Using diffusion distances for flexible molecular shape comparison

Background  

Many molecules are flexible and undergo significant shape deformation as part of their function, and yet most existing molecular shape comparison (MSC) methods treat them as rigid bodies, which may lead to incorrect shape recognition.     

Evidence for histidyl and carboxy groups at the active site of the human placental Na+-H+ exchanger.

The Na+-H+ exchanger of the human placental brush-border membrane was inhibited by pretreatment of the membrane vesicles with a histidyl-group-specific reagent, diethyl pyrocarbonate and with a carboxy-group-specific reagent, N-ethoxycarbonyl-2-ethoxy-1,2-dihydroquinoline. In both cases the inhibition was irreversible and non-competitive in nature. But, if the membrane vesicles were treated with these reagents in the presence of amiloride, cimetidine or clonidine, there was no inhibition. Since amiloride, cimetidine and clonidine all interact with the active site of the exchanger in a mutually exclusive manner, the findings provide evidence for the presence of essential histidyl and carboxy groups at or near the active site of the human placental Na+-H+ exchanger. This conclusion was further substantiated by the findings that Rose Bengal-catalysed photo-oxidation of histidine residues as well as covalent modification of carboxy residues with NN'-dicyclohexylcarbodi-imide irreversibly inhibited the Na+-H+ exchanger and that amiloride protected the exchanger from inhibition caused by NN'-dicyclohexylcarbodi-imide.     

Sodium-gradient-driven, high-affinity, uphill transport of succinate in human placental brush-border membrane vesicles.

1. A high-density-lipoprotein (HDL) conversion factor was partially purified from human plasma by precipitation with (NH4)2SO4, ultracentrifugation, cation-exchange chromatography, anion-exchange chromatography and chromatography on a column of hydroxyapatite. 2. This factor modulates the particle size of HDL by converting a homogeneous population into new populations of particles, some of which are smaller and others larger than those in the original population. 3. The isolated HDL conversion factor appeared as one major band and at least three minor bands on SDS/polyacrylamide-gel electrophoresis; attempts to purify this factor further resulted in loss of conversion activity. 4. Preparations of the HDL conversion factor were stable after heating to 58 degrees C for 1 h, and were shown not to possess proteolytic activity. 5. The conversion factor was distinct from the known apolipoproteins, none of which had HDL conversion activity. 6. Addition of apolipoprotein A-IV had a dose-dependent potentiating effect on the process promoted by the HDL conversion factor.     

A proton gradient is the driving force for uphill transport of lactate in human placental brush-border membrane vesicles

The characteristics of lactate transport in brush-border membrane vesicles isolated from normal human full-term placentas were investigated. Lactate transport in these vesicles was Na+-independent, but was greatly stimulated when the extravesicular pH was made acidic. In the presence of an inwardly directed H+ gradient ([H+]o greater than [H+]i), transient uphill transport of lactate could be demonstrated. This H+ gradient-dependent stimulation was not a result of a H+ diffusion potential. Transport of lactate in the presence of the H+ gradient was not inhibited by 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid or by furosemide, ruling out the participation of an anion exchanger in placental lactate transport. Many monocarboxylates strongly interacted with the lactate transport system, whereas, with the single exception of succinate, dicarboxylates did not. The monocarboxylates pyruvate and lactate, but not the dicarboxylate succinate, when present inside the vesicles, were able to exert a trans-stimulatory effect on the uptake of radiolabeled lactate. Kinetic analyses provided evidence for a single transport system with a Kt of 4.1 +/- 0.4 mM for lactate and a Vmax of 54.2 +/- 9.9 nmol/mg of protein/30 s. Pyruvate inhibited lactate transport competitively, by reducing the affinity of the system for lactate without altering the maximal velocity. It is concluded that human placental brush-border membranes possess a transport system specific for lactate and other monocarboxylates and that this transport system is Na+-independent and is energized by an inwardly directed H+ gradient. Lactate-H+ symport rather than lactate-OH- antiport appears to be the mechanism of the H+ gradient-dependent lactate transport in these membranes.     

Proton gradient-coupled uphill transport of glycylsarcosine in rabbit renal brush-border membrane vesicles

An inward-directed proton gradient energizes the transport of intact glycylsarcosine against a concentration gradient in rabbit renal brush-border membrane vesicles. Dissipation of the proton gradient abolishes the uphill transport. Generation of an inside-negative membrane potential nearly doubles the intravesicular concentration of the dipeptide at the peak of the overshoot without altering the equilibrium value. These data provide direct evidence for peptide-proton cotransport in the renal brush-border membrane.     

Floral morphogenesis and flowering in aseptic cultures ofBrowallia demissa L

Floral buds ofBrowallia demissa, at three stages of development, were cultured on Nitsch and Nitsch basal medium. The supplements used include IAA; several cytokinins— benzyladenine, kinetin and 6-benzyl-9 tetrahydropyran-adenine (SD 8339); gibberellic acid (GA₃); 2, 3, 5-triiodobenzoic acid (TIBA); arginine and cysteine. All three stages of floral buds failed to complete development. In some treatments stages II and III produced callus and/or roots from the morphological basal end. Cytokinins promoted bud formation whereas both IAA and GA₃ depressed bud formation The shoots differentiatedin vitro were capable of setting flowers, fruits and seeds in all the treatments. The seeds were viable. Comparative studies of development of flowersin vivo andin vitro were made. In some treatments the flowers exhibited abnormal corolla, and roecium and gynoecium. Factors affecting normal bud initiation, organization and development are discussed.     

Evidence for an imipramine-sensitive serotonin transporter in human placental brush-border membranes

Serotonin is actively transported into brush-border membrane vesicles isolated from normal human term placentas and an inward-directed NaCl gradient provides the driving force for this process. Uptake is negligible if Na+ is replaced by Li+, K+, Rb+, Cs+ or choline. The presence of Cl- seems necessary for the maximal activity of this Na+-dependent uptake system. Intravesicular K+ (20-40 mM) stimulates serotonin uptake, the stimulation being considerably greater at pH 7.5 than at pH 6.5. But, in the absence of K+, uptake at pH 6.5 was twice the uptake at pH 7.5. Unlabeled serotonin and dopamine inhibit the uptake of radiolabeled serotonin and the IC50 values are 70 nM and 20 microM, respectively. Histamine and 5-hydroxytryptophan do not significantly interact with the system (IC50 greater than 1 mM). Kinetic analysis reveals that serotonin uptake in these vesicles occurs via a single, saturable, high affinity system (Kt = 51 +/- 2 nM; Vmax = 6.4 +/- 0.1 pmol/mg of protein/15 s). The transporter is highly sensitive to inhibition by imipramine (IC50 = 32 nM) and desipramine (IC50 = 160 nM) but relatively insensitive to reserpine and hydralazine.     

Isolation of sodium chloride-tolerant callus line of Cicer arietinum L. cv. BG-203

A NaCl-tolerant callus line of Cicer arietinum has been isolated, as a spontaneous variant, on agar-solidified MS-medium supplemented with 100 mM NaCl. The growth of this line, in the presence of 100 mM NaCl, was comparable to that of the NaCl-sensitive callus line growing in the absence of NaCl. Regarding relative tolerance of the two callus lines towards NaCl (0 to 200 mM), the tolerant line performed poorly in the absence of NaCl and exhibited optimal growth at 50 mM NaCl. The tolerance persisted even after three passages of 4-wk each, tested so far, away from the selective agent.