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Glossary of Technical Terms

  • 13C
    Carbon isotope used in NMR experiments.
  • 15N
    Nitrogen isotope used in NMR experiments.
  • 1H
    Hydrogen isotope used in NMR experiments.
  • 2D NMR
    Two dimensional NMR
  • 3-10 helix
    A secondary structure motif that occurs most often as a single turn transition. Similar to an alpha helix, but more tightly coiled. Has 3 residues per helical turn, and 10 atoms in the ring closed by the hydrogen bond.
  • 3D NMR
    See multidimensional NMR.
  • 4D NMR
    See multidimensional NMR.
  • A form DNA
    A conformation of DNA that has tilted base pairs and more base pairs per turn than does B DNA. The A form is seen in unhydrated DNA (fibres or crystals of oligonucleotides).
  • active site
    The region of a protein that binds substrates and that is involved in chemical reactions. Generally an active site contains very specific amino acids that participate in the binding.
  • acylation
    A post-translation modification of a protein that involves the addition of acetyl or myristoyl groups usually on the N-terminal end of a protein. This occurs after the removal of the initiator methionine.
  • adenine (A)
    A nitrogenous base that occurs in nucleotides of DNA and RNA and pairs through hydrogen bonding complementarity with thymine (in DNA) or uracil (in RNA).
  • adenosine triphosphate
    A molecule consisting of a ribose sugar molecule at the center with an attached adenine base on one side and a string of phosphates on the other. The phosphates are critical for the activity of the ATP molecule.
  • ADIT
    ADIT, the AutoDep Input Tool, is used by the structural biology community for the deposition and validation of data to be included in the PDB archive. It is also used internally by the PDB for data processing.
  • alanine (ala, A)
    An amino acid with a non-polar sidechain. Alanine is weakly hydrophobic.
  • alignment
    The result produced by the comparison of two or more gene or protein sequences in order to determine their degree of base or amino acid similarity.
  • allosteric protein
    A protein that changes among two or more structural conformations upon binding to a small molecule called an effector. This binding occurs at a site different from the proteins active site and enhances or reduces the protein's reactivity towards its normal ligand.
  • alpha carbon
    The carbon in an amino acid to which the side chain is attached.
  • alpha helix
    A secondary structural motif of a protein. It is characterized by hydrogen bonds between the carbonyl group (-C=O) of one amino acid and the amino (N-H) group of the amino acid 4 residoes below it along the helix. The helix makes one complete turn every 3.6 amino acids.
  • amide
    A molecule containing a nitrogen covalently linked to a carbonyl carbon.
  • amide bond
    see peptide bond
  • amine
    A molecule containing nitrogen with a single bond to a carbon chain and two other single bonds to hydrogen or carbon.
  • amino acid
    Any of the subunit building blocks, containing both an acidic and amino group, that are covalently linked to form proteins. Proteins are built from twenty naturally occurring amino acids.
  • amino acid motif
    see motif
  • angstrom
    A unit of length equal to 10-10 meters. It is commonly used to measure atomic dimensions.
  • antibody
    A protein produced by an organism in order to neutralize or destroy foreign substances
  • area detector
    An x-ray detector that can collect diffraction data from many different positions simultaneously as compared with a diffractometer. Image plates, CCDs, multiwire detectors, and film detectors are all considered types of area detectors.
  • arginine (arg, R)
    Amino acid with a charged basic side chain containing an amino group.
  • asparagine (asn, N)
    Amino acid with a uncharged, polar side chain containing an amide group.
  • aspartic acid (asp, D)
    Amino acid with a charged acidic side chain containing a carboxyl group. The ionised form is known as aspartate.
  • asymmetric unit
    The smallest part of a crystal structure to which space group symmetry can be applied to produce the entire crystal. The asymmetric unit may contain a whole molecule, a portion of a molecule, or multiple molecules and does not necessarily represent the functional unit of the molecule under investigation.
  • atom
    The smallest unit of a chemical element that has the characteristics of that element. An atom is composed of protons and neutrons in a nucleus that is surrounded by electrons.
  • ATP
    see adenosine triphosphate
  • B-factor
    See temperature factor
  • B-form DNA
    A right-handed double-helical conformation of DNA usually seen in solution.
  • bacteria
    Prrimitive, one-celled microrganisms without a nucleus.
  • beamline
    Location at a synchrotron where scientists can use experimental instruments to access X-ray radiation that has been generated at the core facility.
  • beta sheet
    A secondary structural motif of a protein. It is characterized by 2 or more amino acid chains lying side-by-side where hydrogen bonds are formed between carbonyl groups (C=O) of one chain and amino groups (N-H) of the adjacent chain. This arrangement forms a sheet-like structure.
  • bioinformatics
    The application of computer and statistical techniques to the management of large amounts of biological data.
  • biological assembly
    The biologically functional molecule which may be different from the crystallographic assymetric unit (see asymmetric unit).
  • BioMagResBank
    Biological Magnetic Resonance Data Bank (BMRB), a publicly-accessible depository for NMR data of proteins, peptides, and nucleic acids.
  • BLAST
    A set of programs used to perform fast sequence alignmnents between two or more gene or protein sequences. The program is used to search a protein or nucleotide sequence database for a match against a query protein or nucleotide sequence. The statistical significance of each match is given in order to indicate the degree of similarity between related or homologous sequences.
  • carbohydrate
    A chemical compound containing only carbon, hydrogen and oxygen. Examples include starches and sugars.
  • carbonyl group
    A carbon double bonded to an oxygen. Each residue in a protein contains a carbonyl group as part of the main chain.
  • carboxyl group
    A carbonyl group with a hydroxyl group (OH) attached to the carbon in addition to the doubly bonded oxygen. A carboxyl group occurs at the C-terminus of proteins. The hydroxyl group is eliminated during peptide bond formation when additional amino acids are attached
  • cartesian coordinates
    An X-Y-Z coordinate system with the axes at 90 degrees to each other.
  • CATH
    A hierarchical classification of protein structural relationships which groups proteins at four major levels: Class(C), Architecture(A), Topology(T) and Homologous superfamily (H).
  • chemical shift
    An atomic property that varies depending on the chemical and magnetic properties of an atom and its arrangement within a molecule.
  • chain
    A linear biopolymer such as a polypeptide (protein) or polynucleotide (DNA and RNA). Chains in the PDB are assigned chain IDs, such as A, B, C.
  • chromosome
    The structure in the cell nucleus that contains all of the cellular DNA together with a number of proteins that compact and package DNA
  • coenzyme
    see prosthetic group
  • cofactor
    see prosthetic group
  • configuration
    The covalent linkages that generate a molecule. In order to change the configuration of a molecule, bonds have to be broken and new bonds have to be made
  • conformer
    Conformers have different nonsuperimposible three-dimensional arrangements of atoms. They can be interconverted without the breakage of covalent bonds.
  • constraint (X-ray)
    During crystallographic refinement, a fixed value may be placed on a parameter. For example, early on in the refinement process, all occupancies might be constrained to values of 1.0. This constraint might be removed later on in the refinement process so that the occupancies could reflect alternative conformations.
  • correlation spectroscopy
    A 2D NMR method that establishes connectivities of spin-spin coupled protons.
  • COSY
    see correlation spectroscopy
  • covalent bond
    A bond that exists between two atoms if they share electrons between them. One pair of electrons forms a single bond, whereas two pairs form a double bond.
  • CPK model
    A spacefilling three-dimensional representation of a molecule. Given the centers of the molecule atoms and the relative van der Waals radii, a spherical CPK-type representation of a molecule can be built.
  • cryo-electron microscopy
    Electron microscopy performed at a very low temperature in order to visualize systems that are in motion. This method also provides the ability to examine structures that are too large or complex for X-ray or NMR analysis
  • cryo-EM
    see cryo-electron microscopy
  • crystal
    A homogeneous solid in which molecules are arranged in a regular, repeating network.
  • crystallization
    The formation and growth of a crystalline solid by freezing a liquid, evaporating a solution, or precipitating a solid from solution.
  • crystallization components
    Components of the solution(s) used to produce crystals. Includes the molecule to be crystalized and precipitants.
  • crystallography
    see X-ray crystallography
  • cysteine (cys, C)
    Amino acid with a uncharged, polar side chain containing an sulfhydryl group. Cysteine can form covalent disulfide links within protein structures.
  • cytosine (C)
    A nitrogenous base that occurs in nucleotides of DNA and RNA and pairs through hydrogen bonding complementarity with guanine.
  • dalton
    A unit of mass equal to one twelfth of a carbon-12 atom. Daltons are used to specify the mass of molecules.
  • data (NMR)
    In NMR spectroscopy, the initial data collected include high-resolution multidimensional NMR spectra which reveal correlations between atoms that lie either within a few bonds of each other (J coupling) or within a short distance of each other (NOE coupling). NMR resonances are then assigned to specific atoms in the molecule and couplings are assigned to pairs or groups of atoms. These couplings are then used to produce a list of restraints that specify that particular atoms in the final model be near each other. Finally, a computer program is used to produce a model of the molecule which fits all of the restraints.
  • data (X-ray)
    In X-ray crystallography, the initial data include the measured positions and intensities of the reflections in the diffraction pattern produced by the macromolecular crystal. The relative phases of the waves that produced the diffraction pattern are also determined. An electron-density map of the molecule is then computed from the positions, intensities and phases of all of the reflections. A model of the molecule contained within the crystal is then built to fit the electron-density map.
  • deoxyribonucleic acid
    see DNA
  • deoxyribose
    the type of sugar found in DNA
  • diffraction (X-ray)
    When a macromolecular crystal is irradiated with an X-ray beam, the electrons surrounding each atom in the molecule bend, or diffract, the X-ray beam. As the beam exits the crystal, the scattered X-rays produce spots, or a diffraction pattern, on a photographic film or detector.
  • diffractometer
    An x-ray detector that collects diffraction data one reflection at a time.
  • dihedral angle
    The spatial relationship of four atoms (A, B, C, D) that are not necessarily sequentially connected that is defined by the angle between the plane containing atoms A, B, and C and the plane containing atoms B, C, and D.
  • dimer
    Protein composed of 2 chains or subunits.
  • disordered regions (NMR)
    In NMR spectroscopy, disordered regions of molecules result in high variability between the models of the ensemble. Atom positions in these regions are very uncertain.
  • disordered regions (X-ray)
    In X-ray crystallography, disordered regions of molecules appears as weak regions of electron density and as regions with high temperature factors. Atom positions in these regions are very uncertain.
  • disulfide bond
    Covalent bond formed between the sulfur atoms of two cysteine residues in a protein. Disulfide bonds often stabilize protein structure or link multiple proteins in a complex.
  • DNA
    DNA or deoxyribonucleic acid is the molecule that encodes genetic information necessary for all cellular functions. DNA is composed of the sugar deoxyribose, phosphate groups, and the bases adenine , thymine (T), guanine (G) and cytosine (C). The DNA molecule is normally a double helix in which the two strands are bound through complementarity of the bases. Cs from one strand hydrogen bind to Gs of the other strand and vice versa. Similarly, As and Ts hydrogen bind to each other.
  • domain
    A distinct area in a protein of specific tertiary structure that folds independently and possesses its own function
  • electron microscopy
    Imaging technique that uses a beam of high energy electrons to produce a magnified image of an object.
  • electron-density map
    A depiction of the electron cloud surrounding a molecule. In crystallography, an atomic model is built to fit an electron density map.
  • electrostatic
    A non-bonded interaction between protein molecules. Electrostatic attraction between oppositely charged ions holds them close together.
  • ensemble
    A collection of alternative models that each fits a set of NMR experimental data. A single model may be chosen by averaging the atomic positions of the set of models and then minimizing the energy of the result (see minimized average structure) or choosing a representative model from the ensemble (see representative conformer).
  • entity
    A unique molecule under investigation, and can be one of three types: polymer, non-polymer and water. Entities are described only once, even in those structures that contain multiple observations of an entity. For example, in a DNA molecule containing two identical chains the entity would be one of the individual chains rather than the double helix.
  • enzyme
    A macromolecule that is capable of catalyzing, or speeding up, specific biochemical reactions without being permanently altered or consumed. The term enzyme usually refers to proteins, but some RNA molecules can also function as enzymes.
  • enzyme classification
    A hierarchical classification of enzymes grouped according to function.
  • eukaryote
    A eukaryote is an organism, such as a plant or an animal, whose cells contain a nucleus distinct and separate from the cytoplasm.
  • experimental model
    Experimental models are derived from experimental methods involving either X-ray diffraction or NMR spectroscopy. In contrast, theoretical models include homology models and models obtained from simulations of folding and molecular dynamics.
  • fold
    Families of proteins are classified based on their secondary structural units of helices and sheets . Each different topology is considered as a fold.
  • fourier transformation
    A mathematical process that performs a conversion between real space and reciprocal space. Short distances in real space become long distances in reciprocal space, and vice versa. Using a Fourier transformation, a computer program can convert an X-ray diffraction pattern into an electron density map.
  • fractional coordinates
    Coordinates in which the positions of atoms are described with respect to the sides of a unit cell.
  • functional genomics
    The study of what genes do in different biological processes, including how they contribute to or cause disease.
  • GenBank
    The NIH sequence database that contains an annotated collection of all publicly available DNA sequences. Each entry includes a description of the sequence, information on the source organism, protein translation for coding regions, and bibliographic references.
  • gene
    A segment of DNA that encodes a specific protein or a protein subunit.
  • gene expression
    The process by which a gene's coded information is translated into proteins.
  • genetic code
    The set of triplet letters in DNA (or mRNA) that encode specific amino acids
  • genetics
    The scientific study of heredity.
  • genome
    All of the genetic material in the chromosomes of a particular organism.
  • genomics
    The science of searching for genes associated with disease.
  • genotype
    All of the genes possessed by a particular individual.
  • genotyping
    A procedure by which DNA sequence differences between individuals are used to study inheritance.
  • glutamic acid (glu, E)
    Amino acid with a charged acidic side chain containing a carboxyl group. The ionised form is known as glutamate.
  • glutamine (gln, Q)
    Amino acid with a uncharged, polar side chain containing an amide group.
  • glycine (gly,G)
    Amino acid with no side chain. Glycine is weakly hydrophobic. Glycine is often located at bends or folds in proteins.
  • glycosidic bond
    Covalent bond linking sugars in polysaccharides.
  • glycosylation
    The addition of carbohydrate groups to particular residues on a protein.
  • guanine (G)
    A nitrogenous base that occurs in nucleotides of DNA and RNA and pairs through hydrogen bonding complementarity with cytosine.
  • hairpin turn
    Bends that occur between two antiparallel beta-sheets or helices. Hairpin turns usually contain proline residues.
  • helix-turn-helix motif
    A domain found in some DNA-binding proteins that consists of a recognition helix and a stabilizing helix separated by a short loop.
  • hertz
    A hertz is defined as one cycle per second and is used to measure the frequency of electromagnetic radiation.
  • heterodimer
    Protein composed of 2 different chains or subunits.
  • heterotetramer
    Protein composed of 4 different chains or subunits.
  • heterotrimer
    Protein composed of 3 different chains or subunits.
  • histidine (his, H)
    Amino acid with a uncharged, polar side chain that contains a heterocyclic aromatic group.
  • homodimer
    Protein composed of 2 identical chains or subunits.
  • homology
    Similarity in sequence or structure that is due to a shared ancestry and points to a potentially common function.
  • homotetramer
    Protein composed of 4 identical chains or subunits.
  • homotrimer
    Protein composed of 3 identical chains or subunits.
  • hydrogen bond
    A weak bond between a hydrogen atom (that is covalently attached to another atom) and an electronegative atom (nitrogen or oxygen). Hydrogen bonds are important in many biological interactions.
  • hydrophilic
    "Water loving". Functional groups, amino acids, molecules, or domains that prefer to be in an aqueous environment are termed hydrophilic. Hydrophilic groups tend to make favorable intereactions with water, usually through hydrogen bonds.
  • hydrophobic
    "Water hating". Functional groups, amino acids, molecules, or domains that prefer to be in a non-aqueous (lipid) environment because they cannot make favorable interactions with water.
  • immunoglobulin (Ig)
    Specific proteins, also know as antibodies, that are produced by derivatives of B lymphocytes and which help protect organisms from antigens. An immunoglobulin is a tetrameric protein composed of two identical light chains and two identical heavy chains.
  • in situ
    Maintenance or study of an organism within its native environment.
  • in vitro
    A biological or chemical experiment that is performed outside an organism, for example in a test tube.
  • in vivo
    A biological or chemical experiment that is performed within an organism.
  • inhibitor
    A molecule that blocks or suppresses the biological activity of another molecule.
  • ion
    An atom or group of atoms that have either gained or lost electrons and as a result bears an electrical charge. Positively charged ions are called cations and negatively charged ions are called anions.
  • isoleucine (ile, I)
    An amino acid with a nonpolar, hydrophobic sidechain.
  • isomer
    One of two or more molecules with identical chemical compositions, but differing in the arrangement of their atoms. Two isomers may have different physical, chemical, and biological properties.
  • isotope
    A form of a chemical element that contains the same number of protons but a different number of neutrons than other forms of the element. Isotopes are often used to trace atoms or molecules in a metabolic pathway. In NMR, only one isotope of each element contains the correct magnetic properties to be useful.
  • kilodalton
    A unit of mass equal to 1,000 daltons (see Dalton)
  • kinase
    An enzyme that attaches a phosphate to a protein.
  • laue diffraction
    One of the oldenst and most common X-ray crystallography techniques. A single macromolecular crystal is irradiated with a beam of X-rays which are diffracted by the crystal. The scattered X-rays then produce spots, or a diffraction pattern, on a photographic film.
  • leucine (leu, L)
    An amino acid with a nonpolar, hydrophobic sidechain.
  • ligand
    A molecule that binds specifically to another molecule (usually a protein or nucleic acid) to form a complex. A ligand can be another protein, but is often a small molecule.
  • luzzati plot (X-ray)
    A way of estimating the overall or average precision of atom positions in a refined crystallographic model. The Luzzati plot provides an estimate of the upper limit of error in the atomic coordinates.
  • lysine (lys, K)
    Amino acid with a charged basic side chain containing an amino group.
  • macromolecule
    A large molecule that is a polymer of smaller units joined together, such as DNA, RNA, protein, or carbohydrate
  • MAD
    see multi-wavelength anomalous diffraction
  • megahertz
    A unit of measurement equal to 1,000,000 hertz (see hertz).
  • messenger RNA
    see mRNA
  • metalloprotease
    A class of protease characterized by a metal ion at its active site.
  • methionine (met, M)
    Amino acid with a sulphur-containing, nonpolar, hydrophobic side chain.
  • microbiology
    The science of microscopic organisms.
  • minimized average conformation
    A single model derived from an ensemble set of NMR structures by averaging the atomic positions of the set of models and then minimizing the energy of the result.
  • minimized average structure
    see minimized average conformation
  • mmCIF
    The macromolecular Crystallographic Information File (mmCIF) is a file format that is used to describe the features of a macromolecular structure. The mmCIF file is suitable for data archiving and data exchange.
  • molecular biology
    The study of nucleic acids and proteins in relation to the mechanisms of gene expression and gene manipulation.
  • molecular chaperone
    A protein that assists in the folding of a second protein into its active conformation.
  • molecule
    The smallest unit of a substance that has the characteristics of that substance. A molecule consists of one or more atoms bound together.
  • monosaccharide
    A carbohydrate that cannot be decomposed to a simpler carbohydrate.
  • motif
    A small structural pattern that is conserved among a variety of proteins and generally corresponds with a particular function
  • mRNA
    An RNA molecule that is transcribed from DNA and is translated into the amino acid sequence of a polypeptide.
  • multi-wavelength anomalous diffraction
    A technique used in X-ray crystallography that uses X-rays of different wavelengths, thereby relieving crystallographers from having to make several different metal-containing crystals.
  • multidimensional (three- and four-dimensional) NMR
    Together with advances in isotope labeling techniques of biomacromolecules, this technology has the advantage of resolving severe overlaps in 2D spectra and providing additional structural and dynamic information.
  • multimeric structure
    A molecular structure consisting of several identical or different subunits held together by weak bonds.
  • native conformation
    The physiological conformation of a protein.
  • NMR
    Nuclear magnetic resonance is a property that magnetic active nuclei have in a magnetic field when responding to applied electromagnetic pulses or perturbations. The measurements of such responses provide rich structural, dynamic, and kinetic information about the molecule.
  • NOESY
    see nuclear overhauser effect spectroscopy
  • non-polar molecule
    A molecule that has a uniformly distributed electronic charge.
  • Nuclear Magnetic Resonance (NMR)
    see NMR
  • nuclear overhauser effect spectroscopy
    An NMR technique that provides information about the distances between hydrogen nuclei to help determine protein structure.
  • nucleic acid
    A large molecule composed of nucleotide subunits.
  • nucleoside
    Nucleotide precursor containing a nitrogenous base and a sugar molecule, but not a phosphate group.
  • nucleotide
    The subunit of DNA or RNA that contains a nitrogenous base (adenine, guanine, cytosine, or thymine in DNA; adenine, guanine, cytosine, or uracil in RNA); a sugar (deoxyribose in DNA and ribose in RNA); and a phosphate group.
  • nucleus
    A membrane-bound organelle that contains DNA.
  • occupancy (X-ray)
    The occupancy of an atom is a measure of the fraction of molecules in the crystal in which the atom is actually present in the position specified by the model. If all of the molecules in the crystal are identical, then occupancies for all of the atoms are 1.00. Otherwise, two or more conformations may be observed for a small region of an atom, such as a side chain. The atoms are then given occupancies equal to the fraction of side chains in each distinct conformation.
  • oligosaccharide
    A compound composed of a small number of monnosaccharide units. Oligosaccharides are frequently found attached to proteins at the surface of cells.
  • omega
    The angle of rotation of the bond between the nitrogen and the carbonyl carbon in a peptide bond.
  • PDB
    See Protein Data Bank
  • pentamer
    Protein composed of 5 chains or subunits.
  • peptide
    A molecule composed of two or more amino acids linked by peptide bonds. Long peptides are generally referred to as polypeptides or proteins.
  • peptide bond
    A covalent bond linking two amino acids between their carboxyl (COOH) and amino (NH2) groups. Also known as amide bonds. Such linkages form peptides and proteins.
  • phenylalanine (phe, F)
    An amino acid with a large nonpolar sidechain. Phenylalanine is hydrophobic and is often found burried within protein structures.
  • phi
    The torsion angle of the alpha carbon-nitrogen bond of each amino acid.
  • phosphate
    A chemical group composed of one phosphorous atom bound to four oxygen atoms. It can be transferred to proteins and other biological molecules for short-term energy storage, or else for regulatory or structural purposes.
  • phosphodiester bond
    A bond between two sugar groups and a phosphate group. Such bonds link nucleotides together to form the sugar-phosphate-sugar backbone of DNA and RNA.
  • phosphorylation
    The covalent attachment of a phosphoryl (PO3--) ion onto a hydroxyl group of an amino-acid within a protein, or on a sugar. Phosphorylation is a critical step in many biochemical processes such as enzyme activity control. Phosphorylation is performed by enzymes that are referred to as kinases.
  • photosynthesis
    The biochemical process by which green plants, algae, and some bacteria use the sun's energy to synthesize organic compounds.
  • plasmid
    An autonomously replicating, extrachromosomal DNA molecule that is distinct from the normal bacterial genome. It is usually in the form of circular double-stranded DNA and it is used as a cloning vector.
  • polar molecule
    A molecule which has partial positive electronic charge in one part of the molecule and a complementary negative charge in another part.
  • polymer
    A large molecule formed by joining small molecules (monomers) together.
  • polypeptide
    A long string of amino acids linked by peptide bonds.
  • polysaccharide
    A biological polymer composed of multiple sugar subunits.
  • post-translational modification
    Alterations made to a protein after its synthesis, such as the addition of phosphate groups, carbohydrate or fatty acid chains. These modifications may be critical for protein function.
  • prenylation
    A post-translation modification of a protein that involves the covalent attachment of prenyl groups to proteins. The prenyl groups include the 15-carbon farnesyl groups and the 20-carbon geranylgeranyl groups.
  • primary structure
    The linear sequence of amino acids in a protein.
  • prokaryote
    An organism whose cells do not contain a nucleus such as in bacteria or blue-green algae.
  • proline (pro, P)
    An amino acid with a nonpolar cyclic sidechain. Proline is weakly hydrophobic.
  • prosthetic group
    A small molecule or metal that interacts with a protein to confer activity. The heme group of hemoglobin is an example of a prosthetic group. Prosthetic groups are also called cofactors or coenzymes.
  • protein
    A large biological molecule composed of a long string of amino acids joined by peptide bonds. . The order and identity of these amino acids is determined by the DNA sequence of the gene coding for the protein. Proteins perform a wide variety of functions and can serve as enzymes, antibodies, hormones, or structural components.
  • Protein Data Bank
    The single repository of experimentally determined structures of proteins, nucleic acids and complex biomolecular assemblies as mangaged by the Worldwide Protein Data Bank. PDB can also refer to a particular file format for describing structures.
  • protein families
    Sets of proteins with related structure, function, or sequence.
  • proteolysis
    In general, the degradation of proteins carried out by specific enzymes. With respect to the post-translational modification of proteins, proteolysis involves the removal of the initiator methionine or of signal sequences.
  • proteomics
    The study of the identity and function of the entire protein complement of a given tissue, cell, or organism at a particular time.
  • purine
    A bicyclic nitrogenous base found in DNA and RNA. Adenine and guanine are purines.
  • pyrimidine
    A monocyclic nitrogenous base found in DNA and RNA. Thymine, cytosine, and uracil are pyrimidines.
  • quaternary structure
    The arrangement of multiple tertiary structure domains or subunits into higher order spacial arrangements.
  • R-factor
    A mesure of the agreement between experimental crystallographic data and the atomic model representing that data.
  • R-free
    An R-factor calculated using only a selected group of reflections that were not included in the refinement procedure. R-free is intended to provide a quality control for the refinement process. See R-factor.
  • Ramachandran map
    see Ramachandran plot
  • Ramachandran plot
    A two-dimensional plot showing the backbone conformational angles psi versus phi in a polypeptide. Various regions of the plot indicate specific secondary conformation. The phi angle is around the C-N bond and the psi angle is around the CA-C bond. Ramachandran plots are used to identify areas in a structure with geometric problems.
  • receptor
    Proteins found on the cell surface to which other molecules selectively bind causing a reaction within the cell.
  • reciprocal space
    A concept that is critical for the interpretation of X-ray diffraction patterns. The diffraction space is usually called the reciprocal space because of the inverse relationship between the real spacing in the object and the angle of diffraction. The further out you go in reciprocal space, the more the diffraction pattern becomes sensitive to objects that are in close proximity in "real space". This reflects the principal of Fourier transforms that linear scaling in one space corresponds to the inverse scaling in the other space. Short distances in real space become long distances in reciprocal space, and vice versa.
  • refinement (NMR)
    The process of improving the agreement between the molecular model and the experimental NMR data. Simulated annealing or some other molecular dynamics program is used to fold the initial model using simulated forces that impose correct bond lengths and angles, provide weak van der Waals repulsions, and satisfy the restraints derived from NMR. The resulting model is examined for problems such as van der Waals collisions, and for large deviations from conformational restraints. Models that have such problems are eliminated. The whole simulated folding process is repeated until a number of models (an ensemble) are identified that make chemical sense are are consistent with the NMR-derived restraints.
  • refinement (X-ray)
    The process of improving the agreement between the molecular model and the experimental diffaction data. Fitting models to the electron density map is an iterative process. The initial model contains phase and other errors, and certain measures are taken during the refinement process to correct these errors. For example, certain constraints and restraints may be imposed on the model during refinement. The success of refinement is indicated in part by a decreasing R-factor and the elimination of residues from unfavorable regions in the Ramachandran plot.
  • relaxation
    If a system is disturbed from its state of equilibrium it relaxes to that state, and the process is referred to as relaxation. The branch of kinetics concerned with such processes is known as relaxation kinetics. Relaxation techniques include temperature jump and pressure jump.
  • representative conformer
    A single model chosen from an ensemble set of NMR structures as being representative of the set.
  • resonance assignments
    A process in which resonances in NMR spectra are assigned to specific atoms in the molecule.
  • restraint (NMR)
    Refers to the atomic distances and conformational angles that are determined from NMR couplings or correlations. T hese restraints specify which pairs of atoms are near each other through bonds or through space. The building of an NMR model complies with these restraints.
  • restraint (X-ray)
    During refinement of a crystallographic model, a restraint or condition may be applied to specific parameters. For example, the condition that all bond lengths and bond angles fall within a certain range of values.
  • ribonucleic acid
    see RNA
  • ribose
    the type of sugar found in RNA
  • ribosomal RNA
    see rRNA
  • ribosome
    Particle composed of ribosomal RNAs and proteins that is the site of protein synthesis.
  • Rms deviations (NMR)
    A measure for the precision of the NMR-derived models within an ensemble.
  • RNA
    RNA is a usually single-stranded nucleic acid similar to DNA but containing the sugar ribose rather than deoxyribose and the base uracil (U) rather than thymine (T). RNA has structural, genetic, and enzymatic roles. There are three major types of RNA: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).
  • ROESY
    see rotating frame overhauser enhancement spectroscopy
  • rotamer
    Conformation of a protein side chain arising from rotations around single bonds. Each amino acid has a set of preferred rotations that are defined by chi angles.
  • rotating frame overhauser enhancement spectroscopy
    An advanced form of NOESY which is ideal for large molecules.
  • rRNA
    One of the structural and functional components of ribosomes.
  • saccharide
    An organic compound containing sugar.
  • SCOP
    Acronym for the 'Structural Classification Of Proteins' database. The database contains proteins whose 3D structure is available and also provides information on known structural and evolutionary relationships.
  • secondary structure
    The arrangement a protein arising from hydrogen bonding interactions within contiguous segments of the polypeptide backbone. The two main types of secondary structure are the alpha helix and the beta-pleated sheet.
  • selenoproteins
    A post-translational modification of a protein that involves the incorporation of the unique amino acid selenocysteine.
  • sequence alignment
    The result of a linear comparison between two or more gene or protein sequences in order to determine their degree of nucleic or amino acid similarity.
  • serine (ser,S)
    Amino acid with a uncharged, polar side chain containing a hydroxyl group.
  • side chain
    The variable group in an amino acid that is attached to the alpha carbon.
  • signal transduction
    The process involving the transmission of chemical, electrical, or biological signals into and within a cell.
  • similarity (homology) search
    A method for predicting the structure and function of a newly sequenced gene.This method is based on the detection of significant sequence similarity to a protein of known structure and function, or of a sequence pattern that is characteristic of a protein family.
  • solid state NMR
    NMR experiments performed in a solid phase.
  • solution NMR
    NMR experiments performed in a liquid or liquid crystal phase.
  • solvent accessibility
    The surface area of a biomolecule that is exposed to solvent in its native, folded state. Helps to identify which amino acids are on the surface of a folded molecule and are therefore available to interact with other molecules.
  • space group
    In X-ray crystallography, the space group describes how unit cells pack and how to generate an array of molecules from the original unit cell.
  • stereochemistry
    The study of how the shape of a molecule affects its chemistry.
  • structural biology
    A field of study that focuses on the determination of the three-dimensional structures of biomolecules in order to better understand their function.
  • structural genomics
    A field of study dedicated to determining a large number of protein structures based on gene sequences. The goal is to be able to generate approximate structural models of any protein based on its nucleic acid sequence, and thereby infer its biological function.
  • structural parameters
    Refers to the bond lengths, bond angles, and conformational angles in a model.
  • structure prediction
    The use of algorithms to predict the secondary, tertiary and sometimes even quarternary structure of proteins from their sequences. Since the folded tertiary structure of a protein governs how it functions, being able to predict a protein's structure from its sequence is useful for infering its biological function.
  • structure-based drug design
    A methodology for designing new drugs that uses the three-dimensional structure of a target molecule.
  • substrate
    A molecule that binds to an enzyme and is subsequently chemically modified.
  • subunit
    A single polypeptide chain of a protein consisting of two or more polypeptides.
  • sulfation
    An irreversible post-translational modification of a protein that involves the addition of sulfate to tyrosine groups.
  • UniProt
    A database of protein sequences. Each entry contains the sequence of a protein along with a short description of its features and function(s), if known.
  • synchrotron
    A large instrument used to generate very intense X-rays. Synchrotrons have been key in shortening data collection time in X-ray diffraction experiments.
  • temperature factor
    A measure of how much the position of an atom deviates from that given in the atomic coordinates. This deviation is due to thermal motion and crystal imperfections. Temperature factors are also termed B-factors.
  • tertiary structure
    The arrangement of the secondary structure elements of a protein arising from interactions of the side chains including the formation of disulfide bonds between cysteine residues as well as non-covalent forces.
  • tetramer
    Protein composed of 4 chains or subunits.
  • theoretical model
    Theoretical models are produced by methods other than X-ray diffraction and NMR spectroscopy. Theoretical models include homology models and models derived from simulations of folding and molecular dynamics.
  • threonine (thr,T)
    Amino acid with a uncharged, polar side chain containing a hydroxyl group.
  • thymine (T)
    A nitrogenous base that occurs in nucleotides of DNA and pairs through hydrogen bonding complementarity with adenine.
  • TOCSY
    See TOtal Correlation SpectroscopY
  • torsion angle
    see dihedral angle
  • TOtal Correlation SpectroscopY
    An NMR method for correlating all the spins that are mutually coupled. It is useful in identifying spin systems such as each individual amino acid residue.
  • transcription
    The process of copying (by RNA polymerase) genetic information from the DNA by the synthesis of a complementary single strand of mRNA.
  • transfer RNA
    See tRNA
  • transgenic animals
    Animals (usually mice) that have had a foreign gene inserted into their genome by recombinant DNA technology.
  • translation
    The process in which the information encoded in mRNA is read and the corresponding sequence of amino acids is synthesized. This process is perfomed by tRNA and the ribosome (containing rRNA).
  • transmembrane protein
    A protein that spans the cell membrane. These proteins may have hydrophobic regions that are compatible with the lipid nature of the membrane as well as hydrophilic regioins that are compatible with the aqueous environment both inside and outside the cell.
  • trimer
    Protein composed of 3 chains or subunits.
  • tRNA
    RNA molecule thata carries amino acids to the ribosome during protein synthesis.
  • tryptophan (trp, W)
    Amino acid with a uncharged, polar side chain that contains a heterocyclic aromatic group.
  • tyrosine (tyr, Y)
    Amino acid with a uncharged, polar side chain containing an aromatic phenolic group.
  • unexplained density (X-ray)
    Empty density may be due to ions like phosphate and sulfate from the solvent or reagents like mercaptoethanol, dithiothreitol, or detergents used in the purification or crystallization of the protein. Unexplained density may also be due to small molecules like cofactors tha co-purified with the protein of interest.
  • unit cell
    The minimum repeat unit within a crystal which can be used to generate the entire crystal structure using only translation. Fractional coordinates are used to describe positions in the unit cells. These are fractions of a, b, and c (the axes) and these coordinates are similar to the x, y, and z of cartesian coordinates. Several unit cells can often be defined for the same arrangement. However, the convention is to choose the unit cell with the highest symmetry.
  • uracil (U)
    A nitrogenous base that occurs in nucleotides of RNA and pairs through hydrogen bonding complementarity with adenine.
  • valine (val, V)
    An amino acid with a nonpolar, hydrophobic sidechain.
  • van der Waals forces
    Weak interactions, including hydrogen bonds, occurring between atoms and molecules whey they are in close proximity.
  • van der Waals radius
    The radius of the electron cloud surrounding an atom that defines how close another atom or molecule can approach.
  • virus
    An infectious microbe that requires a host cell in which to reproduce. It consists of proteins and either DNA or RNA.
  • X-ray crystallography
    A method used to determine the detailed three-dimensional structure of molecules present in a crystal in which an X-ray beam is aimed at the crystal and the resulting scattered rays are studied.
  • Z DNA
    A left-handed form of DNA present under physiological conditions It contains short GC segments that are methylated and may play a role in regulating gene expression in eukaryotes.
  • Z value
    Refers to the number of molecules in the cell. It is dependent on the symmetry of the crystal. Increasing the unit cell axis or changing from a primative cell to a centered cell can change the Z value.