Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different from the inverse problem of protein design.
Protein structure prediction is one of the most important goals pursued by computational biology and addresses Levinthal's paradox. Accurate structure prediction has important applications in medicine (for example, in drug design) and biotechnology (for example, in novel enzyme design).
Starting in 1994, the performance of current methods is assessed biennially in the Critical Assessment of Structure Prediction (CASP) experiment. A continuous evaluation of protein structure prediction web servers is performed by the community project Continuous Automated Model EvaluatiOn (CAMEO3D).
Protein structure and Terminology Proteins are chains of amino acids joined together by peptide bonds. Many conformations of this chain are possible due to the rotation of the main chain about the two torsion angles φ and ψ at the Cα atom. This conformational flexibility is responsible for differences in the three-dimensional structure of proteins.
The peptide bonds in the chain are polar, i.e. they have separated positive and negative charges (partial charges) in the carbonyl group, which can act as hydrogen bond acceptor and in the NH group, which can act as hydrogen bond donor. These groups can therefore interact in the protein structure. Proteins consist mostly of 20 different types of L-α-amino acids (the proteinogenic amino acids). These can be classified according to the chemistry of the side chain, which also plays an important structural role. Glycine takes on a special position, as it has the smallest side chain, only one hydrogen atom, and therefore can increase the local flexibility in the protein structure. Cysteine in contrast can react with another cysteine residue to form one cystine and thereby form a cross link stabilizing the whole structure.
Protein structure arises from a sequence of secondary structure elements, such as α helices and β sheets. In secondary structures, regular patterns of H-bonds are formed between the main chain NH and CO groups of spatially neighboring amino acids, and the amino acids have similar Φ and ψ angles.
Formation of these secondary structures efficiently satisfies the hydrogen bonding capacities of the peptide bonds. The secondary structures can be tightly packed in the protein core in a hydrophobic environment, but they can also be present at a polar protein surface. Each amino acid side chain has a limited volume to occupy and a limited number of possible interactions with other nearby side chains, a situation that must be taken into account in molecular modeling and alignments.Yousif, Ragheed Hussam, et al. "Exploring the Molecular Interactions between Neoculin and the Human Sweet Taste Receptors through Computational Approaches." Sains Malaysiana 49.3 (2020): 517-525.
α-helix
The α-helix is the most abundant type of secondary structure in proteins. The α-helix has 3.6 amino acids per turn with an H-bond formed between every fourth residue; the average length is 10 amino acids (3 turns) or 10 Å but varies from 5 to 40 (1.5 to 11 turns). The alignment of the H-bonds creates a dipole moment for the helix with a resulting partial positive charge at the amino end of the helix. Because this region has free NH2 groups, it will interact with negatively charged groups such as phosphates. The most common location of α-helices is at the surface of protein cores, where they provide an interface with the aqueous environment. The inner-facing side of the helix tends to have hydrophobic amino acids and the outer-facing side hydrophilic amino acids. Thus, every third of four amino acids along the chain will tend to be hydrophobic, a pattern that can be quite readily detected. In the leucine zipper motif, a repeating pattern of leucines on the facing sides of two adjacent helices is highly predictive of the motif. A helical-wheel plot can be used to show this repeated pattern. Other α-helices buried in the protein core or in cellular membranes have a higher and more regular distribution of hydrophobic amino acids, and are highly predictive of such structures. Helices exposed on the surface have a lower proportion of hydrophobic amino acids. Amino acid content can be predictive of an α-helical region. Regions richer in alanine (A), glutamic acid (E), leucine (L), and methionine (M) and poorer in proline (P), glycine (G), tyrosine (Y), and serine (S) tend to form an α-helix. Proline destabilizes or breaks an α-helix but can be present in longer helices, forming a bend.
β-sheet
β-sheets are formed by H-bonds between an average of 5–10 consecutive amino acids in one portion of the chain with another 5–10 farther down the chain. The interacting regions may be adjacent, with a short loop in between, or far apart, with other structures in between. Every chain may run in the same direction to form a parallel sheet, or in the reverse direction to form an antiparallel sheet, or the chains may form a mixed sheet. The pattern of hydrogen bonding is different in the parallel and antiparallel configurations. Each amino acid in the interior strands of the sheet forms two H-bonds with neighboring amino acids, whereas each amino acid on the outside strands forms only one bond with an interior strand. Looking across the sheet at right angles to the strands, more distant strands are rotated slightly counterclockwise to form a left-handed twist. The Cα-atoms alternate above and below the sheet in a pleated structure, and the R side groups of the amino acids alternate above and below the pleats. The Φ and Ψ angles of the amino acids in sheets vary considerably in one region of the Ramachandran plot. It is more difficult to predict the location of β-sheets than of α-helices. The situation improves somewhat when the amino acid variation in multiple sequence alignments is taken into account.
Deltas Parts of the protein may have fixed three-dimensional structure without regular structures. They should not be confused with disordered or unfolded segments of proteins or random coil, an unfolded polypeptide chain lacking any fixed three-dimensional structure. These parts are frequently called "deltas" (Δ) because they connect β-sheets and α-helices. Deltas are usually located at protein surface, and therefore mutations of their residues are more easily tolerated. Having more substitutions, insertions, and deletions in a certain region of a sequence alignment maybe an indication of some delta. The positions of introns in genomic DNA may correlate with the locations of loops in the encoded protein . Deltas also tend to have charged and polar amino acids and are frequently a component of active sites.
Protein classification
Proteins may be classified according to both structural and sequential similarity. For structural classification, the sizes and spatial arrangements of secondary structures described in the above paragraph are compared in known three-dimensional structures. Classification based on sequence similarity was historically the first to be used. Initially, similarity based on alignments of whole sequences was performed. Later, proteins were classified on the basis of the occurrence of conserved amino acid patterns. Databases that classify proteins by one or more of these schemes are available. In considering protein classification schemes, it is important to keep several observations in mind. First, two entirely different protein sequences from different evolutionary origins may fold into a similar structure. Conversely, the sequence of an ancient gene for a given structure may have diverged considerably in different species while at the same time maintaining the same basic structural features. Recognizing any remaining sequence similarity in such cases may be a very difficult task. Second, two proteins that share a significant degree of sequence similarity either with each other or with a third sequence also share an evolutionary origin and should share some structural features also. However, gene duplication and genetic rearrangements during evolution may give rise to new gene copies, which can then evolve into proteins with new function and structure.
Terms used for classifying protein structures and sequences The more commonly used terms for evolutionary and structural relationships among proteins are listed below. Many additional terms are used for various kinds of structural features found in proteins. Descriptions of such terms may be found at the CATH Web site, the Structural Classification of Proteins (SCOP) Web site, and a Glaxo Wellcome tutorial on the Swiss bioinformatics Expasy Web site.
Active site a localized combination of amino acid side groups within the tertiary (three-dimensional) or quaternary (protein subunit) structure that can interact with a chemically specific substrate and that provides the protein with biological activity. Proteins of very different amino acid sequences may fold into a structure that produces the same active site. Architecture is the relative orientations of secondary structures in a three-dimensional structure without regard to whether or not they share a similar loop structure. Fold (topology) a type of architecture that also has a conserved loop structure. Blocks is a conserved amino acid sequence pattern in a family of proteins. The pattern includes a series of possible matches at each position in the represented sequences, but there are not any inserted or deleted positions in the pattern or in the sequences. By way of contrast, sequence profiles are a type of scoring matrix that represents a similar set of patterns that includes insertions and deletions. Class a term used to classify protein domains according to their secondary structural content and organization. Four classes were originally recognized by Levitt and Chothia (1976), and several others have been added in the SCOP database. Three classes are given in the CATH database: mainly-α, mainly-β, and α–β, with the α–β class including both alternating α/β and α+β structures. Core the portion of a folded protein molecule that comprises the hydrophobic interior of α-helices and β-sheets. The compact structure brings together side groups of amino acids into close enough proximity so that they can interact. When comparing protein structures, as in the SCOP database, core is the region common to most of the structures that share a common fold or that are in the same superfamily. In structure prediction, core is sometimes defined as the arrangement of secondary structures that is likely to be conserved during evolutionary change. Domain (sequence context) a segment of a polypeptide chain that can fold into a three-dimensional structure irrespective of the presence of other segments of the chain. The separate domains of a given protein may interact extensively or may be joined only by a length of polypeptide chain. A protein with several domains may use these domains for functional interactions with different molecules.