Information about Helix Bundle
A helix bundle is a small protein fold composed of three or four alpha helices and held together by nonlocal hydrophobic interactions.
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.
Classification & external resources
ICD-10 B20-B24
ICD-9 042 - 044
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A structural domain is an element of overall structure within a protein that is self-stabilizing and often folds independently of the rest of the protein chain.
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Three-helix bundles
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.
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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]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.
References
1. ^ 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. PMID 16797585
2. ^ 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. PMID 9784131
3. ^ 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. PMID 16674165
4. ^ 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. PMID 15698135
5. ^ Branden C, Tooze J. (1999). Introduction to Protein Structure 2nd ed. Garland Publishing: New York, NY.
2. ^ 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. PMID 9784131
3. ^ 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. PMID 16674165
4. ^ 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. PMID 15698135
5. ^ 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
Protein tertiary structure | |
|---|---|
| General | Structural domain |
| All-α folds: | Helix bundle |
| All-β folds: | Immunoglobulin fold |
| α/β folds: | TIM barrel |
| α+β folds: | Ferredoxin fold |
| Irregular folds: | Conotoxin |
Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues.
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In biochemistry and chemistry, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.[1]
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Relationship to primary sequence
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alpha helix (α-helix) is a right-handed coiled conformation, resembling a spring, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier ( hydrogen bonding). (See also helix.
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hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear phobos) refers to the physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water [1].
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Identifiers
Symbol VIL2
Entrez 7430
HUGO 12691
OMIM 123900
RefSeq NM_003379
UniProt P15311
Other data
Locus Chr. 6 q22-q27 Villin is a 92.
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Symbol VIL2
Entrez 7430
HUGO 12691
OMIM 123900
RefSeq NM_003379
UniProt P15311
Other data
Locus Chr. 6 q22-q27 Villin is a 92.
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amino acid is a molecule that contains both amine and carboxyl functional groups. In biochemistry, this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent.
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Molecular dynamics (MD) is a form of computer simulation wherein atoms and molecules are allowed to interact for a period of time under known laws of physics, giving a view of the motion of the atoms.
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To help compare orders of magnitude of different times this page lists times between 10−6 seconds and 10−5 seconds (1 microsecond to 10 microseconds). A microsecond is one millionth of a second.
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native state of a protein is its operative or functional form. All protein molecules are simple unbranched chains of amino acids, but it is by assuming a specific three-dimensional shape that they are able to perform their biological function.
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Distributed computing is a method of computer processing in which different parts of a program run simultaneously on two or more computers that are communicating with each other over a network.
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- Human immunodeficiency virus 1
- Human immunodeficiency virus 2
Classification & external resources
ICD-10 B20-B24
ICD-9 042 - 044
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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. For proteins, a sequence motif is distinguished from a structural motif, a motif formed by the three dimensional
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Protein structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry. Its aim is the prediction of the three-dimensional structure of proteins from their amino acid sequences, sometimes including additional relevant information such as
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This is a list of actin-binding proteins in alphabetical order.
List: 0–9 A B C D E F G H I J K L M N O P Q R S T U V W x Y Z
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List: 0–9 A B C D E F G H I J K L M N O P Q R S T U V W x Y Z
References External links
0–9
- 25kDa
- 25kDa ABP from aorta p185neu
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DNA-binding proteins are proteins that comprise any of many DNA-binding domains and thus have a specific or general affinity to DNA.
DNA-binding proteins include transcription factors which modulate the process of transcription, nucleases which cleave DNA molecules, and
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DNA-binding proteins include transcription factors which modulate the process of transcription, nucleases which cleave DNA molecules, and
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coiled coil is a structural motif in proteins, in which 2-7[1] alpha-helices are coiled together like the strands of a rope (Dimers and trimers are the most common types).
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Steric effects arise from the fact that each atom within a molecule occupies a certain amount of space. If atoms are brought too close together, there is an associated cost in energy due to overlapping electron clouds (Pauli or Born repulsion), and this may affect the molecule's
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hydrophobic effect is the property that nonpolar molecules tend to form intermolecular aggregates in an aqueous medium and analogous intramolecular interactions.[1][2] The name arises from the combination of water in Attic Greek hydro-
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salt bridge, in chemistry, is a laboratory device used to connect the oxidation and reduction half-cells of a galvanic cell (voltaic cell), a type of electrochemical cell. Salt bridge usually comes in two types: glass tube and filter paper.
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globin fold is a common three-dimensional fold in proteins. This fold typically consists of eight alpha helices, although some proteins have additional helix extensions at their termini.
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The term antiparallel may refer to:
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- Antiparallel (biochemistry), the orientation of adjacent molecules
- Antiparallel (mathematics), the placement of parallel lines in relation to an angle
- Antiparallel (electronics), the polarity of devices run in parallel
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dimer refers to a molecule composed of two identical subunits or monomers linked together.
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Chemistry
The molecules in a dimer are connected by covalent bonds or weaker interactions such as hydrogen bonds...... Click the link for more information.
dimer refers to a molecule composed of two identical subunits or monomers linked together.
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Chemistry
The molecules in a dimer are connected by covalent bonds or weaker interactions such as hydrogen bonds...... Click the link for more information.
Rop (also known as repressor of primer) is a small homodimeric four-helix bundle protein formed by the antiparalell interaction of two helix-turn-helix monomers. The protein is expressed in E. coli as a mechanism for regulating the gene copy numbers of plasmids.
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Cytochromes are generally membrane-bound hemoproteins that contain heme groups and carry out electron transport.
They are either found as monomeric proteins (i.e. cytochrome c) or as subunits of bigger enzymatic complexes that catalyze redox reactions.
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They are either found as monomeric proteins (i.e. cytochrome c) or as subunits of bigger enzymatic complexes that catalyze redox reactions.
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Identifiers
Symbol FTH1
Alt. Symbols FTHL6
Entrez 2495
HUGO 3976
OMIM 134770
RefSeq NM_002032
UniProt P02794
Other data
Locus Chr.
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Symbol FTH1
Alt. Symbols FTHL6
Entrez 2495
HUGO 3976
OMIM 134770
RefSeq NM_002032
UniProt P02794
Other data
Locus Chr.
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Human growth hormone can refer to:
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- For physiology of human growth hormone, see growth hormone.
- For athletic use of HGH, see Growth hormone treatment for bodybuilding
- For deficiency diseases, see growth hormone deficiency.
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Cytokines are a group of proteins and peptides that are used in organisms as signaling compounds. These chemical signals are similar to hormones and neurotransmitters and are used to allow one cell to communicate with another.
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In biochemistry and chemistry, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.[1]
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Relationship to primary sequence
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citation, footnoting or external linking.
A structural domain is an element of overall structure within a protein that is self-stabilizing and often folds independently of the rest of the protein chain.
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