Combining protein evolution and secondary structure

An evolutionary model that combines protein secondary structure and amino acid replacement is introduced. It allows likelihood analysis of aligned protein sequences and does not require the underlying secondary (or tertiary) structures of these sequences to be known. One component of the model describes the organization of secondary structure along a protein sequence and another specifies the evolutionary process for each category of secondary structure. A database of proteins with known secondary structures is used to estimate model parameters representing these two components. Phylogeny, the third component of the model, can be estimated from the data set of interest. As an example, we employ our model to analyze a set of sucrose synthase sequences. For the evolution of sucrose synthase, a parametric bootstrap approach indicates that our model is statistically preferable to one that ignores secondary structure.      

Energetics of threonine uptake by pod wall tissues of Vicia faba L.

Kjeldahl assays showed that the pod wall of Vicia faba fruits behaves as a transitory reservoir of nitrogen. We have studied the properties and energetics of amino-acid uptake during the accumulating stage of pod wall development. A comparative analysis using various inhibitors or activators of the proton pump has been carried out i) on threonine uptake, ii) on the acidifying activity of the tissues, and iii) on the transmembrane potential difference of mesocarp cells. Except for the effect of dicyclohexylcarbodiimide which could not be satisfactorily explained, all other results obtained with ATPase inhibitors, uncouplers and fusicoccin were consistent with the view of a transport energized by the proton-motive force. Adding threonine to a medium containing fragments of pericarp or of endocarp induced a pH change (to-wards more alkaline values) of the medium and a membrane depolarization of the storage cells which depended on the amino-acid concentration added. These data indicate H⁺-threonine cotransport in the pod wall of broad bean. Moreover, because p-chloromercuribenzenesulphonic acid inhibits threonine uptake without affecting the transmembrane potential difference, it is concluded that the threonine carrier possesses a functional SH-group located at the external side of the plasmalemma.Abbreviations CCCP carbonylcyanide- m-chlorophenylhydrazone - DCCD N,N-dicyclohexylcarbodiimide - DES diethylstilbestrol - DNP 2,4-dinitrophenol - FC fusicoccin - PCMBS p-chloromercuribenzenesulphonic acid - PD potential difference     

Phloem loading in Vicia faba leaves: Effect of N-ethylmaleimide and parachloromercuribenzenesulfonic acid on H+ extrusion,K+ and sucrose uptake

The effects of a penetrating (NEM) and a non-penetrating (PCMBS) sulfhydryl-specific reagent on proton extrusion, ⁸⁶Rb and [U-¹⁴C]sucrose uptake by Vicia faba leaves have been studied. Proton extrusion was strongly or completely inhibited by 0.1 mM NEM. ⁸⁶Rb and [U-¹⁴C]sucrose uptake were markedly reduced by NEM concentrations equal to or higher than 0.5 mM. Under our experimental conditions, PCMBS (1 mM) exerted a strong inhibition on [¹⁴C]sucrose uptake but did not inhibit proton extrusion and ⁸⁶Rb uptake. The sensitivity of phloem loading to PCMBS is thought to be a consequence of sugar-carrier blockage and not of inhibition of the proton pump.Abbreviations CCCP carbonylcyanide-m-chlorophenylhydrazone - DES diethylstilbestrol - DCCD dicyclohexylcarbodiimide - FC Fusicoccin - NEM N-ethylmaleimide - PCMBS p-chloromercuribenzenesulfonic acid