[3] Macromolecules and water: Probing with osmotic stress

Va, Parsegian; Rp, Rand; Dc, Rau

doi:10.1016/0076-6879(95)59039-0

Cited by 407 publications

(566 citation statements)

References 37 publications

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“…The increasing density requires a gradual decrease in the distance between the DNA strands, down to ∼25-28 Å, as observed experimentally (Cerritelli et al, 1997). This is accompanied by rapid growth in the DNA-DNA interaction energy, including both electrostatic repulsions and hydration forces (Parsegian et al, 1995). Orthogonal views of the final conformations of all structures are shown in Supplementary Data (Supplementary Figures 1-5).…”

Section: Structure Development During Packagingmentioning

confidence: 87%

The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape

Petrov

Boz

Harvey

2007

Journal of Structural Biology

108

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The packaging of double-stranded DNA into bacteriophages leads to the arrangement of the genetic material into highly-packed and ordered structures. Although modern experimental techniques reveal the most probable location of DNA inside viral capsids, the individual conformations of DNA are yet to be determined. In the current study we present the results of molecular dynamics simulations of the DNA packaging into several bacteriophages performed within the framework of a coarse-grained model. The final DNA conformations depend on the size and shape of the capsid, as well as the size of the protein portal, if any. In particular, isometric capsids with small or absent portals tend to form concentric spools, whereas the presence of a large portal favors coaxial spooling; slightly and highly elongated capsids result in folded and twisted toroidal conformations, respectively. The results of the simulations also suggest that the predominant factor in defining the global DNA arrangement inside bacteriophages is the minimization of the bending stress upon packaging.

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Section: Structure Development During Packagingmentioning

confidence: 87%

The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape

Petrov

Boz

Harvey

2007

Journal of Structural Biology

108

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“…In these cases, a molecular weight cutoff is expected, because PEGs beyond a certain size are fully excluded from the cavity. 37,38 The values of DDG seen for the two FecA sites in Table I increase more dramatically for the largest molecular weight PEGs, which might be due to some exclusion from a cavity that is formed after the Ton box unfolds.…”

Section: Discussionmentioning

confidence: 98%

Osmolytes modulate conformational exchange in solvent‐exposed regions of membrane proteins

Jiménez¹,

Cao²,

Kim³

et al. 2010

Protein Science

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Site-directed spin labeling (SDSL) was used to investigate local structure and conformational exchange in two bacterial outer-membrane TonB-dependent transporters, BtuB and FecA. Protecting osmolytes, such as polyethylene glycols (PEGs) are known to modulate a substrate-dependent conformational equilibrium in the energy coupling motif (Ton box) of BtuB. Here, we demonstrate that a segment that is N-terminal to the Ton box in BtuB, is in conformational exchange between ordered and disordered states with or without substrate. Protecting osmolytes shift this equilibrium to favor the more ordered, folded state. However, a segment of BtuB that is C-terminal to the Ton box that is not solvent exposed is insensitive to PEGs. Protecting osmolytes also modulate a conformational equilibrium in the Ton box of FecA, with larger molecular weight PEGs producing the largest shifts in the conformational free energy. These data indicate that solvent-exposed regions of these transporters undergo conformational exchange and that regions of these transporters that are involved in protein-protein interactions sample multiple conformational substates. The sensitivity to solute provides an explanation for differences seen between two high-resolution structures of BtuB, which each likely represent one conformation from a subset of states that are normally sampled by the protein. This work also illustrates how SDSL and osmolytes may be used to characterize and quantitate conformational equilibria in membrane proteins.

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“…Excluded osmolytes can stabilize native protein, RNA, and DNA structures, promote the assembly of macromolecular complexes, and strongly increase ligand affinity, see, for example, (4,30,31). The exclusion of small solutes and salts from macromolecular surfaces and cavities necessarily means that water is included, i.e., a preferential hydration.…”

Section: Discussionmentioning

confidence: 99%

“…Different structures, conformations, or assemblies have different numbers of included or excess water molecules. Excluded osmolytes modulate the equilibrium between two states through their osmotic pressure acting on the difference in the numbers of included or excess water molecules (4,32).…”

Section: Discussionmentioning

confidence: 99%

“…For a linear interdependence, the slope ∂Π PEG /∂Π solute is simply given by the solute osmotic pressure, Π 0 , and the difference in PEG osmotic pressures at a constant interaxial spacing with and without added osmolyte, the apparent Π excess . For a concentration m of solute (4) and ( HPC precipitates from dilute solution as the temperature is increased to about 42°C in water.…”

Section: Thermodynamic Analysismentioning

confidence: 99%

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Assessing the Interaction of Urea and Protein-Stabilizing Osmolytes with the Nonpolar Surface of Hydroxypropylcellulose

Stanley

Rau

2008

Biochemistry

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The interaction of urea and several naturally occurring protein stabilizing osmolytes, glycerol, sorbitol, glycine betaine, trimethylamine oxide (TMAO), and proline, with condensed arrays of a hydrophobically modified polysaccharide, hydroxypropylcellulose (HPC), has been inferred from the effect of these solutes on the forces acting between HPC polymers. Urea interacts only very weakly. The protein stabilizing osmolytes are strongly excluded. The observed energies indicate that the exclusion of the protein stabilizing osmolytes from protein hydrophobic side chains would add significantly to protein stability. The temperature dependence of exclusion indicates a significant enthalpy contribution to the interaction energy in contrast to expectations from 'molecular crowding' theories based on steric repulsion. The dependence of exclusion on the distance between HPC polymers rather indicates that perturbations of water structuring or hydration forces underlie exclusion.Solutes are widely used to modulate the stability of native or folded conformations of proteins and nucleic acids (1-7). There are several naturally occurring osmolytes that cells synthesize to protect proteins in response to denaturing environmental conditions such as heat shock. Stabilization of compact structures typically results from an increased exclusion of solutes from the unfolded or more open conformations. There is an unfavorable interaction of solutes with exposed surfaces. The exclusion of osmolytes from surfaces necessarily means the inclusion of water and has quite naturally been termed a preferential hydration (6). Excluded, stabilizing osmolytes that are naturally occurring include glycerol, sorbitol, glycine betaine, proline, and trimethylamine oxide (TMAO) (8). Denaturation results when there are favorable interactions of solutes with exposed surface; more solutes are 'bound' or included with unfolded structures. Urea is probably the best known denaturant. The nature of the interaction between the solute and the macromolecule that results in exclusion or inclusion has not been satisfactorily characterized. Crowding theories that have been successful for the interaction of macromolecules (9) have been reformulated for small solute-macromolecule forces (10). This, however, does not explain the chemical specificity of the interaction. Bolen and coworkers, for example, have concluded (8,11,12) that the inclusion of urea and the exclusion of stabilizing osmolytes from proteins are dominated by the interaction of these small molecules with the peptide backbone with little contribution from the exclusion of these polar solutes from hydrophobic side chains. One method for elucidating the physics of the interaction is to measure the distance dependence of the force through either a radial distribution function of solutes †

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[3] Macromolecules and water: Probing with osmotic stress

Cited by 407 publications

References 37 publications

The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape

The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape

Osmolytes modulate conformational exchange in solvent‐exposed regions of membrane proteins

Assessing the Interaction of Urea and Protein-Stabilizing Osmolytes with the Nonpolar Surface of Hydroxypropylcellulose

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