Protein Design: Getting to the bottom of the TIM barrel

In the design of a supported timber beam subjected to a distributed load, both the beam's physical dimensions and the timber's characteristics, such as its grade and species, are critical. These factors determine the allowable stress values, which are crucial for calculating the necessary beam depth to ensure structural integrity and safety.
The design begins with analyzing the beam as a free body to identify moments and force balances, thereby determining support reactions. Next, the...

The design of prismatic beams, structural elements with a uniform cross-section, focuses on ensuring safety and structural integrity under load. The design process begins by determining the allowable stress, either from material properties tables, or by dividing the material's ultimate strength by a safety factor. This safety factor is essential for accommodating uncertainties, and varies depending on the material—timber, steel, or concrete—with each having unique strength and...

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.
α-Helix containing multi-pass transmembrane proteins
Multi-pass transmembrane proteins such as...

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...

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...