Conformational ability

In a recent series of papers, Kilian 9,50 52) proposed a new phenomenological approach to rubber elasticity and suggested a molecular network might be considered as a formelastic fluid the conformational abilities of which were adequately characterized by the model of a van der Waals conformational gas with weak interaction. The ideal network is treated as an ideal conformational gas. According to... 

The last step to liberating all the inherent potential of these early nucleoproteinic systems of RNA and protein was found in the dual conformational abilities of the small 2 -deoxy-D-ribose cycle to account for a conformationally amplifying switch between A- and B-type nucleic acid versions [7 a, 8 c, 33]. The discovery of the information store of DNA enabled the systems to separate the replication of a more densely packed DNA message from the informational and functional instruments needed in the hitherto existing nucleic-acid-protein interaction schemes and promoted by this... 

A series of water-soluble calix[n]arenes (n = 4 - 8) with different conformational abilities were investigated as artificial ribonucleases that hydrolyze cytidine-2, 3 -cyclophosphate at pH 2 and 30°C [56]. Best results were obtained with calix[4]arene 12, which inaeased the rate by 16 times (Scheme 4.9). 

Drake and Baltz, 1976). The instability of DNA and the occurrence of mutations is considered briefly in Section II. The ability of DNA to denature (unwind) is essential, on the one hand, for replication and in order to serve as a template for RNA synthesis, and, on the other hand, may lead to irreversible changes. This ability is similar to the conform-ability of enzymes, which is essential for enzymatic action but which may lead to irreversible denaturation. 

Small size, ruggedness, simple cabling and the ability to operate the equipment under adverse conditions in the field has also been design goals. The system should also conform with the regulations necessary for the CE-marking (i. e. standards and directives for EMC, Electrical Safety and Machine Safety). 

Harder P, Grunze M, Dahint R, Whitesides G M and Laibinis P E 1998 Molecular conformation in oligo(ethylene glycol)-terminated self-assembled monolayers on gold and silver surfaces determines their ability to resist protein adsorption J. Rhys. Chem. B 102 426-36... 

Nevertheless, the technique suffers from a severe time scale problem -the trajectories are computed for (at most) a few nanoseconds. This is far too short compared to times required for many processes in biophysics. For example, the ii to T conformational transition in hemoglobin lasts tens of microseconds [1], and the typical time for ion migration through the gramicidin channel is hundreds of nanoseconds. This limits (of course) our ability to make a meaningful comparison to experiments, using MD. 

The molecular mechanics force fields available include MM+, OPLS, BIO+, and AMBER. Parameters missing from the force field will be automatically estimated. The user has some control over cutoff distances for various terms in the energy expression. Solvent molecules can be included along with periodic boundary conditions. The molecular mechanics calculations tested ran without difficulties. Biomolecule computational abilities are aided by functions for superimposing molecules, conformation searching, and QSAR descriptor calculation. 

Some of the other features of this program are the ability to compute transition states, coordinate driving, conformation searches, combinatorial tools, and built-in visualization. The builder includes atoms and fragments for organics, inorganics, peptides, nucleotides, chelates, high-coordination geometries, and... 

The ability of receptors to couple to G-proteins and initiate GTPase activity may also be independent of ligand. Thus, specific mutations in a- and P-adrenergic receptors have led to receptors that mediate agonist-independent activation of adenylyl cyclase (69,70). These mutations presumably mimic the conformational state of the ligand-activated receptor when they are activated conventionally by ligands. 

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