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Does Water Play a Structural Role in the Folding of Small Nucleic Acids?
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ABSTRACT
Nucleic acid structure and dynamics are known to be closely coupled to local environmental conditions and, in particular, to the ionic character of the solvent. Here we consider what role the discrete properties of water and ions play in the collapse and folding of small nucleic acids. We study the folding of an experimentally well-characterized RNA hairpin-loop motif (sequence 5'-GGGC[GCAA]GCCU-3') via ensemble molecular dynamics simulation and, with nearly 500 µS of aggrega...
Related newspaper, magazine, and journal articles from HighBeam Research
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Protein Hydrophobic Collapse and Early Folding Steps Observed in a Microfluidic Mixer
Biophysical Journal
; ABSTRACT We demonstrate that the sub-millisecond protein folding process referred to as "collapse" actually consists of at least two separate processes. We observe the UV fluorescence spectrum from naturally occurring tryptophans in three well-studied proteins, cytochrome c, apomyoglobin, and
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Nanosecond temperature jump relaxation dynamics of cyclic [beta]-hairpin peptides
Biophysical Journal
; ABSTRACT The thermal unfolding of a series of 6-, 10-, and 14-mer cyclic [beta]-hairpin peptides was studied to gain insight into the mechanism of formation of this important secondary structure. The thermodynamics of the transition were characterized using temperature dependent Fourier transform
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PlayStation 3 geared to fight aliens, demons and disease
Oakland Tribune
; ... lift for Stanford University research that until now relied on help from an assortment of home computers around the world. A news conference at Stanford Thursday described a plan that will let PS3 owners contribute to a major scientific study by simply running ...
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PlayStation 3 can fight aliens, demons and disease
Oakland Tribune
; ... lift for Stanford University research that until now relied on help from an assortment of home computers around the world. A news conference is scheduled at Stanford this morning to describe a plan that will let PS3 owners contribute to a major scientific ...
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Good gaming : PS3 can help research
Oakland Tribune
; ... lift for Stanford University research that until now relied on help from an assortment of home computers around the world. A news conference is scheduled at Stanford this morning to describe a plan that will let PS3 owners contribute to a major scientific ...
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PlayStation3 can fight disease between games
Oakland Tribune
; ... lift for Stanford University research that until now had relied on help from an assortment of home computers around the world. A news conference is scheduled at Stanford this morning to describe a plan that will let PS3 owners contribute to a major scientific ...
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Kinetic Pathways of [beta]-Hairpin (Un)folding in Explicit Solvent
Biophysical Journal
; ABSTRACT We examine the dynamical (un)folding pathways of the C-terminal [beta]-hairpin of protein G-B1 at room temperature in explicit solvent, by employing transition path sampling algorithms. The path ensembles contain information on the folding kinetics, including solvent motion. We determine
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Monte Carlo Studies of Folding, Dynamics, and Stability in [alpha]-Helices
Biophysical Journal
; ABSTRACT Folding simulations of polyalanine peptides were carried out using an off-lattice Monte Carlo simulation technique. The peptide was represented as a chain of residues, each of which contains two interaction sites: one corresponding to the C^sup α^ atom and the other to the side chain.
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Extent of hydrogen-bond protection in folded proteins: A constraint on packing architectures
Biophysical Journal
; ABSTRACT Progressive structuring and ultimately exclusion of water by hydrophobes surrounding backbone hydrogen bonds turn the latter into guiding factors of protein folding. Here we demonstrate that an arrangement of five hydrophobes yields an optimal hydrogen-bond stabilization. This motif is
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Folding Trp-Cage to NMR Resolution Native Structure Using a Coarse-Grained Protein Model
Biophysical Journal
; ABSTRACT We develop a coarse-grained protein model with a simplified amino acid interaction potential. Using this model, we perform discrete molecular dynamics folding simulations of a small 20-residue protein-Trp-cage-from a fully extended conformation. We demonstrate the ability of the Trp-cage
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