Proteins are an important class of biological macromolecules present in all biological organisms, made up of such elements as carbon, hydrogen, nitrogen, phosphorus, oxygen, and sulfur. Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl The term macromolecule by definition implies "large Molecule " A chemical element is a type of Atom that is distinguished by its Atomic number; that is by the number of Protons in its nucleus. Carbon (kɑɹbən is a Chemical element with the symbol C and its Atomic number is 6 Hydrogen (ˈhaɪdrədʒən is the Chemical element with Atomic number 1 Nitrogen (ˈnaɪtɹəʤɪn is a Chemical element that has the symbol N and Atomic number 7 and Atomic weight 14 Phosphorus, (ˈfɒsfərəs is the Chemical element that has the symbol P and Atomic number 15 Oxygen (from the Greek roots ὀξύς (oxys (acid literally "sharp" from the taste of acids and -γενής (-genēs (producer literally begetteris the Sulfur or sulphur (ˈsʌlfɚ see spelling below) is the Chemical element that has the Atomic number 16 All proteins are polymers of amino acids. A polymer is a large Molecule ( Macromolecule) composed of repeating Structural units typically connected by Covalent Chemical bonds In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this The polymers, also known as polypeptides consist of a sequence of 20 different L-α-amino acids, also referred to as residues. Peptides (from the Greek πεπτίδια, "small digestibles" are short Polymers formed from the linking in a defined order of α- Amino For chains under 40 residues the term peptide is frequently used instead of protein. Peptides (from the Greek πεπτίδια, "small digestibles" are short Polymers formed from the linking in a defined order of α- Amino To be able to perform their biological function, proteins fold into one, or more, specific spatial conformations, driven by a number of noncovalent interactions such as hydrogen bonding, ionic interactions, Van der Waals' forces and hydrophobic packing. A hydrogen bond results from a Dipole-dipole force between an Electronegative atom and a Hydrogen atom bonded to Nitrogen, Oxygen An ionic bond (or electrovalent bond) is a type of Chemical bond that can often form between Metal and Non-metal Ions (or The Van der Waals equation is an Equation of state that can be derived from a special form of the potential between a pair of molecules (hard-sphere repulsion In Chemistry, hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear phobos) refers to the physical property of In order to understand the functions of proteins at a molecular level, it is often necessary to determine the three dimensional structure of proteins. This is the topic of the scientific field of structural biology, that employs techniques such as X-ray crystallography or NMR spectroscopy, to determine the structure of proteins. Structural biology is the branch of Molecular biology concerned with the Architecture and shape of biological Macromolecules especially Proteins X-ray crystallography is a method of determining the arrangement of Atoms within a Crystal, in which a beam of X-rays strikes a crystal and scatters Protein nuclear magnetic resonance spectroscopy (usually abbreviated protein NMR) is a field of Structural biology in which NMR spectroscopy is used

A number of residues are necessary to perform a particular biochemical function, and around 40-50 residues appears to be the lower limit for a functional domain size. Biochemistry is the study of the chemical processes in living Organisms It deals with the Structure and function of cellular components such as A protein domain is a part of protein sequence and structure that can evolve, function and exist independently of the rest of the protein chain Protein sizes range from this lower limit to several thousand residues in multi-functional or structural proteins. However, the current estimate for the average protein length is around 300 residues. Very large aggregates can be formed from protein subunits, for example many thousand actin molecules assemble into a collagen filament. In Structural biology, a protein subunit or subunit protein is a single Protein Molecule that assembles (or " coassembles " Actin is a globular roughly 42-kDa Protein found in all eukaryotic cells (except for Nematode sperm where it may be present at concentrations of

Levels of protein structure

Protein structure, from primary to quaternary structure.

Biochemistry refers to four distinct aspects of a protein's structure:

• Primary structure - the amino acid sequence of the peptide chains.
• Secondary structure - highly regular sub-structures (alpha helix and strands of beta sheet) which are locally defined, meaning that there can be many different secondary motifs present in one single protein molecule. A common motif in the Secondary structure of Proteins the alpha helix (α-helix is a right-handed coiled conformation resembling a spring, in which The β sheet (also β-pleated sheet) is the second form of regular Secondary structure in Proteins consisting of beta strands connected laterally
• Tertiary structure - three-dimensional structure of a single protein molecule; a spatial arrangement of the secondary structures. It also describes the completely folded and compacted polypeptide chain.
• Quaternary structure - complex of several protein molecules or polypeptide chains, usually called protein subunits in this context, which function as part of the larger assembly or protein complex.

In addition to these levels of structure, a protein may shift between several similar structures in performing its biological function. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as chemical conformation, and transitions between them are called conformational changes. In Chemistry, conformational isomerism is a form of Stereoisomerism in which Molecules with the same Structural formula (same connectivity

The primary structure is held together by covalent or peptide bonds, which are made during the process of protein biosynthesis or translation. A peptide bond is a Chemical bond formed between two Molecules when the Carboxyl group of one molecule reacts with the Protein biosynthesis (synthesis is the process in which cells build Proteins The term is sometimes used to refer only to protein translation but more These peptide bonds provide rigidity to the protein. The two ends of the amino acid chain are referred to as the C-terminal end or carboxyl terminus (C-terminus) and the N-terminal end or amino terminus (N-terminus) based on the nature of the free group on each extremity.

The various types of secondary structure are defined by their patterns of hydrogen bonds between the main-chain peptide groups. In Protein structure, the DSSP algorithm is the standard method for assigning Secondary structure to the Amino acids of a protein given the atomic-resolution However, these hydrogen bonds are generally not stable by themselves, since the water-amide hydrogen bond is generally more favorable than the amide-amide hydrogen bond. Thus, secondary structure is stable only when the local concentration of water is sufficiently low, e. g. , in the molten globule or fully folded states. A molten globule ( MG) is a stable partially folded Protein state found in mildly denaturing conditions such as low PH (generally pH = 2 mild Protein folding is the physical process by which a Polypeptide folds into its characteristic and functional three-dimensional structure.

Similarly, the formation of molten globules and tertiary structure is driven mainly by structurally non-specific interactions, such as the rough propensities of the amino acids and hydrophobic interactions. However, the tertiary structure is fixed only when the parts of a protein domain are locked into place by structurally specific interactions, such as ionic interactions (salt bridges), hydrogen bonds and the tight packing of side chains. The tertiary structure of extracellular proteins can also be stabilized by disulfide bonds, which reduce the entropy of the unfolded state; disulfide bonds are extremely rare in cytosolic proteins, since the cytosol is generally a reducing environment. In Chemistry, a disulfide bond is a single Covalent bond derived from the coupling of Thiol groups

Structure of the amino acids

An α-amino acid

An α-amino acid consists of a part that is present in all the amino acid types, and a side chain that is unique to each type of residue. The C_α atom is bound to 4 different molecules (the H is omitted in the diagram); an amino group, a carboxyl group, a hydrogen and a side chain, specific for this type of amino acid. An exception from this rule is proline, where the hydrogen atom is replaced by a bond to the side chain. Proline (abbreviated as Pro or P) is an α- Amino acid, one of the twenty DNA -encoded amino acids Because the carbon atom is bound to four different groups it is chiral, however only one of the isomers occur in biological proteins. The term chiral (pronounced /ˈkaɪɹ(əl̩/ is used to describe an object that is non- superimposable on its mirror image This article is about the chemical concept For "isomerism" of atomic nuclei see Nuclear isomer. Glycine however, is not chiral since its side chain is a hydrogen atom. A simple mnemonic for correct L-form is "CORN": when the C_α atom is viewed with the H in front, the residues read "CO-R-N" in a clockwise direction. A mnemonic device (nəˈmɒnɪk is a Memory aid Commonly met mnemonics are often verbal something such as a very short poem or a special word used to help a person remember

CO-R-N rule

The side chain determines the chemical properties of the α-amino acid and may be any one of the 20 different side chains:

The 20 naturally occurring amino acids can be divided into several groups based on their chemical proporties. Important factors are charge, hydrophobicity/hydrophilicity, size and functional groups. The nature of the interaction of the different side chains with the aqueous environment plays a major role in molding protein structure. Hydrophobic side chains tends to be buried in the middle of the protein, whereas hydrophilic side chains are exposed to the solvent. Examples of hydrophobic residues are: Leucine, isoleucine, phenylalanine, and valine, and to a lesser extent tyrosine, alanine and tryptophan. The charge of the side chains plays an important role in protein structures, since ion bonding can stabilize proteins structures, and an unpaired charge in the middle of a protein can disrupt structures. Charged residues are strongly hydrophilic, and are usually found on the out side of proteins. Positively charged side chains are found in lysine and arginine, and in some cases in histidine. Negative charges are found in glutamate and aspartate. The rest of the amino acids have smaller generally hydrophilic side chains with various functional groups. Serine and threonine have hydroxylgroups, and aspargine and glutamine have amide groups. Some amino acids have special properties such as cysteine, that can form covalent disulfide bonds to other cysteines, proline that is cyclical, and glycine that is small, and more flexible than the other amino acids. In Chemistry, a disulfide bond is a single Covalent bond derived from the coupling of Thiol groups

The peptide bond

Two amino acids

Bond angles for ψ and ω

Two amino acids can be combined in a condensation reaction. A condensation reaction is a Chemical reaction in which two Molecules or moieties ( Functional groups) combine to form one single molecule together with By repeating this reaction, long chains of residues (amino acids in a peptide bond) can be generated. This reaction is catalysed by the ribosome in a process known as translation. Catalysis is the process in which the rate of a Chemical reaction is increased by means of a Chemical substance known as a catalyst Ribosomes ( from ribo nucleic acid and "Greek soma ( meaning body") are complexes of RNA and Protein that Protein biosynthesis (synthesis is the process in which cells build Proteins The term is sometimes used to refer only to protein translation but more The peptide bond is in fact planar due to the delocalization of the electrons from the double bond. A peptide bond is a Chemical bond formed between two Molecules when the Carboxyl group of one molecule reacts with the The electron is a fundamental Subatomic particle that was identified and assigned the negative charge in 1897 by J The rigid peptide dihedral angle, ω (the bond between C₁ and N) is always close to 180 degrees. In Aerospace engineering, the Dihedral is the Angle between the two wings see Dihedral. The dihedral angles φ (the bond between N and Cα) and psi ψ (the bond between Cα and C₁) can have a certain range of possible values. These angles are the degrees of freedom of a protein, they control the protein's three dimensional structure. They are restrained by geometry to allowed ranges typical for particular secondary structure elements, and represented in a Ramachandran plot. A Ramachandran plot (also known as a Ramachandran map or a Ramachandran diagram) developed by Gopalasamudram Narayana Ramachandran, is a way to visualize A few important bond lengths are given in the table below. In Molecular geometry, bond length or bond distance is the average distance between nuclei of two bonded Atoms in a Molecule.

Primary structure

Main article: Primary structure

The sequence of the different amino acids is called the primary structure of the peptide or protein. A picometre ( American spelling: picometer, symbol pm) is a unit of Length in the Metric system, equal to one trillionth In Biochemistry, the primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including In Biochemistry, the primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including Counting of residues always starts at the N-terminal end (NH₂-group), which is the end where the amino group is not involved in a peptide bond. The primary structure of a protein is determined by the gene corresponding to the protein. A specific sequence of nucleotides in DNA is transcribed into mRNA, which is read by the ribosome in a process called translation. Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known Transcription is the synthesis of RNA under the direction of DNA Messenger ribonucleic acid ( mRNA) is a molecule of RNA encoding a chemical "blueprint" for a Protein product The sequence of a protein is unique to that protein, and defines the structure and function of the protein. The sequence of a protein can be determined by methods such as Edman degradation or tandem mass spectrometry. Edman degradation, developed by Pehr Edman, is a method of sequencing Amino acids in a Peptide. Mass spectrometry is an analytical technique that identifies the chemical composition of a compound or sample based on the Mass-to-charge ratio of charged particles Often however, it is read directly from the sequence of the gene using the genetic code. The genetic code is the set of rules by which information encoded in genetic material ( DNA or RNA sequences is translated into Proteins Post-transcriptional modifications such as disulfide formation, phosphorylations and glycosylations are usually also considered a part of the primary structure, and cannot be read from the gene.

Secondary structure

Main article: Secondary structure

By building models of peptides using known information about bond lengths and angles, the first elements of secondary structure, the alpha helix and the beta sheet, were suggested in 1951 by Linus Pauling and coworkers. In Biochemistry and Structural biology, secondary structure is the general three-dimensional form of local segments of Biopolymers such as A common motif in the Secondary structure of Proteins the alpha helix (α-helix is a right-handed coiled conformation resembling a spring, in which The β sheet (also β-pleated sheet) is the second form of regular Secondary structure in Proteins consisting of beta strands connected laterally Linus Carl Pauling (February 28 1901 – August 19 1994 was an American Scientist, Peace activist, Author and educator. ^[1] Both the alpha helix and the beta-sheet represent a way of saturating all the hydrogen bond donors and acceptors in the peptide backbone. These secondary structure elements only depend on properties that all the residues have in common, explaining why they occur frequently in most proteins. Since then other elements of secondary structure have been discovered such as various loops and other forms of helices. The part of the backbone that is not in a regular secondary structure is said to be random coil. A random coil is a Polymer Conformation where the Monomer subunits are oriented randomly while still being bonded to adjacent Each of these two secondary structure elements have a regular geometry, meaning they are constrained to specific values of the dihedral angles ψ and φ. Thus they can be found in a specific region of the Ramachandran plot.

The left panel shows the hydrogen bonding in an actual α-helix backbone. Note that the nth residue O (Lys 143) bonds to the (n+4)th following residue's N (Arg 147). The actual values of some displayed H-bond distances give you some idea about the variations to expect within a helix. The center panel includes the side chains which were omitted in the left panel for clarity. You see the side chains pointing towards the N-terminal of the chain (lower residue numbers) and thus it is usually possible to determine the direction of the helix quite well during initial model building. A 0. 2 nm electron density is shown in the right panel

Here are some more representation of the same helix.

Backbone

Secondary structure cartoon ("ribbon" or "linguini diagram")

Turns, loops and a few other secondary structure elements such as a 3-10 helix complete the picture. We have now enough pieces to assemble a complete protein, displaying its typical tertiary structure.

Tertiary structure

Main article: tertiary structure

The elements of secondary structure are usually folded into a compact shape using a variety of loops and turns. In Biochemistry and Chemistry, the tertiary structure of a Protein or any other Macromolecule is its three-dimensional structure as defined The formation of tertiary structure is usually driven by the burial of hydrophobic residues, but other interactions such as hydrogen bonding, ionic interactions and disulfide bonds can also stabilize the tertiary structure. The tertiary structure encompasses all the noncovalent interactions that are not considered secondary structure, and is what defines the overall fold of the protein, and is usually indispensable for the function of the protein.

Quaternary structure

Main article: Quaternary structure

The quaternary structure is the interaction between several chains of peptide bonds. In Biochemistry, quaternary structure is the arrangement of multiple folded Protein molecules in a multi-subunit complex The individual chains are called subunits. The individual subunits are not necessarily covalently connected, but might be connected by a disulfide bond. Not all proteins have quaternary structure, since they might be functional as monomers. The quaternary structure is stabilized by the same range of interactions as the tertiary structure. Complexes of two or more polypeptides (i. e. multiple subunits) are called multimers. Specifically it would be called a dimer if it contains two subunits, a trimer if it contains three subunits, and a tetramer if it contains four subunits. Multimers made up of identical subunits may be referred to with a prefix of "homo-" (e. g. a homotetramer) and those made up of different subunits may be referred to with a prefix of "hetero-" (e. g. a heterodimer). Tertiary structures vary greatly from one protein to another. They are held together by glycosydic and covalent bonds.

Side chain conformation

The atoms along the side chain are named with Greek letters in Greek alphabetical order: α, β, γ, δ, є and so on. C_α refers to the carbon atom closest to the carbonyl group of that amino acid, C_β the second closest and so on. The C_α is usually considered a part of the backbone. The dihedral angles around the bonds between these atoms are named χ1, χ2, χ3 etc. E. g. the first and second carbon atom in the side chain of lysine is named α and β, and the dihedral angle around the α-β bond is named χ1. Side chains can be in different conformations called gauche(-), trans and gauche(+). Side chains generally tend to try to come into a staggered conformation around χ2, driven by the minimization of the overlap between the electron orbitals of the hydrogen atoms. A staggered conformation is a Chemical conformation that exists in any open chain single Chemical bond connecting two sp3 hybridised atoms as

Domains, motifs, and folds in protein structure

Many proteins are organized into several units. A structural domain is an element of the proteins overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. A protein domain is a part of protein sequence and structure that can evolve, function and exist independently of the rest of the protein chain Protein folding is the physical process by which a Polypeptide folds into its characteristic and functional three-dimensional structure. Many domains are not unique to the protein products of one gene or one gene family but instead appear in a variety of proteins. History See also History of genetics The existence of genes was first suggested by Gregor Mendel (1822-1884 who in the 1860s studied inheritance A gene family is a set of Genes with a known homology. They are generally biochemically similar Domains often are named and singled out because they figure prominently in the biological function of the protein they belong to; for example, the "calcium-binding domain of calmodulin". Calmodulin ( CaM) (an abbreviation for CAL cium MODUL ated prote' IN') is a calcium-binding protein expressed in all Eukaryotic cells Because they are self-stabilizing, domains can be "swapped" by genetic engineering between one protein and another to make chimeras. Genetic engineering, Recombinant DNA technology, genetic modification/manipulation (GM and gene splicing are terms that apply to the direct Fusion proteins, also known as chimeric proteins, are proteins created through the joining of two or more Genes which originally coded for separate proteins A motif in this sense refers to a small specific combination of secondary structural elements (such as helix-turn-helix). In Proteins the helix-turn-helix ( HTH) is a major Structural motif capable of binding DNA. These elements are often called supersecondary structures. In an unbranched chain-like biological Molecule, such as a Protein or a strand of RNA, a structural motif is a three-dimensional structural Fold refers to a global type of arrangement, like helix-bundle or beta-barrel. A beta barrel is a large Beta-sheet that twists and coils to form a closed structure in which the first strand is hydrogen bonded to the last Structure motifs usually consist of just a few elements, e. g. the 'helix-turn-helix' has just three. Note that while the spatial sequence of elements is the same in all instances of a motif, they may be encoded in any order within the underlying gene. History See also History of genetics The existence of genes was first suggested by Gregor Mendel (1822-1884 who in the 1860s studied inheritance Protein structural motifs often include loops of variable length and unspecified structure, which in effect create the "slack" necessary to bring together in space two elements that are not encoded by immediately adjacent DNA sequences in a gene. A DNA sequence or genetic sequence is a succession of letters representing the Primary structure of a real or hypothetical DNA Molecule Note also that even when two genes encode secondary structural elements of a motif in the same order, nevertheless they may specify somewhat different sequences of amino acids. In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this This is true not only because of the complicated relationship between tertiary and primary structure, but because the size of the elements varies from one protein and the next. Despite the fact that there are about 100,000 different proteins expressed in eukaryotic systems, there are much fewer different domains, structural motifs and folds. Animals Plants fungi, and Protists are eukaryotes (juːˈkærɪɒt or -oʊt Organisms whose cells are organized into complex This is partly a consequence of evolution, since genes or parts of genes can be doubled or moved around within the genome. eVolution is the third Album by eLDee, it was due to be released in 2008 This means that, for example, a protein domain might be moved from one protein to another thus giving the protein a new function. Because of these mechanisms pathways and mechanisms tends to be reused in several different proteins.

Protein folding

Main article: Protein folding

The process by which the higher structures form is called protein folding and is a consequence of the primary structure. Protein folding is the physical process by which a Polypeptide folds into its characteristic and functional three-dimensional structure. A unique polypeptide may have more than one stable folded conformation, which could have a different biological activity, but usually, only one conformation is considered to be the active, or native conformation.

Structure classification

Several methods have been developed for the structural classification of proteins. These seek to classify the data in the Protein Data Bank in a structured order. The Protein Data Bank ( PDB) is a repository for 3-D structural data of Proteins and Nucleic acids These data typically obtained by X-ray crystallography Several databases exist which classify proteins using different methods. SCOP, CATH and FSSP are the largest ones. A ags scop was an Old English poet the Anglo-Saxon counterpart of the Old Norse non [[skald]]. The CATH Protein Structure Classification is a semi-automatic hierarchical classification of protein domains published in 1997 by Christine Orengo Janet Thornton and their colleagues The methods used are purely manual, manual and automated, and purely automated. Work is being done to better integrate the current data. The classification is consistent between SCOP, CATH and FSSP for the majority of proteins which have been classified, but there are still some differences and inconsistencies.

Protein structure determination

Around 90% of the protein structures available in the Protein Data Bank have been determined by X-ray crystallography. The Protein Data Bank ( PDB) is a repository for 3-D structural data of Proteins and Nucleic acids These data typically obtained by X-ray crystallography X-ray crystallography is a method of determining the arrangement of Atoms within a Crystal, in which a beam of X-rays strikes a crystal and scatters This method allows one to measure the 3D density distribution of electrons in the protein (in the crystallized state) and thereby infer the 3D coordinates of all the atoms to be determined to a certain resolution. Inference is the act or process of deriving a Conclusion based solely on what one already knows Roughly 9% of the known protein structures have been obtained by Nuclear Magnetic Resonance techniques, which can also be used to determine secondary structure. Protein nuclear magnetic resonance spectroscopy (usually abbreviated protein NMR) is a field of Structural biology in which NMR spectroscopy is used Note that aspects of the secondary structure as whole can be determined via other biochemical techniques such as circular dichroism. Circular dichroism (CD is a form of Spectroscopy based on the differential absorption of left- and right-handed circularly polarized Light. Secondary structure can also be predicted with a high degree of accuracy (see next section). Cryo-electron microscopy has recently become a means of determining protein structures to high resolution (less than 5 angstroms or 0. Electron cryomicroscopy ( cryo-EM or sometimes cryo-electron microscopy) is a form of Electron microscopy (EM where the sample is studied at Cryogenic 5 nanometer) and is anticipated to increase in power as a tool for high resolution work in the next decade. This technique is still a valuable resource for researchers working with very large protein complexes such as virus coat proteins and amyloid fibers.

Computational prediction of protein structure

The generation of a protein sequence is much simpler than the generation of a protein structure. Peptide sequence or amino acid sequence is the order in which Amino acid residues connected by Peptide bonds lie in the chain in Peptides However, the structure of a protein gives much more insight in the function of the protein than its sequence. Therefore, a number of methods for the computational prediction of protein structure from its sequence have been proposed. Ab initio prediction methods use just the sequence of the protein. Threading uses existing protein structures. Threading is a method for the computational prediction of Protein structure from Amino acid sequence. Homology Modeling to build a reliable 3D model for a protein of unknown structure from one or more related proteins of known structure. In Protein structure prediction, homology modeling, also known as comparative modeling, is a class of methods for constructing an atomic-resolution model of a

Rosetta@home is a distributed computing project which tries to predict the structures of proteins with massive sampling on thousands of home computers. Rosetta@home is a Distributed computing project for Protein structure prediction on the Berkeley Open Infrastructure for Network Computing (BOINC Distributed computing deals with Hardware and Software Systems containing more than one processing element or Storage element concurrent Foldit is a video game designed to use human pattern recognition and puzzle solving abilities to improve existing software. Foldit is an experimental Video game about Protein folding, developed as a collaboration between the University of Washington 's departments of A video game is a Game that involves interaction with a User interface to generate visual feedback on a video device. Pattern recognition is a sub-topic of Machine learning. It is "the act of taking in raw data and taking an action based on the category of the data" A puzzle is a Problem or Enigma that challenges Ingenuity. In a basic puzzle one is intended to piece together objects in a logical way in order to

Software

There are many available software packages, such as free web-based STING, used to visualize and analyze protein structures. STING ( S equence T o and with' IN' G raphics is a free Web-based suite of programs for a comprehensive analysis of the relationship between protein sequence Another example is the FeatureMap3D web-server which can visualize the quality of a protein-protein alignment in 3D and be used to map sequence feature annotation such as the underlying Intron/Exon structure onto a protein structure. Introns, derived from the term "intragenic regions" and also called intervening sequence (IVS are DNA regions in a Gene that are not translated into An exon is a Nucleic acid sequence that is represented in the mature form of an RNA molecule after a portions of a precursor RNA Introns have been

Several packages, such as Quantum Pharmaceuticals software^[2], can be used to predict conformational changes of proteins and its influence on protein's functions.

Several methods have been developed to compare structures of different proteins. Please see structural alignment. Structural alignment is a form of Sequence alignment based on comparison of shape

Computational tools are also frequently employed to check experimental and theoretical models of protein structures for errors (examples: ProSA, NQ-Flipper, Verify3D, ANOLEA, WHAT_CHECK).

References

Further reading

• Habeck M, Nilges M, Rieping W (2005). "Bayesian inference applied to macromolecular structure determination". Physical review. E, Statistical, nonlinear, and soft matter physics 72 (3 Pt 1): 031912. PMID 16241487.   (Bayesian computational methods for the structure determination from NMR data)

External links

• ProSA-web Web service for the recognition of errors in experimentally or theoretically determined protein structures
• NQ-Flipper Check for unfavorable rotamers of Asn and Gln residues in protein structures
• servers That check nearly 200 aspects of protein structure, like packing, geometry, unfavourable rotamers in general of for Asn, Gln and His especially, strange water molecules, backbone conformations, atom nomenclature, symmetry parameters, etc.
• Bioinformatics course. An interactive, fully free, course explaining many of the aspects discussed in this wiki entry.