An examination of the conservation of surface patch polarity for proteins

H P Shanahan1, J M Thornton

  • 1European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD,UK. shanahan@ebi.ac.uk

Abstract

Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Potential Due to a Polarized Object01:29

Potential Due to a Polarized Object

A neutral atom consists of a positively charged nucleus surrounded by a negatively charged electron cloud. When placed in an external electric field, the external electric force pulls the electrons and nucleus apart, opposite to the intrinsic attraction between the nucleus and the electrons. The opposing forces balance each other with a slight shift between the center of masses of the nucleus and the electron cloud, resulting in a polarized atom. On the other hand, a few molecules, like water,...
Polarity of the Cytoskeleton01:18

Polarity of the Cytoskeleton

The intrinsic polarity of cells can be primarily attributed to two factors- i) the asymmetric accumulation of mobile components such are regulatory molecules and subcellular components across the cell and ii) the orientation of polar cytoskeletal filaments that make up the cytoskeletal networks, specifically microfilaments, and microtubules arranged along the axis of polarity. Interactions between the cytoskeletal filaments are crucial for the establishment and maintenance of the polar nature...
Oriented Surfaces01:30

Oriented Surfaces

A surface is called orientable if a consistent choice of unit normal vector can be made at every point on the surface. A thin soap film stretched across a wire loop provides a familiar example. The film separates the air on one side from the air on the other, so one side can be selected as positive and the opposite side as negative. Once this choice is made, a unit normal vector can be assigned smoothly across the entire surface.At each point on the soap film, a unit normal vector points...