PP hairpin

High resolution X-ray analysis of protein structures shows that the conformational categories of the connecting peptides which link the a-helices and -sheets are limited. Such well defined types of folding units, such as aa- and PP-hairpins, and aP- and Pa-arches, are referred to as supersecondary structures. One important step towards building a tertiary structure from secondary structures is to identify these supersecondary structure... 

Hairpin p motif, also called pp hairpin, which consists of two sequential antiparallel P-strands connected by a tight reverse turn. This motif changes the direction of antiparallel P-sheet structures. 

Forward and Reverse Work Distributions Cross at W = AG. In order to obtain AG we can measure the forward and reverse work distributions, Pp(W) and Pr(—W), and look at the work value W where they cross, P-p W ) =Rr(—W ). According to Eq. (41), both distributions should cross at W = AG independently of how far the system is driven out of equilibrium (i.e., independently of the pulling speed). Figure 9 shows experiments on a short canonical RNA hairpin CD4 (i.e., just containing Watson-Crick complementary base pairs) at three different pulling speeds, which agree very well with the FT prediction. 

The sequences of all three pieces of RNA in the E. coli ribosomes are known as are those from many other species. These include eukaryotic mitochondrial, plas-tid, and cytosolic rRNA. From the sequences alone, it was clear that these long molecules could fold into a complex series of hairpin loops resembling those in tRNA. For example, the 16S rRNA of E. coli can fold as in Fig. 29-2A and eukaryotic 18S RNA in a similar way (Fig. 29-4).38/39/67 69 The actual secondary structures of 16S and 18S RNAs, within the folded molecules revealed by X-ray crystallography, are very similar to that shown in Fig. 29-2A. Ribosomal RNAs undergo many posttranscriptional alterations. Methylation of 2 -hydroxyls and of the nucleic acid bases as well as conversion to pseudouridines (pp. 1638-1641) predominate over 200 modifications, principally in functionally important locations that have been found in human rRNA.69a... 

P R E CONTENTS Preface. Stable-Isotope Assisted Protein NMR Spectroscopy in Solution, Brian J. Stockman and John L. Mar-kley. 31P and 1H Two-Dimensional NMR and NOESY-Dis-tance Restrained Molecular Dynamics Methodologies for Defining Sequence-Specific Variations in Duplex Oligonucleotides, David G. Gorenstein, Robert P. Meadows, James T. Metz, Edward Nikonowcz and Carol Beth Post. NMR Study of B- and Z-DNA Hairpins of d[(CG) 3T4(CG)3] in Solution, Sa-toshi Ikuta and Yu-Sen Wang. Molecular Dynamics Simulations of Carbohydrate Molecules, J.W. Brady. Diversity in the Structure of Hemes, Russell Timkovich and Laureano L. Bon-doc. Index. Volume 2,1991, 180 pp. 112.50/E72.50 ISBN 1-55938-396-8... 

R. H. Zhou, B. J. Berne (2002) Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water P. Natl. Acad. Sci. USA 99, pp. 12777-12782... 

V. S. Pande, D. S. Rokhsar (1999) Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. P. Natl. Acad. Sci. USA 96, pp. 9062-9067... 

P. G. Bolhuis (2005) Kinetic pathways of beta-hairpin (un)folding in explicit solvent. Biophys. J. 88, pp. 50-61... 

N. Singhal, C. D. Snow, V. S. Pande (2004) Using path sampling to build better markovian state models Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. J. Chem. Phys. 121, pp. 415-425... 

V. Munoz, R A. Thompson, J. Hofrichter, W. A. Eaton (1997) Folding dynamics and mechanism of beta-hairpin formation. Nature 390, pp. 196-199... 

A. Kolinski, B. Ilkowski, J. Skolnick (1999) Dynamics and thermodynamics of beta-hairpin assembly Insights from various simulation techniques. Biophys. J. 77, pp. 2942-2952... 

G. H. Wei, P. Derreumaux, N. Mousseau (2004) Complex folding pathways in a simple beta-hairpin. Prot. Struct. Func. Bio. 56, pp. 464-474... 

B. Zagrovic, E. Sorin, V. S. Pande (2001) Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. J. Mol. Biol. 313, pp. 151-169... 

B. Y. Ma, R. Nussinov (2000) Molecular dynamics simulations of a beta-hairpin fragment of protein G Balance between side-chain and backbone forces. J. Mol. Biol. 296, pp. 1091-1104... 

A. E. Garcia, K. Y. Sanbonmatsu (2001) Exploring the energy landscape of a beta hairpin in explicit solvent. Proteins 42, pp. 345-354... 

J. Tsai, M. Levitt (2002) Evidence of turn and salt bridge contributions to beta-hairpin stability MD simulations of C-terminal fragment from the B1 domain of protein G. Biophys. Ghem. 101, pp. 187-201... 

G. P. Purohit, Thermal and hydraulic design of hairpin and finned-bundle exchangers, Chemical Engineering, May 16,1983, pp. 62-70. 

The pp and paP motifs are commonly used to connect antiparallel and parallel /3-strands, respectively. The PP motif is frequently connected by a hairpin turn, which provides a compact way of changing the direction of the polypeptide chain. In the same way, the Pap motif provides a compact module where the width of the a-helix is similar to that of the combined width of the two /3-strands. It also provides a hydrophobic core. The dimensions of the Pap motif explain why large parallel sheets that are built with this motif always have a-helices on both sides since there is insufficient space on one side of a sheet to accommodate all of the connecting helices. 

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