Folding dynamics

The version 2.0 assay uses a different set of probes designed to hybridize to genotypes 1 to 6 with equal efficacy (Fig. 4). The new probe set not only enhanced the efficiency of binding to genotypic variants but also lowered the LOQ from 3.5 X 105 to 2 X 105 HCV RNA equivalents/ml (Detmer et al., 1996). The version 2.0 assay displayed almost a 600-fold dynamic range up to 1.2 X 108 RNA equivalents/ml. The LOQ was set at 2 X 105 to ensure a specificity of 95%. The assay was reproducible, with a mean CV of 14% for replicates of low-, middle-, and high-titer sera. Serial dilutions of quality level 1 RNA transcripts (Collins et al,... 

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Ill Nanosecond time scale folding dynamics of a pentapeptide in water. Biochemistry (1991) 30(24) 6054-8. 

De Mori, G.M.S., Colombo, G., Micheletti, C. Study of the villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics. Protein. Struct. Funct. Genet. 2005, 58, 459-71. 

The irreversible Generalized Langevin Equation (iGLE) described in Sec. II. is capable of modeling some of the nonstationary folding dynamics motivated in this section.Such an application is the subject of present work, but it has been mentioned here in order to further motivate the reader to assess the ubiquity of nonstationary phenomenon in physical problems. 

C. D. Snow, H. Nguyen, V. S. Pande, and M. Gruebele. Absolute comparison of simulated and experimental protein folding dynamics. Nature, 420 102-106, 2002. 

A quality assurance sample is run with every batch of samples and results should not differ daily by more than 15%. Profile analysis licensed for commercial clinical diagnostic use may have to meet special requirements. For example, quantification against a five-point standard curve was required for each compound. We prepare a series of calibrants with identical amounts of internal standard, but increasing amounts of reference analyte, typically covering 100-fold dynamic range. 

A. Kolinski and F. Skolnik, Lattice Models of Protein Folding, Dynamics and Thermodynamics, Chapman 8c Hall, London, 1996. 

Monitoring protein folding dynamics by time-resolved ESI-MS... 

Numerous studies have been performed on the dynamic generation from DCLs of either molecular receptors for substrates or substrates for receptors [35-39, 46]. Work in our group has been directed in particular towards the influence of physical and chemical stimuli on the behavior of DCLs, as for instance in the case of the constitutional dynamic reorganization exerted by temperature and protonation on imine libraries [45], the induction of liquid crystal properties by an electric field acting on a dynamic library [47], or component selection induced by cation binding in a folded dynamer chain [48] (see also below). 

In the following sections, we present our recent studies on multibasin protein folding dynamics on minimalistic protein landscapes. Here, we focus on the question of how the time series of scalar quantities can shed light on the underlying configurational energy landscapes and geometry of the state space [41]. 

The Allan variance analyses of energy fluctuations strongly suggests that we utilize some collective coordinates on behalf of the internal DOFs to elucidate the nature of protein folding dynamics. Here, let us examine the versatility of principal component (PC) analysis in scrutinizing the heterogeneous coopera-tivity and dimensionality of multibasin dynamics. 

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