Parallel fold

Concentric (parallel) folds—rock formations parallel to each other such that their respective thicknesses remain constant (see Figure 2-43). 

It is evident from the ductility and strength of polymers that the ties between lamellae must be stronger than the van der Waal s forces holding neighboring, parallel fold planes together. Evidently some molecules (tie molecules) must participate in the growth of two or more adjacent lamellae, thereby providing relatively short molecular links between the lamellae. 

Figure 1 CD spectra for sequences with loop lengths varying. Samples with loops of length 1 or 2 exhibit a peak at 265 nm characteristic of parallel folds (length 2 possibly being polymorphic) the other sequences have a peak at 295 nm, characteristic of anti-parallel folding...

There is also a need for further base-line studies to support this physiological work. Although there are now some algorithms to identify PQS, none of these are very well developed, and further work is required to refine them. It would be valuable to have a model that could predict both the structure (especially antiparallel V5. parallel folds) and the thermodynamic stability of sequences, in the manner currently possible for duplex DNA. This goal will require more detailed analysis of the role of the sequences, and hence a significant extension of the analysis to date. Another issue is that, to date, almost every biophysical study has looked at G-quadruplex formation from a single strand of DNA. There is a need to better understand the equilibrium between quadruplex and duplex structures in a more native context. 

Parallel or concentric folds are those where the strata have been bent into more or less parallel curves in which the thickness of the individual beds remains the same. From Figure 2.5a, it can be observed that, because the thickness of the beds remains the same on folding, the shape of the folds changes with depth and, in fact, they fade out. Parallel folding occurs in competent (relatively strong) beds that may be interbedded with incompetent (relatively weak, plastic) strata. 

Determination of the Structures of Distinct Transition State Ensembles for a Beta-sheet Peptide with Parallel Folding Pathways. 

A ligand such as ethylenediamine is not planar and has a spiral form (gauche) giving rise to further forms. When the direction of one C—C bond in one ethylenediamine is parallel to the 3-fold axis the isomer is termed the le( form, when it is inclined to the axis it is termed the ob form. 

Axes of symmetry. An axis about which rotation of the body through an angle of 2njn (where n is an integer) gives an identical pattern 2-fold, 3-fold, 4-fold and 6-fold axes are known in crystals 5-fold axes are known in molecules. In a lattice the rotation may be accompanied by a lateral movement parallel to the axis (screw axis). 

Figure 2.11 Beta sheets are usuaiiy represented simply by arrows in topology diagrams that show both the direction of each (3 strand and the way the strands are connected to each other along the polypeptide chain. Such topology diagrams are here compared with more elaborate schematic diagrams for different types of (3 sheets, (a) Four strands. Antiparallel (3 sheet in one domain of the enzyme aspartate transcarbamoylase. The structure of this enzyme has been determined to 2.8 A resolution in the laboratory of William Lipscomb, Harvard University, (b) Five strands. Parallel (3 sheet in the redox protein flavodoxin, the structure of which has been determined to 1.8 A resolution in the laboratory of Martha Ludwig, University of Michigan, (c) Eight strands. Antiparallel barrel in the electron carrier plastocyanln. This Is a closed barrel where the sheet is folded such that (3 strands 2 and 8 are adjacent. The structure has been determined to 1.6 A resolution in the laboratory of Hans Freeman in Sydney, Australia. (Adapted from J. Richardson.)...

Polypeptide chains are folded into one or several discrete units, domains, which are the fundamental functional and three-dimensional structural units. The cores of domains are built up from combinations of small motifs of secondary structure, such as a-loop-a, P-loop-p, or p-a-p motifs. Domains are classified into three main structural groups a structures, where the core is built up exclusively from a helices p structures, which comprise antiparallel p sheets and a/p structures, where combinations of p-a-P motifs form a predominantly parallel p sheet surrounded by a helices. 

The most frequent of the domain structures are the alpha/beta (a/P) domains, which consist of a central parallel or mixed P sheet surrounded by a helices. All the glycolytic enzymes are a/p structures as are many other enzymes as well as proteins that bind and transport metabolites. In a/p domains, binding crevices are formed by loop regions. These regions do not contribute to the structural stability of the fold but participate in binding and catalytic action. 

Figure 4.2 A p-a-p motif is a right-handed structure. Two such motifs can be joined into a four-stranded parallel p sheet in two different ways. They can be aligned with the a helices either on the same side of the p sheet (a) or on opposite sides (b). In case (a) the last p strand of motif I (red) is adjacent to the first p strand of motif 2 (blue), giving the strand order 1 2 3 4. The motifs are aligned in this way in barrel structures (see Figure 4.1a) and in the horseshoe fold (see Figure 4.11). In case (b) the first p strands of both motifs are adjacent, giving the strand order 4 3 12. Open twisted sheets (see Figure 4.1b) contain at least one motif alignment of this kind. In both cases the motifs ate joined by an ct helix (green).

The a/p-barrel structure is one of the largest and most regular of all domain structures, comprising about 250 amino acids. It has so far been found in more than 20 different proteins, with completely different amino acid sequences and different functions. They are all enzymes that are modeled on this common scaffold of eight parallel p strands surrounded by eight a helices. They all have their active sites in very similar positions, at the bottom of a funnel-shaped pocket created by the loops that connect the carboxy end of the p strands with the amino end of the a helices. The specific enzymatic activity is, in each case, determined by the lengths and amino acid sequences of these loop regions which do not contribute to the stability of the fold. 

Parallel p-helix domains have a novel fold... 

In addition to the antiparallel p-structures, there is a novel fold called the P helix. In the p-helix structures the polypeptide chain is folded into a wide helix with two or three p strands for each turn. The p strands align to form either two or three parallel p sheets with a core between the sheets completely filled with side chains. 

Jurnak, E, et al. Parallel p domains a new fold in protein structures. Curr. Opin. Struct. Biol. 4 802-806, 1994. 

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