*Loops - Protein StructureDr.SatyavaniIIITA

*Different Levels of Protein StructuresThe primary structure is the sequence of residues in the polypeptide chain.Secondary structure is a local regularly occurring structure in proteins.Alpha helicesBeta sheetsLoops (Coils, Turns)

*Loops of Protein StructuresMost protein structures are built up from Alpha helices and beta strands which are connected by loop regions.

*Loops exhibit greater structural variability than Beta-sheets and Alpha helices.Loop structure therefore is considerably more difficult to predict than the structure of the geometrically highly regular Beta-sheets and Alpha helices.Loops are often exposed to the surface of proteins and contribute to active and binding sites. Consequently, loops are crucial for protein function.

A combination of secondary structure elements forms the stable hydrophobic core of the molecule.The loop regions are at the surface of the molecule.The main Chain C-O and N-H groups of the loop regions, which do not form hydrogen bonds to each other.*

The loop regions are exposed to the solvent and can form hydrogen bonds to water molecules.Loop regions exposed to solvents are rich in charged and polar hydrophilic residues.*

This has been used in several predictions schemes, and it has proved possible to predict loop regions from an amino acid sequence with high degree of confidence than alpha helices or beta sheets, which is ironic since loops have irregular shapes.*

When homologous amino acid sequences from different species are compared, it is found that insertions and deletions of a few residues occur almost exclusively in the loop regions.During evolution cores are much more stable than loops.*

Intron positions are also often found at sites in structural genes that correspond to loop regions in the protein structure.

Since proteins that exhibit sequence homology in general have similar core structures, it is apparent that the specific arrangement of secondary structure elements in the core is rather insensitive to the lengths of the loop regions. *

In addition to their function as connecting units between secondary structure elements, loop regions frequently participate in forming binding sites and enzyme active sites. Thus antigen binding sites in antibodies are built up from six loop regions, which vary in both in length and in amino acid sequence between different antibodies

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Modelling antigen binding site from a known antibody sequence is thus essentially a problem of modelling three-Dimensional structures of loop regions since the core structures of all antibodies are very similar. *

Such model building has been facilitated by the recent findings that loop regions have preferred structures.Surveys of known 3-D structures of loops have shown that they fall into a rather limited set of structures and are not a random collection of possible structures.*

Loop regions that connect two adjacent antiparallel beta strands are called hairpin loops.Short hairpin loops are usually called reverse turns or simply turns. *

Long loop regions are often flexible and can frequently adopt several different conformations, making them invisible in X-Ray structure determinations and undetermined in NMR studies.Such loops are frequently involved in in the function of the protein and can switch from an open confirmation. *

which allows access to the active site, to the closed confirmation, which sheilds reactive groups in the active site from water.Long loops are in many cases susceptable to proteolytic degradation.

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One specific type of long loop, the omega loop, is compact with good internal packing interactions and is therefor quite stable.Other long loops, which by themselves would be attacked by proteolytic enzymes, are stabilized and protected by binding metal ions, especially calcium.*

TurnsTurns are the third of the three "classical" secondary structures. Approximately one-third of all residues in globular proteins are contained in turns that serve to reverse the direction of the polypeptide chain. This is perhaps not so surprising since the diameter of the average globular protein domain is roughly 25 (an extended polypeptide conformation would require ~7 residues to traverse the domain before having to change directions).

Turns are located primarily on the protein surface and accordingly contain polar and charged residues. Antibody recognition, phosphorylation, glycosylation, hydroxylation, and intron/exon splicing are found frequently at or adjacent to turns.

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Gamma TurnThe hydrogen bond between CO of residue i and NH of residue i+2. The dihedral angles of residue i+1 are (70, -60) and (-70, 60) for phi and psi of the classical and inverse gamma turns.

Type I Turn.The hydrogen bond between CO of residue i and NH of residue i+3.The backbone dihedral angles are (-60, -30) and (-90, 0) of residues i+1 and i+2, respectively, for the type I turn. Proline is often found in position i+1 in type I turns as its phi angle is restricted to -60 and its amide nitrogen does not require a hydrogen bond. Glycine is favored in this position in the type II' as it requires a positive (left-handed) phi value.

Type II Turn.The hydrogen bond between CO of residue i and NH of residue i+3. The backbone dihedral angles are (-60, 120) and (80, 0) of residues i+1 and i+2, respectively, for the type II turn.Glycine is favored in this position in the type II' as it requires a positive (left-handed) phi value.

Type III Turn.The hydrogen bond between CO of residue i and NH of residue i+3. This is a single turn of right-handed (III) and left-handed (III') 310 helix. The backbone dihedral angles are (-60, -30) and (-60, -30) of residues i+1 and i+2, respectively, for the classical type III turn.

Preferred Residues for b Sheet and TurnsEight most common residues for beta-sheet Val, Ile, Tyr, Trp,Phe, Leu, Cys, ThrEight least common residues for beta-sheet Glu, Asp, Pro, Ser,Lys, Gly, Ala, AsnEight most common residues for turnsGly, Asn, Pro, Asp,Ser, Cys, Tyr, LysEight least common residues for turnsIle, Val, Met, Leu, Phe, Ala, Glu, Trp

LoopsIn Leszczynski & Rose (1986), out of 67 proteins surveyed, they tabulated 26 % helix, 19% sheet, 26 % turns and 21 % in loops. These loop structures contain between 6 and 16 residues and are compact and globular in structure. Like turns, they generally contain polar residues and hence are predominantly at the protein surface.

b-hairpin LoopAdjacent antiparallel b strands are joined by hairpin loops. Such loops are frequently short and do not have regular secondary structure. Nevertheless, many loop regions in different proteins have similar structures.

Schematic Structural Diagrams of Myoglobin

Richardson DiagramsMyoglobinTriosephosphate isomeraseCylinder for a helices; arrows for b strands, which gives the direction of the strand from N to C; and the ribbons for the remaining part.

Beta Sheet Topology DiagramsBeta sheets are usually represented simply by arrows in topology diagrams that show both the direction of each strand and the way the strands are connected to each other along the polypeptide chain. transcarbamoylaseflavodoxinplastocyanin

Super Secondary Structures (Motifs)Simple combinations of a few secondary structure elements with a specific geometric arrangement are called super secondary structures or motifs.They may have functional and structural significance.Common motifs:Helix-turn-helix b-hairpin, b-meanderb-barrel, Geek keybab

Helix-Turn-Helix MotifTwo helices that are connected by a short loop region in a specific geometric arrangement constitute a helix-turn-helix motif. (a) the DNA-binding motif and (b) the calcium-binding motif, which are present in many proteins whose function is regulated by calcium.

EF-hand Calcium-binding MotifThe calcium atom is bound to one of the motifs in the muscle protein troponin-C through six oxygen atoms: one each from the side chains of Asp (D) 9, Asn (N) 11, and Asp (D) 13; one from the main chain of residue 15; and two from the side chain of Glu (E) 20. In addition, a water molecule (W) is bound to the calcium atom.

Amino Acid Sequences of EF-hand Motifs1 3 5 7 9 12 The side chains of hydrophobic residues on the flanking helices form a hydrophobic core between the a helices

The b Hairpin MotifThe hairpin motif is very frequent in b sheets and is built up from two adjacent b strands that are joined by a loop region. Bovine Trypsin InhibitorSnake Venom Erabutoxin

Greek Key MotifThe Greek key motif is found in antiparallel b sheets when four adjacent b strands are arranged in the pattern shown as a topology diagram in (a). The three dimensional structure of the enzyme Staphylococcus Nuclease shown in (b) in blue and red is also a Greek key motif.

b-a-b MotifTwo adjacent parallel b strands are usually connected by an a helix from the C-terminus of strand 1 to the N-terminus of strand 2.Most protein structures that contain parallel b sheets are built up from combinations of such b-a-b motifs.

b-a-b HandednessThe b-a-b motif can in principle have two "hands."(a) This connection with the helix above the sheet is found in almost all proteins and is called right-handed because it has the same hand as a right-handed a helix. (b) The left-handed connection with the helix below the sheet.

Domain OrganizationSmall protein molecules like the epidermal growth factor, EGF, are comprised of only one domain. Others, like the serine proteinase chymotrypsin, are arranged in two domains that are required to form a functional unit. Many of the proteins that are involved in blood coagulation and fibrinolysis have long polypeptide chains that comprise different combinations of domains.