Polarity as a criterion in protein design

Hypothetical proteins can be tested computationally by determiningwhether or not the designed sequence-structure pair has thecharacteristics of a typical globular protein. We have developedsuch a test by deriving quantities with approximately constantvalue for all globular proteins, based on empirical analysisof the exposed and buried surfaces of 128 structurally knownproteins. The characteristic quantities that best appear tosegregate badly designed or deliberately misfolded proteinsfrom their properly folded natural relatives are the polar fractionof side chains on the protein surface and, independently, inthe protein interior. Three of the seven hypothetical structurestested here can be rejected as having too many polar side-chaingroups in the interior or too few on the protein surface. Inaddition, a recently designed nutritional protein is identifiedas being very much unlike globular proteins. These database-derivedcharacteristic quantities are useful in screening designed proteinsprior to experiment and may be useful in screening experimentallydetermined (X-ray, NMR) protein structures for possible errors.     

Homology Model Adjustment and Ligand Screening with a Pseudoreceptor of the Human Histamine H4 Receptor

A new pseudoreceptor modeling method (PRPS) was applied to the refinement of a homology model of the human histamine H₄ receptor (H₄R), the prediction of a ligand binding site, and virtual screening. Retrieval of two new H₄R ligands demonstrates the biological relevance of the pseudoreceptor model and provides a means for finding new hits and leads in the early phases of drug discovery.

     

Solubility of poly(n-alkylmethacrylate)s in hydrocarbons and in alcohols

Poly(methylmethacrylate) (PMMA), poly(butylmethacrylate) (PBMA), and poly(decylmethacrylate) (PDMA) are completely miscible with toluene at normal pressure from room temperature up to the boiling point of the solvent. In alkanes (C₆ to C₁₀) and 1-pentanol the solubility increases with the length of the side chain of the polymer: PMMA always exhibits a solubility gap within the above temperature range, PBMA shows upper critical solution temperatures (except n-hexane, which is a non-solvent), and PDMA mixes completely with all alkanes under consideration. Alcohols (up to C₄) are non-solvents for PMMA but theta solvents for PBMA and PDMA (except ethanol which is a non-solvent for the latter). The low temperature demixing of ethanol/PBMA is shifted towards lower temperatures by pressure.     

The role of heat-shock and chaperone proteins in protein folding: possible molecular mechanisms

Recently some heat-shock proteins have been linked to functionsof ‘chaperoning’ protein folding in vivo. Here currentexperimental evidence is reviewed and possible requirementsfor such an activity are discussed. It is proposed that onemode of chaperone action is to actively unfold misfolded orbadly aggregated proteins to a conformation from whkh they couldrefold spontaneously; that improperly folded proteins are recognizedby excessive stretches of solvent-exposed backbone, rather thanby exposed hydrophobic patches; and that the molecular mechanismfor unfolding is either repeated binding and dissociation (‘plucking’)or translocation of the protein backbone through a binding cleft(‘threading’), allowing the threaded chain to refoldspontaneously. The observed hydrolysis of ATP would providethe energy for active unfolding. These hypotheses can be appliedto both monomeric folding and oligomeric assembly and are sufficientlydetailed to be open to directed experimental verification.