Sample VHG Document in XML From: http://www.vhg.org.uk/dtd/testvhg.xml Date: 1998-08-28 --> ]> 3-10 helix 3(10) helix

Infrequently used motif of secondary structure, occurs most often as a single turn transition. Similar to , but more tightly coiled than alpha helix, with 3 residues per helical turn, and 10 atoms in the ring closed by the hydrogen bond.

adenine A

A nitrogen-containing, bicyclic, basic purine that occurs in nucleotides of DNA and RNA. It is one member of the base pair A-T (adenine-thymine).

purine thymine alpha helix

Common motif of secondary structure. Polypeptide chain formining a helical arrangement in which one full turn contains 3.6 residues and 13 atoms, and can therefore also be refered to as 3.6 13 helix. Usually right handed but occasionally also left-handed.

amino acid

A compound containing both an acidic and amino group. There are twenty naturally occuring amino acids from which proteins are built.

amino acids aminoacid aminoacids aa alanine ala A

One of the most commonly found amino acids, with a methyl group as a side chain. A non-essential amino acid, it is biosynthesized directly from pyruvate.

arginine arg R

Basic amino acid. Arginine can be made from ornithine by mammals in the Krebs-Henseleit urea cycle but arginine rapidly breaks down to urea.

asparagine asn N

Amino acid with uncharged polar side chain.

aspartic acid asp D

Amino acid with acidic side chain. The ionised form is known as aspartate.

cysteine Cys C

An amino acid with a thiol side chain. Cysteine is neutral, polar and found on the surface of proteins. Cysteine plays a special role in protein structure due to covalent disulphide links.

cystine

A term found in older literature referring to two disulphide linked cysteine residues.

glutamic acid Glu E

Amino acid with acidic side chain. The ionised form is known as glutamate.

glutamine Gln Q

Amino acid with amide side chain, uncharged and polar.

glycine Gly G

Simplest of the naturally occuring amino acids, with no side chain. Glycine is often located at bends or folds in proteins.

histidine His H

Amino acid with imidizole side chain. It's charged state ina protein is very dependent on its local environment.

isoleucine Ile I

Amino acid with a hydrophobic aliphatic side chain. Isomer of leucine.

leucine Leu L

Amino acid with a hydrophobic aliphatic side chain. Isomer of isoleucine.

lysine Lys K

Amino acid with primary amine side chain. Positively charged under physiological conditions.

methionine Met M

Amino acid with sulphur-containing hydrophobic side chain.

phenylalanine noun phe F

Phenylalanine is a naturally occurring aminoacid (L-isomer). The D-isomer can be found in some bacterial metabolites. It is one of the essential amino acids, and is aromatic, hydrophobic, and neutral thus it is found buried in protein structures.

proline Pro P

Cyclic amino acid

serine Ser S

Amino acid with neutral polar side chain.

threonine Thr T

Amino acid with neutral polar side chain

tryptophan Trp W

Amino acid with aromatic side chain

tyrosine Tyr Y

Amino acid with aromatic side chain

valine Val V

Amino acid with aliphatic side chain

amphipathic

A compound containing both hydrophobic and hydrophilic groups. Many cell components are amphipathic and tend to form structures in which the nonpolar, hydrophobic parts are hidden from water, whereas polar, hydrophilic parts are exposed to water.

barrel

All-beta class of protein folds include sandwich and barrel topology. Barrel folds are made of single beta-sheets that twist and coils upon itself, mostly the first strand of the beta-sheet hydrogen bond to the last strand. The strand directions of the two opposite sides of the barrel fold are roughly orthogonal. Most barrel folds are closed. Barrels are defined by the number of beta-sheets (n) and staggering or shear of the sheets (S).

beta sandwich

All-beta class of protein folds include sandwich and barrel topology. Two beta-sheets are usually twisted and packed so their strands are aligned in sandwich folds. There are a few special cases of orthogonal sandwich folds.

beta sheet

Common secondary structure motif in proteins. Polypeptide chain in extended conformation, sheet formed of strands lying either parallel, antiparallel, or both. Beta sheets can be planar,twisted or form barrels.

carbohydrate saccharide

Carbohydrates are polyhydroxy-carbonyl compounds which generally have the sum formula (CH2O)n. An essential component of living organisms, they are used as storage compounds, energy metabolism intermediates, structural building blocks, and for the modification of proteins.

catalysis

Catalysts accelerate chemical reactions by lowering the free energy of activation. They combine with the reactants, giving a transition state with less free energy than the uncatalyzed reaction. Formation of the reactant products regenerates the free catalyst. Enzymic catalysis is the same except for a measurable saturation effect (Michaelis Menten).

catalytic triad

Arrangement of three amino acids Ser-His-Asp(or Glu) which greatly increses the nucleophilic character of the serine.

CATH

A hierarchical classification of protein structural relationships

chaperone

Chaperones are a set of proteins required for formation of proper tertiary structure, acting as catalysts by increasing the rate of the folding processes. Examples include protein disulphide isomerase and BiP.

chiral

Chirality means 'handedness' of molecules. Chirality is the description and classification of the optical and geometrical properties of molecular centres, axises or planes. Thus, chirality gives rise to different types of isomers. Chiral molecules do not coincide with their mirror image.

circular dichroism

Substances that are optically active rotate the plane of linearly polarised light. Optical rotation of proteins is used to determine alpha helix coiling, and factors influencing the transition between alpha helix and random coil.

codon

Specific triplets of mononucleotides in the DNA chain, called codons, correspond to specific amino acids or to start and stop of translation by the ribosome. The 64 possible triplets of bases in a codon code for 22 amino acids and stop codons. The start codon encodes for methionine.

collagen

Fibrous protein rich in glycine and proline that forms distinct triple-stranded helices. Major compound of the extracellular matrix and connective tissues.

configuration

The covalent linkages that make up a molecule. To change the configuration of a molecule one has to break and make new bonds.

conformer

Various nonsuperimposible three-dimensional arrangements of atoms that are interconvertible without breaking covalent bonds are called conformations. Atom naming conventions describe different conformations. Ramachandran used computer models of small polypeptides to find stable conformations.

covalent bond

A covalent bond exists between two atoms if they share electrons between them. One pair of electrons forms a single bond, and two pairs form a double bond. However, in quantum chemical terms an increase in electron density between the atoms also spreads over the rest of the molecule, particularly with delocalised bonding.

crystallography x-ray crystallography

By using X-ray diffraction methods, crystals may be identified, their structure determined, and sizes measured. Crystallography can also be applied to powdered substances that are not crystalline but displaying some regularity of molecular structure. Crystallographic models show covalent skeletons, bond angles and lengths but not the actual space occupied by the molecule.

cytosine C

A nitrogen-containing, cyclic, basic pyrimidine that occurs in nucleotides of DNA and RNA. It is one member of the base pair G-C (guanine-cytosine).

cytoskeleton

Fibrous network in the cytoplasm of an eukaryotic cell that shapes the cell and gives it the ability to move. Cytoskeleton consists mainly of microtubuli, actin and intermediate filaments.

delta helix

Delta helices are left handed helices recently found in an NMR study of LAC repressor head piece.

disulphide bond disulfide bond

The bond formed by oxidation of the thiol groups of two cysteine residues.Often a stabilizing force in protein structure. Found mainly in secretory and membrane bound proteins.

domain

Protein domains are areas of specific tertiary structure. These discrete portions of a protein have their own function. This discrete portions of a protein have their own function or stable folding structure.

electrostatic

Electrostatic attraction between ions of opposite charge holds the ions firmly in place and close together. Electrostatic interactions are one of the non-bonded interactions between protein molecules.

enantiomer

Enantiomers are two mirror images of a chiral molecule. They cannot be structurally superimposed. Each enantiomer rotates plane polarised light in a different direction (either D for clockwise or L for anti-clockwise).

endoplasmic reticulum ER

Cellular organelle in which synthesis of secreted proteins occurs.

enzyme

Macromolecular substance able to catalyze a specific chemical reaction. Originally restricted to proteins, there have been discoveries of RNAs functioning as enzymes (designated ribozymes).

enzyme classification EC

System in which enzymes can be classified in hierachical groups according to function.

enzyme exocytosis

The directed transport of macromolecules from the cell by a vesicle mediated process.

fold

The secondary structural units of helices and sheets form the basis of a classification for families of proteins. Each different topology is considered as a fold.

foldase

Foldases assist in the correct folding of polypeptides.

genetic code

Genetic code is the sequence of codons along the DNA, that can be translated into an amino acid sequence. The DNA sequence of a gene can be used to predict the mRNA sequence, and the genetic code can in turn be used to predict the amino acid sequence.

glycosidic bond

A special kind of acetal bond linking sugars in polysaccharides together.

glycosylation

The addition of oligosaccharides to particular residues on a protein. This modification can be both co-translational and post-translational, occuring in the endoplasmatic reticulum and golgi. Three different forms of glycosylation can be distinguished: N-linked oligosaccharides, O-linked oligosaccharides and glycosyl-phosphatidylinositol (GPI-) anchors.

Golgi

Membrane-bounded organelle in eukaryotic cells which is mainly involved in protein sorting and secretion. Many post-translational modifications occur in the golgi (among others the late stages of glycoslylation).

greek key

Topology for a small number of beta sheet strands in which some interstrand connections go across the end of barrel or, in a sandwich fold, between beta sheets. Named after geometric motif on greek pottery.

guanine G

A nitrogen-containing, bicyclic, basic purine that occurs in nucleotides of DNA and RNA. It is one member of the base pair G-C (guanine-cytosine).

hairpin turn

Beta hairpin turns or bends occur between two antiparallel beta-sheets, usually containing proline residues. There are also helix hairpin turns.

helix

A helical arrangement of a protein chain forming a major part of secondary structure. Can be described by the N m notation where 'N' is number of residues per helical turn and 'm' is number of atoms including hydrogens in the ring closed by the hydrogen bond.

homology

Evolutionary relationship stemming from a common ancestor that is inferred from a sequence comparison between two or more structures.

hydrogen bond

Electrostatic interaction between an hydrogen atom and an electronegative atom, such as oxygen, nitrogen or fluoride. Its strength is 5kJ/mol, and it is enough to fold a polyaminoacid in its characteristic structure. An hydrogen bond is key to the interaction between biological molecules.

isoelectric point

The pH at which a protein carries no net elecric charge.

isomer

Isomer is one of two or more molecules with identical chemical compositions, but differing arrangements of atoms. Two isomers may differ in their physical, chemical, and biological properties.

jellyroll

Jellyroll is a variant of the greek key topology. A small number of beta-sheet strands have interstrand connections. Both ends of a sandwich or a barrel fold are crossed by two interstrand connections.

greek key kinase

Kinase is a generic name for enzymes that attach a phosphate to a protein, opposite in action to phosphatases. These enzymes are important metabolic regulators.

Klotho

Database of biochemical compounds

ligase

Any enzyme that joins substituents together covalently, with ATP cleavage. Ligases form the 6th class of enzymes in the International Classification (EC.6).

lipase

Any enzyme that catalyzes a process involving the cleavage of lipid. There are a range of such enzymes (EC.3.1)

lysosome

Membrane-bounded organelle found in eukaryotes, involved in protein degradation. The lumen of lysosomes has an acidic pH.

mannose

Mannose is a monosaccharide. It is an aldohexose, 2 epimeric to glucose. D-Mannose is part of the core of N-linked oligosaccharides. In high mannose or in hybrid N-linked structures, mannose is found in the outer branches.

MEDLINE

Database of scientific bibliography. References can be searched by different fields like: title, author, journal,substance, etc. MEDLINE is not a public database. However, it is possible to access a subset in molecular genetics at the NCBI.Medline is supported by MESH headings, of which ENTREZ is a subset.

native conformation

Physiologically folded conformation of a protein

NMR nuclear magnetic resonance

Nuclear magnetic resonance is a method of spectroscopy. It uses the magnetic resonance of covalent bonds for imaging, with clinical use for imaging living tissue.

nucleoside

The four bases of DNA are referred to as nucleosides when combined with thri corresponding sugar (ribose or deoxy-ribose). Thus nucleosides are nucleotides without phosphate.

nucleotide

A nucleotide is a subunit of DNA or RNA consisting of purines and pyrimidines (adenine, guanine, thymine, or cytosine in DNA; adenine, guanine, uracil, or cytosine in RNA), a phosphate molecule, and a sugar molecule (deoxyribose in DNA and ribose in RNA). Triplets of nucleotides form codons.

nucleus

Membrane-bound organelle that makes a cell an eukaryote. Contains DNA organized into chromosomes and the enzymes which are involved in DNA replication and transcription.

omega

Angle of rotation of the bond between the nitrogen and the carbonyl carbon in an peptide bond. The angle is usually 180 degrees for a trans peptide bond.

orf open reading frame

The sequence of bases in DNA with no stop codons that may be a coding sequence for proteins.

organelle

A membrane bounded compartment of a eukaryotic cell with a specialized function.

oxidative phosphorylation

Process of energy generation in bacteria and mitochondria where electrons are transferred from nutrients to oxygen, thereby generating ATP. Involves the intermediate generation of a pH gradient across a membrane.

oxidoreductase

Any enzyme that catalyzes a process involved in oxidation, reduction, and electron or proton transfer reactions. Oxidoreductases form the 1st class of enzymes in the International Classification (EC.1).

PCR Polymerase Chain Reaction

Method of amplifying fragments of DNA using a thermostable polymerase.

peptidase

Peptidase is any enzyme that catalyzes a process involving hydrolysis of peptide bonds. Usually, peptidases catalyze degradation of peptides into their amino acids.They mostly include enzymes in EC 3.4 class.

peptide bond

An amide bond linking amino acids between their COOH and NH2 groups. This is essentially a planar bond having some double bond character, so free rotation is not possible.

periplasm

In bacteria, the space between inner and outer membrane.

PEST

Sequence of amino acids in any order (P,E,S,T) that signals cell machinery to degrade that protein.

phi

The torsion angle of the C(alpha)-N bond of each amino acid. limited in angles of rotations as described by Ramachandran plots.

phosphatase

A generic name for enzymes that cleave a phosphate from a protein, that has previously been attached by a kinase. These enzymes are important metabolic regulators.

phosphate

(PO4)3- is the anion of phosphoric acid. Inorganic phosphate can be transferred to many biochemically important molecules. It is transferred as a phosphoric acid anhydride (e.g. in ATP) usually for short term energy storage, or as an ester (with serine, threonine or tyrosine in proteins) for regulatory or structural purposes.

phosphorylate

To covalently attach a phosphoryl (PO3--) ion to a hydroxyl group, usually on an amino-acid residue within a protein, or on a sugar.Phosphorylation is a key activity of biochemical processes such as enzyme activity control. Kinases perform phosphorylation, and phosphatases perform dephosphorylation.

PIR Protein Identification Resource

Protein sequence database, provided by the National Institute of Health. It cross references Genbank, PDB and other sequence databases.

polypeptide

A linear polymer of amino acids linked via peptide bonds. May be as short as 2 amino acids to virtually any length.

primary structure

The amino acid sequence of a polypeptide chain.

prochiral

There are two different prochiral systems. Two chemically identical substituents on an otherwise chiral tetrahedral centre are prochiral. Secondly, sp2 hybridised planar systems with three different substituents are also prochiral.

prokaryote

Any organism made of simple cells without a DNA-containing nucleus. A prokaryote can either be a bacterium, archebacterium or cyanobacterium.

prosthetic

A non-protein substance when combined with a protein. Examples include a heme group in hemoglobin/ myoglobin/cytochromes, nucleic acids in nucleoproteins.

protease

Any enzyme that degrades a protein by hydrolyzing peptide bonds. The distinction between proteases and peptidases is blurred, reflecting the difference between proteins and peptides. Proteases are in the class EC.3.4.21-24.

Protein Data Bank PDB

An archival computer database of 3-D structures of biomolecules. It is maintained by Brookhaven National Laboratory (BNL). PDB also means a particular file format as well as the archive.

proteolysis

To hydrolyze the peptide bond in proteins or peptides.

-CONH- + H20 ----> -CO2H + H2N-

This is an exergonic reaction yielding an acid and an amine.

psi

The torsion angle of the C(alpha)-C bond of each amino acid. Limited in angles of rotations as described by Ramachandran plots.

purine

A nitrogen-containing, bicyclic, basic compound that occurs in nucleotides of DNA and RNA. The purines in DNA and RNA are adenine and guanine.

pyrimidine

A nitrogen-containing, cyclic, basic compound that occurs in nucleotides of DNA and RNA. The pyrimidines in DNA are cytosine and thymine. Those in RNA, are cytosine and uracil.

pyruvate

Part of the flow of phosphate groups from high energy phosphate donors to low energy acceptors via the ATP-ADP system. Pyruvate serves as an acceptor of electrons in glycolysis. It also mobilises acetyl CoA when carbohydrates are used in respiration, prior to the Krebs cycle. Its formula is CH3-C(=O)-CO2H.

quaternary structure

The spatial relationship between polypeptide chains in a protein with several subunits.

Ramachandran plot

A diagramatic representation of rotational angles, phi and psi, possibly occuring in a polypeptide, considering steric constraints from van der Waals radii of each atom.

RasMOL

A molecular graphics program for the visualisation of proteins, nucleic acids, and small molecules. The program is aimed at display, teaching, and generation of publication quality images. The program reads in a molecule co-ordinate file then interactively displays the molecule.

receptor

Receptors allow the interaction between messengers and the messaging process. They cover a wide range of biological processes.

reverse turn

Reverse turns are the turns most often found in peptides and proteins.About one third of all residues in globular proteins are contained in turns that reverse the direction of the polypeptide chain.

ribosome

Particle composed of ribosomal RNAs and proteins. Catalyzes translation of mRNAs to proteins.

RNA ribonucleic acid

A macromolecule composed of ribonucleotides linked by phosphodiester bonds. RNA occurs in cells mainly as tRNA, mRNA and rRNA.

RNAse

Any enzyme that catalyzes hydrolysis of phosphodiester bonds in RNA. The specificities as well as the structures of different ribonucleases are very different.

Rossmann fold dinucleotide binding fold

A super secondary structure most often comprised of two beta-alpha-beta-alpha-beta units that can bind dinucleotides.

rotamer

A conformer describable by rotation about a (sungle) bond. For an amino acid side chain, the positions of atoms are defined by the chi angles. Amino acids have chi angle preferences caused by differing shapes of their side chains. Thus a set of commonly observed chi angle combinations (each combination represents a rotamer), may be assigned to each amino acid.

rRNA ribosomal RNA

Ribosomal RNA; forms part of the structure of ribosomes and is mainly responsible for their translational activity. In prokaryotes, there are three kinds of rRNA; in eukaryotes, there are four.

SCOP

acronym of Structural Classification Of Proteins. Database developed by MRC Laboratory of Molecular Biology and Centre for Protein Engineering in Cambridge, UK. Consists of all proteins whose 3D structure is available, providing structural and evolutionary relationships where possible.

secondary structure

The local spatial arrangement of a polypeptide chain backbone without regard to side chain conformation. Often used to characterize structural entities such as helices, and beta structures.

SEQNET

A UK-based database and software service for sequence and structure based at Daresbury Laboratory, UK. Daresbury is also the UK node of EMBNET.

sheet

Sheets are a major class of secondary structure of polypeptide chains. They can be parallel, antiparallel, mixed, planar or twisted.

subunit

A single polypeptide chain of a protein comprised of two or more polypeptides.

supersecondary structure

This merges with tertiary structures of proteins. It covers beta hairpin turns, beta- and alpha- corners, helix hairpins, and increasingly complex motifs.

swiss3d

Database at ExPASy containing many different formats of images of proteins whose crystal structures are available.

SwissProt

Data base of protein sequences. Each entry contains bibliography, a short description of the protein, pointers to other data bases and the sequence.

tertiary structure

The three dimensional structure of the entire polypeptide chain including side chains.

thymine T

A nitrogen-containing, cyclic, basic pyrimidine that occurs in nucleotides of DNA and RNA. It is one member of the base pair A-T (adenine-thymine).

topoisomerase

Enzymes EC.5.99.1.2 and 3 which cuts DNA and un/winds it. Topo I cuts one strand and topo II cuts at two phosphates, 4 base pairs apart (like a restriction enzyme).

torsion angle

The spatial relationship of 4 atoms i,j,k and l is described by a torsion which is the angle that vector i-j must be turned clockwise to cover k-l when viewing along vector j-k. There are two main torsion angles of a protein the psi and phi angles that define the conformation of the polypeptide backbone.

transcription

The process of reading DNA and synthesizing a complementary strand of mRNA, performed by RNA polymerase. In eukaryotes, transcription occurs in the nucleus and is therefore spatially separated from translation.

transferase

Any enzyme that catalyzes a process catalysing reactions in which groups are transferred. Transferases form the 2nd class of enzymes in the International Classification (EC.2).

translation

The process of reading mRNA and synthesizing a corresponding peptide, performed by the ribosome. Translation occurs in the cytoplasm.

tRNA transfer RNA

Transfer RNA is an adaptor molecule that carries amino acids the ribosome during protein synthesis. They contain about 75-90 mononucleotide units. Each of the 20 amino acids has at least one corresponding tRNAs, and some have multiple tRNAs.

uracil U

A nitrogen-containing, cyclic, basic pyrimidine that occurs in nucleotides of RNA. It is able to form a base pair A-U (adenine-uracil).

unidentified reading frame urf

The sequence of bases in DNA with no stop codons that is a coding sequence for proteins. However, as yet there is doubt about which gene, if any, they belong to.

van der Waals

Van der Waals are weak interactions, which play a major part in protein structure.

zinc finger

A secondary structure motif that is coordinated with a Zn atom. Involved in binding DNA as a transcription factor. The zinc is coordinated with either cys or his residues.

zipper

An example of protein super secondary structures. They look like zips, and can unzip and reform. They are a type of coiled coil structure.