Protein folding dynamics

Karplus M. and Weaver D. L. Protein-folding dynamics - the diffusion-collision model and experimental-data. Prot. Sri. (1994) 3(4) 650-668. 

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. 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... 

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. 

Clearly, these studies of protein folding dynamics are only the first steps in obtaining the solution to a very complex problem. Nevertheless, they provide insights that are relevant to experiments and suggest refinements needed in improved treatments of protein folding. 

See also a-Helix, / -Sheet, Factors Determining Secondary and Tertiary Structure, Thermodynamics of Protein Folding, Dynamics of Protein Folding, Covalent Modifications to Regulate Enzyme Activity (from Chapter 11). 

See also Thermodynamics of Protein Folding, Dynamics of Protein Folding,... 

The tolerance of the protein folding process to noise in the interaction parameters and sequence modifications [93] was also studied using a 3x3x4 target structure [94]. The conclusions were in agreement with the qualitative picture of real protein folding dynamics and thermodynamics [93]. Such studies are important because they may provide some insights into how specific the protein sequence has to be in order to maintain the structural uniqueness of the native conformation. 

In Equation 11.22, is the equilibrium constant between the exchange incompetent and competent states that is related to protein folding dynamics (Eq. 11.23) (see Section 1.3). R is... 

Scheraga HA, Khalili M, Liwo A (2007) Protein-folding dynamics overview of molecular simulation techniques. Annu Rev Phys Chem 58 57... 

Brewer, S.H., Song, B.B., Raleigh, D.P., Dyer, R.B. Residue specific resolution of protein folding dynamics using isotope-edited infrared temperature jump spectroscopy. Biochemistry 46, 3279-3285 (2007)... 

Schuler, B., Hofmann, H. Single-molecule spectroscopy of protein folding dynamics -expanding scope and timescales. Curr. Opin. Struct Biol. 23, 36-47 (2013)... 

M. Karplus and D. L. Weaver, Protein-folding dynamics. Nature 260, 404-406 (1976). 

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