Cross-Talk between Overlap Interactions in Biomolecules: A Case Study of the β-Turn Motif

Noncovalent interactions play a pivotal role in regulating protein conformation, stability and dynamics. Among the quantum mechanical (QM) overlap-based noncovalent interactions, n→π* is the best understood with studies ranging from small molecules to β-turns of model proteins such as GB1. However, these investigations do not explore the interplay between multiple overlap interactions in contributing to local structure and stability. In this work, we identify and characterize all noncovalent overlap interactions in the β-turn, an important secondary structural element that facilitates the folding of a polypeptide chain. Invoking a QM framework of natural bond orbitals, we demonstrate the role of several additional interactions such as n→σ* and π→π* that are energetically comparable to or larger than n→π*. We find that these interactions are sensitive to changes in the side chain of the residues in the β-turn of GB1, suggesting that the n→π* may not be the only component in dictating β-turn conformation and stability. Furthermore, a database search of n→σ* and π→π* in the PDB reveals that they are prevalent in most proteins and have significant interaction energies (∼1 kcal/mol). This indicates that all overlap interactions must be taken into account to obtain a comprehensive picture of their contributions to protein structure and energetics. Lastly, based on the extent of QM overlaps and interaction energies, we propose geometric criteria using which these additional interactions can be efficiently tracked in broad database searches.     

15-甲基-双环[10,3,0]十五碳-1(12)-烯-13-酮的晶体结构及分子稳定构象

15-甲基-双环[10,3,0]十五碳-1(12)-烯-13-酮的单晶属空间群P2_1/n,晶胞参数:a=0.4838(1)nm,b=1.3949(2)nm,c=2.1645(4)nm,β=92.07(1)°,Z=4.其中平面五员环呈刚性。另一个含烯十二员环的实际构象与分子力学计算的最稳定构象一致。     

Syntheses,Crystal Structures and Properties of the Tetrametaphosphimates MII2(PO2NH)4 · 8 H2O with MII = Mg,Mn, Co and Zn

Mg₂(PO₂NH)₄ · 8 H₂O ( 1 ), Mn₂(PO₂NH)₄ · 8 H₂O ( 2 ), Co₂(PO₂NH)₄ · 8 H₂O ( 3 ) and Zn₂(PO₂NH)₄ · 8 H₂O ( 4 ) were obtained as microcrystalline powders by combining aqueous solutions of K₄(PO₂NH)₄ · 4 H₂O and MX₂ · y H₂O (M = Mg, Mn, Co, Zn; X = Cl, NO₃). Single crystals were obtained by crystallization in gelatine gels in U‐tubes or test‐tubes. 2 and 4 were characterized by thermogravimetry and 4 was additionally characterized by temperature dependend in situ powder diffractometry. The structures of 1 , 2 , 3 and 4 were found to be isotypic and were solved by single‐crystal X‐ray methods: P 2₁/c, Z = 2 ( 1 : a = 645.4(2), b = 1050.1(2), c = 1283.3(3) pm, β = 104.66(3)°; 2 : a = 648.7(2), b = 1063.1(2), c = 1310.8(3) pm, β = 103.93(3)°; 3 : a = 643.3(2), b = 1049.0(2), c = 1286.7(3) pm, β = 104.28(3)°; 4 : a = 644.18(5), b = 1049.22(7), c = 1282.43(8) pm, β = 104.122(6)°). The structure is composed of MO₆ octahedra and (PO₂NH)₄^4— anions. The P₄N₄ rings of the (PO₂NH)₄^4— anions exhibit a slightly distorted chair conformation, which is supported by IR data and has been described by torsion angles, Displacement Asymmetry Parameters and Puckering Parameters. Via M²⁺ ions and hydrogen bonds, the tetrametaphosphimate anions are connected forming layers perpendicular to [100]. These layers are connected by hydrogen bonds.     

Stabilization of a high energy molecular conformation by specific intermolecular forces, a novel planar benzylideneaniline system

The system containing six benzylideneanilines (BA) has been studied: Group 1:

Study of the Properties of Electrodeposited Polypyrrole Films

Experimental and theoretical methods have been used for characterization of the properties of polypyrrole films. The AFM studies show that the morphology of polypyrrole (PPy) films on polycrystalline gold electrodes at the first stages of synthesis depends on the structure of the metal surface. It was established that mobility of anions depends remarkably on the rate of electrodeposition of the polymer film. If PPy film was deposited at relatively low current density, mobility of ClO^- ₄ anion was not high enough to guarantee electroneutrality during redox cycling and cations take part in this process especially when Li⁺ cations were replaced by more mobile ⁺ cations. Semiempirical (AM1 and PM3) quantum-chemical methods were used for theoretical studies. It was established that different size and charge of the anions together with the variation in doping levels give rise to a different optimal conformation of oligopyrrole cations which, in turn, define the resulting polymer to be either all-anti (common linear chains) or all-syn (formation of helical structures) or a combination of the two.     

Nucleation of β-hairpin structure in a pyrrole amino acid containing peptide

Synthesis and conformational studies of two short peptides containing pyrrole amino acids (1, Paa), Boc-Paa-Paa-d-Pro-Gly-Xaa-Paa-Paa-OMe (2: Xaa=Ala; 3: Xaa=Val), were carried out in which it was established that replacement of Ala in 2 with a Val residue helps peptide 3 to adopt a well-defined β-hairpin conformation in a nonpolar solvent, like CDCl₃.     

Synthesis of an unsymmetrically doubly bridged calix[4]arene in the 1,3-alternate conformation

We report the synthesis of the first calix[4]arene constrained to a 1,3-alternate conformation by one crown ether and one di-aza-benzo crown ether bridgings. Preliminary binding properties are also given.     

Characteristic lengths and the structure of salt free polyelectrolyte solutions. A small angle neutron scattering study

We have studied salt free semi dilute polyelectrolyte solutions by small angle neutron scattering. Specific labelling associated with an extrapolation method has allowed the separation of the form factor of a single polyelectrolyte chainS ₁(q) and the structure factorS ₂(q). Two lengths are deduced from these two factors: the persistence lengthb _t which characterizes the electrostatic interactions along the chain by a fitting ofS ₁(q) with calculation of the scattering function for a wormlike chain, and fromS ₂(q),q _m ^–1 which characterizes the interactions between chains. These two lengths vary in the same way with the concentration of polyions (b _t C _p ^–1/2 ,q _m ^–1 C _p ^–1/2 ) and a constant relation exists between them: only one length is then necessary to describe the structure of polyelectrolyte soltuion on this semidilute concentration range.Laboratoire Commun CEA-CNRS.     

PREPARATION OF PERFLUOROOCTANOYL-MODIFIED POLY(VINYL-ALCOHOL)S AND THEIR ADSORPTION AT AN AIR-WATER INTERFACE

Perfluorooctanoyl modified poly(vinyl alcohol)s (FPVA) were prepared by means of substituting a small amountof hydroxyl groups on the backbone of poly(vinyl alcohol), for which the initial degree of polymerization is equal to 1750.The substitution extent, defined by the number of substituting units in a chain, for the four FPVA samples was in the range of0.5-5 perfluorooctanoyl groups per chain. The FPVA samples with the highest substitution extent still had good solubility inwater. It was shown by experimental measurement at 30.0±0.1℃ that the surface tension of the aqueous solution of thehighest substituted FPVA decreased to 16.6 mN/In at a higher concentration, e.g about 0.1 g/mL. Obviously,macromolecules of FPVA exhibit a very strong tendency to adsorb at the air-water interface, because the hydrophobicperfluorooctanoyl groups in FPVA have a very high surface activity as they are in small molecular fluorinated surfactants.The chain conformation of such a model polymer adsorbed on the air-water interface was also discussed.     

Conformation of poly(L-glutamic acid) in aqueous solutions of linear amphiphiles with a cationic group at both ends

The conformations of poly(l-glutamic acid) [P(Glu)] in solutions of the bipolar amphiphile 1,20-icosanediylbis(alkylammonium chloride) [C20(RA)₂], where RA includes trimethylammonium (TMA), dimethylammonium (DMA), or methylammonium (MA), were investigated with measurements of the circular dichroism spectra at 10–35 °C. All C20(RA)₂ induced an α-helix of P(Glu) in the aqueous solutions. The residue molar ellipticity at 222 nm showed a similar dependence on the amphiphile concentration (C _s) below 0.5 of the ratio of 2C _s to the residue concentration (C _p) of P(Glu), but it separated into three directions at 2C _s/C _p>0.5. C20(MA)₂ induced an α-helix of P(Glu) at 2C _s/C _p<0.5 followed by a helix aggregate at 2C _s/C _p>0.5. C20(DMA)₂ and C20(TMA)₂ also induced an α-helix, but a helix aggregate. C20(TMA)₂ indicated a strong temperature dependence and did not induce a complete α-helix at 35 °C. Received: 20 June 2001 Accepted: 6 September 2001