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A helix bundle is a small protein fold composed of three or four alpha helices and held together by nonlocal hydrophobic interactions. A representation of the 3D structure of myoglobin, showing coloured alpha helices. ...
In biochemistry, the tertiary structure of a protein is its overall shape. ...
A diagram of the alpha helix structure of amino acids In proteins, the α helix is a major structural motif in secondary structure. ...
In chemistry, hydrophobic or lipophilic species, or hydrophobes, tend to be electrically neutral and nonpolar, and thus prefer other neutral and nonpolar solvents or molecular environments. ...
Three-helix bundles
 An example of the three-helix bundle fold, the headpiece domain from the protein villin as expressed in chickens (PDB ID 1QQV). Three-helix bundles are among the smallest and fastest known cooperatively folding structural domains.[1] The three-helix bundle in the villin headpiece domain is only 36 amino acids long and is a common subject of study in molecular dynamics simulations because its microsecond-scale folding time is within the timescales accessible to simulation. Although a famous early simulation[2] approached but did not converge to the native state, more extensive sampling using distributed computing methods has been used to observe successful folding events.[3] The 40-residue HIV accessory protein has a very similar fold and has also been the subject of extensive study.[4] There is no general sequence motif associated with three-helix bundles, so they cannot necessarily be predicted from sequence alone. Three-helix bundles often occur in actin-binding proteins and in DNA-binding proteins. Within a protein, a structural domain (domain) is an element of overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. ...
Trinomial name Gallus gallus domesticus A chicken (Gallus gallus domesticus) is a type of domesticated bird which is often raised as a type of poultry. ...
An amino acid residue is what is left of an amino acid once a molecule of water has been lost (an H+ from the nitrogenous side and an OH- from the carboxylic side) in the formation of a peptide bond. ...
Molecular dynamics (MD) simulation is a special discipline of molecular modelling. ...
To help compare orders of magnitude of different times this page lists times between 10−6 seconds and 10−5 seconds (1. ...
In biochemistry, the native state of a protein is its operative or functional form. ...
Distributed computing is decentralised and parallel computing, using two or more computers communicating over a network to accomplish a common objective or task. ...
Human immunodeficiency virus (commonly known as HIV, and formerly known as HTLV-III and lymphadenopathy-associated virus) is a retrovirus that is the cause of the disease known as AIDS, or Acquired Immunodeficiency Syndrome, a syndrome where the immune system begins to fail, leading to many life-threatening opportunistic infections. ...
In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance. ...
Protein structure prediction is one of the most significant technologies pursued by computational structural biology and theoretical chemistry. ...
Actin-binding proteins // A Actin-Binding Proteins (and Drugs) Abl Actinfilin Actup Angiogenin AbLIM Actin-Interacting MAPKKK Ssk2p Adducin Anillin Abp1p Actin-regulating kinases Adseverin (scinderin) Annexins ABP50 (EF-1a) Actin-Related Proteins Afadin Aplyronine ABP120 Actobindin AFAP-110 Archvillin ABP140 Actopaxin Affixin Arginine Kinase ABP280 (Filamin) Actophorin a-actinin...
DNA-binding proteins are a broad class of protein molecules that possess certain structural motifs (e. ...
Four-helix bundles Four-helix bundles typically consist of four helices packed in a coiled-coil arrangement with a sterically close-packed hydrophobic core in the center. Pairs of adjacent helices are often additionally stabilized by salt bridges between charged amino acids. The helix axes typically are oriented about 20 degrees from their neighboring helices, a much shallower incline than in the larger helical structure of the globin fold.[5] A coiled coil is a structural motif found in many proteins. ...
Steric effects are the interaction of molecules dictated by their shape and/or spatial relationships. ...
The hydrophobic effect is the property that nonpolar molecules like to self-associate in the presence of aqueous solution. ...
A salt bridge, in chemistry, is a laboratory device used to connect the oxidation and reduction half-cells of a galvanic cell (electrochemical cell). ...
An example of the globin fold, the oxygen-carrying protein myoglobin (PDB ID 1MBA) from the mollusc Aplysia limacina. ...
The specific topology of the helices is dependent on the protein - helices that are adjacent in sequence are often antiparallel, although it is also possible to arrange antiparallel links between two pairs of parallel helices. Because dimeric coiled-coils are themselves relatively stable, four-helix bundles can be dimers of coiled-coil pairs, as in the Rop protein. Other examples of four-helix bundles include cytochrome, ferritin, human growth hormone, and cytokines.[5] Although sequence is not conserved among four-helix bundles, sequence patterns tend to mirror those of coiled-coil structures in which every fourth and seventh residue is hydrophobic. Two antiparallel molecules run side-by-side in opposite directions. ...
Sucrose, or common table sugar, is composed of glucose and fructose. ...
Sucrose, or common table sugar, is composed of glucose and fructose. ...
Cytochromes are generally membrane-bound proteins that contain heme groups and carry out electron transport or catalyse reductive/oxidative reactions. ...
Ferritin is a globular protein found mainly in the liver, which can store about 4500 iron (Fe3+)ions in a hollow protein shell made of 24 subunits. ...
For physiology of human growth hormone, see growth hormone. ...
Cytokines is a group of proteinaceous signalling compounds that like hormones and neurotransmitters are used extensively for inter-cell communication. ...
References - ^ Wickstrom L, Okur A, Song K, Hornak V, Raleigh DP, Simmerling CL. (2006). The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure. J Mol Biol 60(5):1094-107.
- ^ Duan Y, Kollman PA. (1998). Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282(5389):740-4.
- ^ Jayachandran G, Vishal V, Pande VS. (2006). Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece. J Chem Phys 124(16):164902.
- ^ Herges T, Wenzel W. (2005). In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field. Phys Rev Lett 94(1):018101.
- ^ a b Branden C, Tooze J. (1999). Introduction to Protein Structure 2nd ed. Garland Publishing: New York, NY.
External links - SCOP cytochrome c fold
- SCOP nucleic acid-binding three-helix bundles
- SCOP four-helix bundles
- SCOP Rop-like proteins
- SCOP all-alpha proteins
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