C-H…O hydrogen bond mediated chain reversal in a peptide containing g-amino acid residue, determined directly from powder X-ray diffraction data

The finding that peptides containing -amino acid residues give rise to folding patterns hitherto unobserved in -amino acid peptides[1] has stimulated considerable interest in the conformational properties of peptides built from , and residues,[2] as the introduction of additional methylene (CH2) units into peptide chains provides further degrees of conformational freedom.

A C-H…O hydrogen bond stabilized polypeptide chain reversal motif at the C-terminus helices in proteins.

The serendipitous observation of a C–Hcdots, three dots, centeredO hydrogen bond mediated polypeptide chain reversal in synthetic peptide helices has led to a search for the occurrence of a similar motif in protein structures. From a dataset of 634 proteins, 1304 helices terminating in a Schellman motif have been examined. The C–Hcdots, three dots, centeredO interaction between the T−4 CαH and T+1 C=O group (Ccdots, three dots, centeredO≤3.5 Å) becomes possible only when the T+1 residue adopts an extended β conformation (T is defined as the helix terminating residue adopting an αL conformation). In all, 111 examples of this chain reversal motif have been identified and the compositional and conformational preferences at positions T−4, T, and T+1 determined. A marked preference for residues like Ser, Glu and Gln is observed at T−4 position with the motif being further stabilized by the formation of a side-chain–backbone Ocdots, three dots, centeredH–N hydrogen bond involving the side-chain of residue T−4 and the N–H group of residue T+3. In as many as 57 examples, the segment following the helix was extended with three to four successive residues in β conformation. In a majority of these cases, the succeeding β strand lies approximately antiparallel with the helix, suggesting that the backbone C–Hcdots, three dots, centeredO interactions may provide a means of registering helices and strands in an antiparallel orientation. Two examples were identified in which extended registry was detected with two sets of C–Hcdots, three dots, centeredO hydrogen bonds between (T−4) CαHcdots, three dots, centeredC=O (T+1) and (T−8) CαHcdots, three dots, centeredC=O (T+3).

Probing the role of the C-H center dot center dot center dot O hydrogen bond stabilized polypeptide chain reversal at the C-terminus of designed peptide helices. Structural characterization of three decapeptides

The structural characterization in crystals of three designed decapeptides containing a double D-segment at the C-terminus is described. The crystal structures of the peptides Boc-Leu-Aib-Val-Xxx-Leu-Aib-Val- (D)Ala-(D)Leu-Aib-OMe, (Xxx = Gly 2, (D)Ala 3, Aib 4) have been determined and compared with those reported earlier for peptide 1 (Xxx = Ala) and the all L analogue Boc-Leu-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-OMe, which yielded a perfect right-handed a-helical structure. Peptides 1 and 2 reveal a right-handed helical segment spanning residues 1 to 7, ending in a Schellman motif with Ala(8) functioning as the terminating residue. Polypeptide chain reversal occurs at residue 9, a novel feature that appears to be the consequence of a C-(HO)-O-... hydrogen bond between residue 4 (CH)-H-alpha and residue 9 CO groups. The structures of peptides 3 and 4, which lack the pro R hydrogen at the C-alpha atom of residue 4, are dramatically different. Peptide 3 adopts a right-handed helical conformation over the 1 to 7 segment. Residues 8 and 9 adopt at conformations forming a C-terminus type I' beta-turn, corresponding to an incipient left-handed twist of the polypeptide chain. In peptide 4, helix termination occurs at Aib(6), with residues 6 to 9 forming a left-handed helix, resulting in a structure that accommodates direct fusion of two helical segments of opposite twist. Peptides 3 and 4 provide examples of chiral residues occurring in the less favored sense of helical twist; (D)Ala(4) in peptide 3 adopts an alpha(R) conformation, while (L)Val(7) in 4 adopts an alpha(L) conformation. The structural comparison of the decapeptides reported here provides evidence for the role of specific C-(HO)-O-... hydrogen bonds in stabilizing chain reversals at helix termini, which may be relevant in aligning contiguous helical and strand segments in polypeptide structures.

Conformational studies of the triphenylphosphazenyl side chain in cyclophosphazenes. I. Crystal and molecular structure of N3P3C15(NPPh3)

The title compound, C t8H~sC15NaP4, crystallizes in the monoclinic space group P2~/n with a = 20.14 (2), b = 8.69 (1), c = 14.92 (2) A, fl = 98.8 (3) ° , Z = 4. The structure was determined from visual data and refined to R = 0-069 for 1450 reflections. The cyclophosphazene ring is non-planar. The exocyclic NPPh 3 group exhibits type I conformation [R. A. Shaw (1975). Pure Appl. Chem. 44, 317-341] in which the N-P bond is perpendicular to the adjacent P-CI bond.

Analysis of side-chain conformation in proteins

The crystal structures of a number of globular proteins are currently available. An analysis of the distribution of side-chains among different allowed conformations in these proteins has been carried out. The observed conformations of individual residues are discussed on the basis of well-known stereochemical criteria. The population distribution of side-chains in different allowed regions in conformational space can be explained largely on the basis of simple steric considerations. In addition to examining the conformational behaviour of individual residues, some population distributions of conformational angles of general interest involving groups of residues have also been analyzed.

Covalent attachment of two important dicopper(II) systems in a one-dimensional polymeric chain: An x-ray structure of [Cu2(en)2(OH)2·Cu2(O2CMe)4](PF6)2·0.5EtOH]α showing the shortest Cucdots, three dots, centeredCu Distance in the tetraacetato core

Reaction of Cu2(O2CMe)4(H2O)2 with 1,2-diaminoethane(en) in ethanol, followed by the addition of NH4PF6, led to the formation of a covalently linked 1D polymeric copper(II) title complex showing alternating [Cu2(en)2(OH)22+] and [Cu2(O2CMe)4] units in the chain and the shortest Cucdots, three dots, centeredCu separation of 2.558(2) Å in the tetraacetato core.

The top 100 questions of importance to the future of global agriculture

Despite a significant growth in food production over the past half-century, one of the most important challenges facing society today is how to feed an expected population of some nine billion by the middle of the 20th century. To meet the expected demand for food without significant increases in prices, it has been estimated that we need to produce 70-100 per cent more food, in light of the growing impacts of climate change, concerns over energy security, regional dietary shifts and the Millennium Development target of halving world poverty and hunger by 2015. The goal for the agricultural sector is no longer simply to maximize productivity, but to optimize across a far more complex landscape of production, rural development, environmental, social justice and food consumption outcomes. However, there remain significant challenges to developing national and international policies that support the wide emergence of more sustainable forms of land use and efficient agricultural production. The lack of information flow between scientists, practitioners and policy makers is known to exacerbate the difficulties, despite increased emphasis upon evidence-based policy. In this paper, we seek to improve dialogue and understanding between agricultural research and policy by identifying the 100 most important questions for global agriculture. These have been compiled using a horizon-scanning approach with leading experts and representatives of major agricultural organizations worldwide. The aim is to use sound scientific evidence to inform decision making and guide policy makers in the future direction of agricultural research priorities and policy support. If addressed, we anticipate that these questions will have a significant impact on global agricultural practices worldwide, while improving the synergy between agricultural policy, practice and research. This research forms part of the UK Government's Foresight Global Food and Farming Futures project.

Global solutions describing the collapse of a spherical or cylindrical cavity

The collapse of a spherical (cylindrical) cavity in air is studied analytically. The global solution for the entire domain between the sound front, separating the undisturbed and the disturbed gas, and the vacuum front is constructed in the form of infinite series in time with coefficients depending on an ldquoappropriaterdquo similarity variable. At timet=0+, the exact planar solution for a uniformly moving cavity is assumed to hold. The global analytic solution of this initial boundary value problem is found until the collapse time (=(gamma–1)/2) for gamma le 1+(2/(1+v)), wherev=1 for cylindrical geometry, andv=2 for spherical geometry. For higher values of gamma, the solution series diverge at timet — 2(beta–1)/ (v(1+beta)+(1–beta)2) where beta=2/(gamma–1). A close agreement is found in the prediction of qualitative features of analytic solution and numerical results of Thomaset al. [1].

Barrier crossing in one and three dimensions by a long chain

We consider the Kramers problem for a long chain polymer trapped in a biased double-well potential. Initially the polymer is in the less stable well and it can escape from this well to the other well by the motion of its N beads across the barrier to attain the configuration having lower free energy. In one dimension we simulate the crossing and show that the results are in agreement with the kink mechanism suggested earlier. In three dimensions, it has not been possible to get an analytical `kink solution' for an arbitrary potential; however, one can assume the form of the solution of the nonlinear equation as a kink solution and then find a double-well potential in three dimensions. To verify the kink mechanism, simulations of the dynamics of a discrete Rouse polymer model in a double well in three dimensions are carried out. We find that the time of crossing is proportional to the chain length, which is in agreement with the results for the kink mechanism. The shape of the kink solution is also in agreement with the analytical solution in both one and three dimensions.

Connectionist approach for global optimization

A connectionist approach for global optimization is proposed. The standard function set is tested. Results obtained, in the case of large scale problems, indicate excellent scalability of the proposed approach

Double Aromaticity in the 3,5-Dehydrophenyl Cation and in Cyclo[6]carbon

The presence of two (4n+2)-electron conjugated systems in perpendicular planes results in considerable aromatic stabilization. Despite having two fewer hydrogens, the 6 pi e-2 sigma e 3,5-dehydrophenyl cation (C6H3+, 1) is 32.7 (CCSD(T)/6-31G**) and 35.2 kcal/mol (RMP4sdtq/6-3iG*//RMP2(fu)/6-31G*) more stable than the phenyl cation (evaluated by an isodesmic reaction involving benzene and m-dehydrobenzene (4)). Cation 1, the global C6H3+ minimum, is 11.7,24.2, 11.8, and 30.4 kcal/mol lower in energy than the 2,6- (11) and 3,4-dehydrophenyl (12) cations as well as the open-chain isomers 13 and 14 (RMP4sdtq/6-31G*//RMP2(fu)/6-31G* + ZPE(RMP2(fu)/6-31G*)). The stability of 1 is increased hyperconjugatively by 2,4,6-trisilyl substitution. The double aromaticity of 1 is indicated by the computed magnetic susceptibility exaltations (IGLO/II//RMP2(fu)/6-31G*) of -5.2, -6.8, -15, and -23.2 relative to 11, 12, 13, and 14, respectively. Thus, 1 fulfills the geometric, energetic, and magnetic criteria of aromaticity. The double aromaticity of the D-6h cyclo[6]carbon is apparent from the same criteria

Protonation and deprotonation induced organo/hydrogelation: Bile acid derived gelators containing a basic side chain

Two bile acid derived molecules containing basic amino groups are reported to be efficient and unusual gelators of organic and aqueous solvents.

Why is there a short-term increase in global precipitation in response to diminished CO2 forcing?

Recently, it was found that a reduction in atmospheric CO2 concentration leads to a temporary increase in global precipitation. We use the Hadley Center coupled atmosphere-ocean model, HadCM3L, to demonstrate that this precipitation increase is a consequence of precipitation sensitivity to changes in atmospheric CO2 concentrations through fast tropospheric adjustment processes. Slow ocean cooling explains the longer-term decrease in precipitation. Increased CO2 tends to suppress evaporation/precipitation whereas increased temperatures tend to increase evaporation/precipitation. When the enhanced CO2 forcing is removed, global precipitation increases temporarily, but this increase is not observed when a similar negative radiative forcing is applied as a reduction of solar intensity. Therefore, transient precipitation increase following a reduction in CO2-radiative forcing is a consequence of the specific character of CO2 forcing and is not a general feature associated with decreases in radiative forcing. Citation: Cao, L., G. Bala, and K. Caldeira (2011), Why is there a short-term increase in global precipitation in response to diminished CO2 forcing?, Geophys. Res. Lett., 38, L06703, doi:10.1029/2011GL046713.