A semi-analytical description of protein folding that incorporates detailed geometrical information

Much has been done to study the interplay between geometric and energetic effects on the protein folding energy landscape. Numerical techniques such as molecular dynamics simulations are able to maintain a precise geometrical representation of the protein. Analytical approaches, however, often focus on the energetic aspects of folding, including geometrical information only in an average way. Here, we investigate a semi-analytical expression of folding that explicitly includes geometrical effects. We consider a Hamiltonian corresponding to a Gaussian filament with structure-based interactions. The model captures local features of protein folding often averaged over by mean-field theories, for example, loop contact formation and excluded volume. We explore the thermodynamics and folding mechanisms of beta-hairpin and alpha-helical structures as functions of temperature and Q, the fraction of native contacts formed. Excluded volume is shown to be an important component of a protein Hamiltonian, since it both dominates the cooperativity of the folding transition and alters folding mechanisms. Understanding geometrical effects in analytical formulae will help illuminate the consequences of the approximations required for the study of larger proteins.     

Noncovalent interaction-driven stereoselectivity of copper(II) complexes with cyclodextrin derivatives of L- and D-carnosine

L-Carnosine (β-alanyl-L-histidine, LCar) is the most widely and abundantly distributed copper(II)-coordinating endogenous dipeptide. Though its physiological role has not been completely understood yet, many functions have been proposed for this compound. LCar might be crucial in the potential reduction or prevention of several pathologies in which the metal ions are thought to be involved. The potential therapeutic applications of LCar are drastically limited because of hydrolysis by specific dipeptidases (carnosinases). D-Carnosine (DCar), the enantiomer of the naturally occurring dipeptide, shows the same properties as those of LCar, but it is not hydrolyzed by carnosinases. Chemical modification of LCar has been proposed as a promising strategy to reduce its enzymatic hydrolysis; conjugation of a carbohydrate moiety may also improve site-specific transport to different tissues, which would enhance the peptide bioavailability. On this basis, we have functionalized DCar with β-cyclodextrin (CDDCar) and characterized the compound via NMR. The copper(II) binding properties of the new DCar derivative were investigated by spectroscopic techniques (UV-vis, circular dichroism, electron paramagnetic resonance) and potentiometric measurements. The results surprisingly revealed a pronounced difference from the analogous LCar derivative (CDLCar), especially concerning the dimeric species. The spectroscopic data show that this stereoselectivity is driven by noncovalent interactions, namely, hydrogen bonds, CH-π interactions, and steric and hydrophobic effects of the cyclodextrin cavity.     

Isomerization dynamics of the 2-phenylazo-1,3-dimethylimidazolium cation photoexcited to the S2 (π, π*) state as studied by transient absorption spectroscopy in the time domain of 10(-13) to 10(3) seconds

Photoinduced isomerization of a novel photochromic cation, [2PA-Mmim](+) (2-phenylazo-1,3-dimethylimidazolium cation), was studied by optical spectroscopic methods. The UV-Vis absorption spectra of the [2PA-Mmim](+) cation show two prominent bands starting around 410 and 520 nm, corresponding to the S(0)-S(2) (π, π*) and S(0)-S(1) (n, π*) transitions, respectively. The photoisomerization mechanism is studied by femtosecond time-resolved transient absorption experiments performed after S(0)-S(2) (π, π*) excitation in several solvents with different viscosity, including ionic liquids. The transient absorption signals at two representative wavelengths were fitted by bi-exponential functions, which yield four decay components. The photoisomerization mechanism is discussed in light of the relaxation schemes available for azobenzene. Only one of the components depends on the solvent viscosity and it changes from 1.2 ps (dichloromethane, 0.4 cP) to 5.6 ps ([Bmim][BF(4)], 93 cP). This component is assigned to a molecule at the S(1) state, which is responsible for the "rotational" isomerization. The weak dependence on the solvent viscosity of this component is explained in terms of local change in the viscosity as a result of local heating due to excess energy released at S(2)-S(1) internal conversion. The other three components of ～0.4, 1.0 and 10 ps are attributed to relaxation processes of the molecule at S(2), S(1) and S(0) states, respectively. The quantum yields for the forward E-Z photoisomerization are ～0.15 after S(2) excitation. The backward Z-E isomerization is slow with a lifetime of 1 hour and an activation energy of 91 kJ mol(-1) through an "inversion" mechanism.     

Control of the Solid‐State Chiral Optical Properties of a Supramolecular Organic Fluorophore Containing 4‐(2‐Arylethynyl)‐Benzoic Acid

The solid‐state chiral optical properties of a 4‐(2‐arylethynyl)‐benzoic acid/amine supramolecular organic fluorophore can be controlled by changing the arylethynyl group of the achiral 4‐(2‐arylethynyl)‐benzoic acid component molecule rather than the chirality of the amine component molecule.     

Thermochemistry of Alane Complexes for Hydrogen Storage: A Theoretical and Experimental Investigation

Knowledge of the relative stabilities of alane (AlH(3)) complexes with electron donors is essential for identifying hydrogen storage materials for vehicular applications that can be regenerated by off-board methods; however, almost no thermodynamic data are available to make this assessment. To fill this gap, we employed the G4(MP2) method to determine heats of formation, entropies, and Gibbs free energies of formation for 38 alane complexes with NH(3-n)R(n) (R = Me, Et; n = 0-3), pyridine, pyrazine, triethylenediamine (TEDA), quinuclidine, OH(2-n)R(n) (R = Me, Et; n = 0-2), dioxane, and tetrahydrofuran (THF). Monomer, bis, and selected dimer complex geometries were considered. Using these data, we computed the thermodynamics of the key formation and dehydrogenation reactions that would occur during hydrogen delivery and alane regeneration, from which trends in complex stability were identified. These predictions were tested by synthesizing six amine-alane complexes involving trimethylamine, triethylamine, dimethylethylamine, TEDA, quinuclidine, and hexamine and obtaining upper limits of ΔG° for their formation from metallic aluminum. Combining these computational and experimental results, we establish a criterion for complex stability relevant to hydrogen storage that can be used to assess potential ligands prior to attempting synthesis of the alane complex. On the basis of this, we conclude that only a subset of the tertiary amine complexes considered and none of the ether complexes can be successfully formed by direct reaction with aluminum and regenerated in an alane-based hydrogen storage system.     

Pushing exercise program to correct glottal incompetence

A voice therapy program using pushing exercises to correct glottal incompetence is described. The program utilizes various types of instrumentation to determine whether or not a given patient is likely to benefit from the treatment. The program also provides feedback of target voices. Three cases with incomplete glottal closure and subsequent vocal dysphonia characterized by an asthenic breathy quality are used to illustrate the program. Details of the program, termination criteria, and problems and precautions learned from treating 29 patients over a 3-year period are presented.     

Graphs with small boundary

For a pair of vertices x and y in a graph G, we denote by d_G(x,y) the distance between x and y in G. We call x a boundary vertex of y if x and y belong to the same component and d_G(y,v)?d_G(y,x) for each neighbor v of x in G. A boundary vertex of some vertex is simply called a boundary vertex, and the set of boundary vertices in G is called the boundary of G, and is denoted by B(G).In this paper, we investigate graphs with a small boundary. Since a pair of farthest vertices are boundary vertices, |B(G)|?2 for every connected graph G of order at least two. We characterize the graphs with boundary of order at most three. We cannot give a characterization of graphs with exactly four boundary vertices, but we prove that such graphs have minimum degree at most six. Finally, we give an upper bound to the minimum degree of a connected graph G in terms of |B(G)|.     

Determination of fructosyl amino acids and fructosyl peptides in protease-digested blood sample by a flow-injection system with an enzyme reactor.

A flow-injection system with an enzyme reactor was proposed for the measurement of fructosyl amino acids and fructosyl peptides in protease-digested blood samples. A fructosyl-amino acid oxidase (FAOX-TE) and two fructosyl-peptide oxidases (FPOX-CE and FPOX-CET) were covalently immobilized onto an inert support. They were used as the enzyme reactor in a FIA system with a hydrogen peroxide electrode. In particular, the FPOX-CET reactor possessed high selectivity for the detection of fructosyl valine (FV) and fructosyl valyl histidine (FVH) and an excellent operational stability. The proposed FIA system with the FPOX-CET reactor responded linearly to the concentration of FV over the dynamic range of 7.8 x 10(-6) to 5.8 x 10(-4) M. The present method could be successfully applied to the assay of FV and FVH in the protease-digested blood samples.