvent-excluded surface area calculations.

Main Results:

  • The new method accurately predicts diffusion coefficients for structures ranging from peptides to proteins.
  • Results are comparable to explicit molecular simulations.
  • The approach surpasses statistical mass-based predictions, which often use limited data.

Conclusions:

  • This method provides accurate and computationally feasible predictions of diffusion coefficients.
  • It leverages chemical identity, enabling differentiation of structures with similar masses.
  • The approach offers a valuable tool for biophysical and computational chemistry research.