Gramicidin study

P.K. Hu]cherjee cUid H. Paulus, Biological function of gramicidin —studies on gramicidin-negative mutants, Proe. Natl. Aoad. Sai. USA 74, 780 (1977). 

Staphylococcal a-hemolysin is another widely studied pore-forming toxin. It is used by infectious bacteria to perforate host animal cells by a mechanism that is distinct from that of gramicidin. Several aspects of the stmcture and function of this heptameric protein complex have been smdied. 

Tyrocidine [8011-61-8] is a mixture of three closely related components. Tyrocidine studies on mechanism of action (98), biosynthesis on multien2yme complexes (93,99,100), and chemistry (101) are available, and tyrothricin production is discussed (102). Although the mechanism of action of linear gramicidins has been well researched, such work on tyrocidine is more limited it appears that tyrocidine damages membranes (103,104). 

A good understanding of the properties of water is thus essential as we move to more complicated systems. We have been involving in the study of aqueous solution of many important biological molecules, such as acetylcholine, Gramicidin, deoxydinucleoside phosphate and proflavin, and DNA, etc., first at the Monte Carlo level and slowly moving to the molecular dynamics simulations. We will discuss some of the new results on the hydration structure and the dynamics of B- and Z-DNA in the presence of counterions in the following. 

Although rum ammonia levels are not routinely measured, it is a useful indicator of Reye s syndrome and should be monitored in newborns at risk of developing hyperammonemia Ammonia is produced in many analytically useful enzyme reactions and the ammonium ISE has been used as the base sensor in several enzyme electrodes (see next section). In addition to valinomycin, other antibiotics such as the nonactin homalogs and gramicidins also behave as ionophores. The nonactin homolo were originally studied for their ability to selectively bind potassiiun ions It was then discovered that ammonium ions were preferred over potassium ions, and the selectivity coefficient Knh+ = 0.12 was reported. Since ammonia is present at fairly low levels in serum, this selectivity is not sufficient to to accurately measure NH4 in the presence of K. An extra measure of selectivity can be gained by using a gas permeable membrane to separate the ammonia gas from the sample matrix... 

X-ray diffraction studies on gramicidin commenced as early as 1949 218-219> and this early work pointed to a helical structure 220). Recent work by Koeppe et al. 221) on gramicidin A crystallised from methanol (/%) and ethanol (.P212121) has shown that the helical channel has a diameter of about 5 A and a length of about 32 A in both cases. The inclusion complexes of gramicidin A with CsSCN and KSCN (P212121) have channels that are wider (6-8 A) and shorter (26 A) than the uncomplexed dimer 221 222). Furthermore there are two cation binding sites per channel situated either 2.5 A from either end of the channel or 2.5 A on each side of its centre 222) Unfortunately these data do not permit a choice to be made from the helical models (i)—(iv) and it is not certain if the helical canals studied are the same as those involved in membrane ion transport. 

Major effort has therefore been applied to study of the helical channels by non-erystallographic methods in order to discriminate unambigously between the likely models. This has resulted in the gramicidin ion channel not only being the first clearly identified example but also the most characterised in structural terms. The bulk of... 

It should be noted that in forming this dimeric channel structure all the hydrogen bonds are parallel to the channel axis and that the inner surface is lined with the polar polypeptide groups. In addition the various lipophilic side chains coat the outer wall of the structure and are thus in contact with the lipid hydrocarbon chains. The resulting gramicidin A channel is a most efficient means of ion transport with approximately 107 sodium ions traversing the channel per second, under conditions of 1 M NaCl, 100 mV applied potential and a temperature of 25 °C 225). The detailed mechanism by which this can be achieved is under active study 226). 

The bonding of K+ and Na+ to A-methylacetamide is of interest64 in studies of the interaction of these ions with peptides and proteins, and particularly studies of the ion transport through transmembrane channels such as the gramicidin channel. Roux and Karplus35 have used the complexation of the given alkali ion with two N-methylacetamide molecules and two water molecules as a model for interactions occurring in transmembrane channels. 

Roux, B. 1993. Non-additivity in Cation-peptide Interactions. A Molecular Dynamics and Ab Initio Study of Na+ in the Gramicidin Channel. Chem. Phys. Letters 212,231-240. 

Other workers began to study the structure of gramicidin. Christensen and coworkers12 isolated crystalline tryptophane and leucine from a hydrolysate. They found no evidence for a fatty acid component and established that phenylalanine, proline and hydroxyproline were absent from a hydrolysate. These workers isolated alanine diox-pyridate from a hydrolysate and also established that gramicidin contained a compound with vicinal hydroxy and amino groups. They speculated that this compound might be serine or isoserine and proposed that gramicidin contains two tryptophane, 2 leucine, 2 or 3 alanine and 1 hydroxyamino residues or a multiple of this composition. 

Rothchild and Stanley studied the conformation of Gramicidin A using Raman spectroscopy52. Two types of conformation were found depending on the solvent used. 

As was mentioned in Section 2, x-ray diffraction was used in an effort to establish the structure of the gramicidin complex25 29 29. These studies were frustrated by the fact that the gramicidin was not chemically pure but was a mixture of components. 

Low and Richards used a density gradient column to study the density of crystals of "mixed gramicidin fractions"56. 

The conformation of gramicidin in aqueous solution has been extensively studied. A lipophilic left-handed helical structure has been proposed for gramicidin A 0 1 1. it was proposed that the mode of action of gramicidin is due to the formation of ion transport channels across biological membranes. 

Bamberg and coworkers have studied the single channel conductance of gramicidins A, B and C80 81. Significant differences between gramicidin A and B were found. 

Circular dichroism at high pressures has been used to study the conformation of a derivative of gramicidin A in trifluoroethanol solutions87. 

Kyogoku and Kawano have prepared an extensive review of the use of NMR techniques to study the conformation of gramicidin and other antibiotics in solution88. 

Lotz and coworkers have used poly (y-benzyl-D-L-glutamate) as a stereochemical model to study the conformation of gramicidin A89. 

Conduction along water wires may as well be the dominant mechanism in the permeation of protons in channels an MD study of proton transport through a gramicidin channel can be found in, for example, [156]. 

Arseniev, A. S., Barsukov, I. L., Bystrov, V. F., Lomize, A. L. and Ovchinnikov, Y. A. (1985). 1H-NMR study of gramicidin-A transmembrane ion channel head-to-head right handed single stranded helices, FEBS Lett., 186, 168-174. 

Osterberg and Norinder [42] further analyzed a subset of the ATPase data published by Litman et al. [39]. The ATPase activity values were correlated by multivariate statistics with calculated descriptors (MolSurf descriptors) related to physicochemical properties suchaslipophilicity, polarity, polarizability and hydrogen bonding. After exclusion of one outlier and large molecules such as valinomycin, gramicidin S and so on, which were not handled by the MolSurf software, only 21 compounds were included in the study. Two models were derived model 1, based on... 

Similarly, iterative NRPSs operate in a linear fashion but utilize at least one domain or module multiple times for the synthesis of a single NRP product. Thus, peptides assembled by iterative synthetases contain short, repeating units of peptide building blocks. In such systems, the terminal PCP-TE (or infrequendy PCP-C) didomain is responsible for both condensation of the repeating peptide units and chain release from the assembly line. NRPs biosynthesized in this manner include enniatin, enterobactin, bacillibactin, " gramicidin and the depsi-peptides valinomycin and cereulide. Of these examples, condensation of the precursor peptides for both enterobactin and gramicidin S has been extensively studied and will be discussed in detail. 

Guevremont R, Ding L, Ells B, Barnett DA, Purves RW (2001) Atmospheric pressure ion trapping in a tandem FAIMS-FAIMS coupled to a TOFMS studies with electrospray generated gramicidin S ions. J Am Soc Mass Spectrom 12(12) 1320-1330... 

Roux, B. (1990) Theoretical study of ion transprot in the gramicidin A channel. Harvard University, Cambridge, MA. 

Gramicidin S is a cyclic decapeptide with a characteristic CD spectrum that qualitatively resembles that of an a-helixj185-189 but numerous studies described below strongly support the structure predicted by Hodgkin and O ugh ton11751 and by Schwyzer et alJ176l in which 13-turns (type II ) at the D-Phe-L-Pro sequences link two extended tripeptide sequences (Val-Orn-Leu) that form an antiparallel (3-structure. 

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