[25] Analyzing solvent reorganization and hydrophobicity

Lee, B.

doi:10.1016/0076-6879(95)59061-7

Cited by 30 publications

(18 citation statements)

References 25 publications

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“…2). (Corrections suggested by Sharp et al (1991aSharp et al ( , 1991b roughly double these values but the validity of the suggested corrections is still being debated (Ben-Naim, 1994;Honig & Yang, 1995;Lee, 1995)). Since the middle of this range (25 cal/A2) is close to the estimates based on pure hydrocarbons, it seems parsimonious to use that value as an estimate of the hydrophobic effect and accept that there is an uncertainty of roughly +30% (Fig.…”

Section: A Suggested Approachmentioning

confidence: 99%

Hydrophobicity regained

Karplus

1997

Protein Science

175

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A widespread practice is to use free energies of transfer between organic solvents and water (AGEansfer) to define hydrophobicity scales for the amino acid side chains. A comparison of four AGEansfer scales reveals that the values for hydrogen-bonding side chains are highly dependent on the non-aqueous environment. This property of polar side chains violates the assumptions underlying the paradigm of equating AGEansfer with hydrophobicity or even with a generic solvation energy that is directly relevant to protein stability and ligand binding energetics. This simple regaining of the original concept of hydrophobicity reveals a flaw in approaches that use AGEansfer values to derive generic estimates of the energetics of the burial of polar groups, and allows the introduction of a "pure" hydrophobicity scale for the amino acid residues.Keywords: amino acids; atomic solvation parameters; hydrophobic effect; hydrophobicity; protein folding; protein stabilityThe hydrophobic effect describes the thermodynamics of the partitioning of non-polar compounds between water and a nonaqueous phase. The hallmarks of the hydrophobic effect are that the transfer of non-polar compounds into water at ambient temperature is unfavorable due to a decrease in entropy and is associated with a large increase in heat capacity. Although the molecular details that give rise to the hydrophobic effect are still debated (Blokzijl & Engberts, 1993), this has not hindered it from becoming the dominant paradigm for understanding protein folding and stability (e.g

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Section: A Suggested Approachmentioning

confidence: 99%

Hydrophobicity regained

Karplus

1997

Protein Science

175

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“…The following conclusions can be drawn from Lee's data [24,25]. (1) The work of making a cavity in water is much larger than in liquid alkane and this difference Tab.…”

Section: Quasi-experimental Estimates Of the Work Of Making A Cavity mentioning

confidence: 98%

“…Saturated hydrocarbons, which serve as models for the side chains of leucine, isoleucine and valine, are preferentially excluded from aqueous solution and have unfavorable solvation free energies. The basic cause is the large unfavorable work of making a cavity in water, which exceeds the favorable van der Waals interaction energy (see Refs [24,25] and Section 6.2.4). Figure 6.3 shows a direct proportionality between the transfer free energy DG and ASA for transfer of alkanes from aqueous solution to the vapor phase.…”

Section: Solvation Free Energies Of Amidesmentioning

confidence: 99%

“…Modern theories of solvation indicate that the gas-liquid transfer process can be formally divided into two steps of an insertion model of solvation: see discussion by Lee [24,25] and basic theory by Widom [26]. In step 1 thermal fluctuations create a cavity in the liquid with a size and shape appropriate for containing the solute.…”

Section: Quasi-experimental Estimates Of the Work Of Making A Cavity mentioning

confidence: 99%

“…Then the transfer free energy gives the free energy change for transferring the solute from a fixed position in the gas phase to a fixed position in the liquid phase [23]. The solute in the gas phase can be treated as an ideal gas [24,25] Transfer free energies of linear alkanes (from 1 to 10 carbon atoms) from liquid alkane to water, measured from hydrocarbon solubility in water. They are plotted against water-accessible surface area (ASA in Å 2 ).…”

Section: Quasi-experimental Estimates Of the Work Of Making A Cavity mentioning

confidence: 99%

See 2 more Smart Citations

Weak Interactions in Protein Folding: Hydrophobic Free Energy, van der Waals Interactions, Peptide Hydrogen Bonds, and Peptide Solvation

Baldwin¹

2005

Protein Folding Handbook

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Protein‐Carbohydrate Interaction: Fundamental Considerations

Burkhalter¹,

Dimick²,

Toone³

et al. 2000

Carbohydrates in Chemistry and Biology

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A major-if not the major-rationale for the study of carbohydrate chemistry derives from the roles played by glycoconjugates in biology [l]. In almost all such roles a carbohydrate ligand must bind to a protein receptor. There exists, then, tremendous potential to modulate biological activity through the creation of high affinity mimics of native saccharide receptors; such compounds have potential therapeutic value in the treatment of viral, parasitic, mycoplasmal and bacterial infections, and the treatment of a range of human cancers [ 2 ] . The study of proteincarbohydrate interaction, then, forms a key focus of this discipline of carbohydrate chemistry and biology.The development of inhibitors of carbohydrate-mediated biological recognition is impeded by the exceptionally weak bindings that typify protein-carbohydrate interaction [ 3 ] . In this chapter we consider the energetic issues central to proteincarbohydrate interaction. We devote some space to a consideration of the general forces and interactions that provide both affinity and specificity during association in aqueous solution. A range of phenomena observed during protein-carbohydrate association appear to be dependent on the assay used to evaluate 'binding'; we therefore consider the some of the more commonly utilized assays of protein carbohydrate interaction and delineate the microscopic events each assay is designed to evaluate. Finally, the last ten years has seen tremendous activity in the development of multivalent carbohydrate ligands; we thus explore the energetic issues surrounding multivalency in ligand binding.Throughout, we endeavor to relate energetic issues directly to protein-carbohydrate interaction. We stress, however, that a tremendous body of literature pertaining to the very issues central to protein-carbohydrate interaction exists in the context of other binding systems. Where appropriate, we draw on the lessons and experience of these adjacent disciplines in our consideration of the biophysical aspects of protein-carbohydrate interaction.

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[25] Analyzing solvent reorganization and hydrophobicity

Cited by 30 publications

References 25 publications

Hydrophobicity regained

Hydrophobicity regained

Weak Interactions in Protein Folding: Hydrophobic Free Energy, van der Waals Interactions, Peptide Hydrogen Bonds, and Peptide Solvation

Protein‐Carbohydrate Interaction: Fundamental Considerations

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