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Biomedical subjects

L A Kuhn

Publications and source records attributed to L A Kuhn.

At least 19 recordsLinked to original sources
PubMed1992

The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures.

To characterize water binding to proteins, which is fundamental to protein folding, stability and activity, the relationships of 10,837 bound water positions to protein surface shape and residue type were analyzed in 56 high-resolution crystallographic structures. Fractal atomic density and accessibility algorithms provided an objective characterization of deep grooves in solvent-accessible protein surfaces. These deep grooves consistently had approximately the diameter of one water molecule, suggesting that deep grooves are formed by the interactions between protein atoms and bound water molecules. Protein surface topography dominates the chemistry and extent of water binding. Protein surface area within grooves bound three times as many water molecules as non-groove surface; grooves accounted for one-quarter of the total surface area yet bound half the water molecules. Moreover, only within grooves did bound water molecules discriminate between different side-chains. In grooves, main-chain surface was as hydrated as that of the most hydrophilic side-chains, Asp and Glu, whereas outside grooves all main and side-chains bound water to a similar, and much decreased, extent. This identification of the interdependence of protein surface shape and hydration has general implications for modelling and prediction of protein surface shape, recognition, local folding and solvent binding.

Algorithms↗
PubMed1991

Transplanted LDL and mannose-6-phosphate receptor internalization signals promote high-efficiency endocytosis of the transferrin receptor.

The internalization signals of several constitutively recycling receptors have recently been identified as regions of four or six amino acids that include an aromatic residue, usually tyrosine. Here, we show that transplanted signals from the low density lipoprotein receptor (LDLR) and cation-independent mannose-6-phosphate receptor (Man-6-PR) promote rapid internalization of the transferrin receptor (TR), directly establishing that recognition signals are interchangeable, self-determined structural motifs and that signals from type I membrane proteins are active in a type II receptor. We also show that the chemical and spatial patterns of critical residues in both four- and six-residue internalization motifs are consistent with a tight turn structure. A six-residue LDLR signal is needed for activity in TR, suggesting that an amino-terminal aromatic side chain is obligatory. In contrast, the carboxy-terminal aromatic side chain in the TR signal can be replaced by a large hydrophobic residue. Thus, internalization signals apparently require an aromatic amino-terminal residue and either an aromatic or large hydrophobic carboxy-terminal residue rather than a conserved tyrosine per se. Consistent with this conclusion, predicted internalization signals from the poly-Ig receptor, YSAF, and asialoglycoprotein receptor (ASGPR) subunit H1, YQDL, also promote internalization of TR.

Amino Acid Sequence↗
PubMed1990

Transferrin receptor internalization sequence YXRF implicates a tight turn as the structural recognition motif for endocytosis.

Using detailed functional studies on 24 human transferrin receptor mutants, we identified YXRF as the internalization sequence. Provided that at least 7 residues separate this tetrapeptide from the transmembrane region, changing the tetrapeptide position within the TR cytoplasmic domain does not reduce internalization activity. Thus, any conformational determinant for internalization must be localized to the YXRF sequence. Twenty-eight tetrapeptide analogs of YXRF, found by an unbiased search of all known three-dimensional protein structures, significantly favored tight turns similar to a type I turn. Of the ten tetrapeptides most closely related to YXRF, eight were surface exposed and had tight-turn conformations, as were four of five tetrapeptides with sequences related to the low density lipoprotein receptor internalization motif, NPXY. The internalization sequences of both receptors contain aromatic residues with intervening hydrogen-bonding residues. Thus, two distinct internalization sequences favor a common structural chemistry and implicate an exposed tight turn as the recognition motif for high efficiency endocytosis.

Amino Acid Sequence↗
PubMed1990

Elucidating the structural chemistry of glycosaminoglycan recognition by protein C inhibitor.

Glycosaminoglycans (GAGs) including heparin accelerate the inhibition of serine proteases by serine protease inhibitors (serpins), an essential process in regulating blood coagulation. to analyze the molecular basis for GAG recognition by the plasma serpin protein C inhibitor (PCI; also known as plasminogen activator inhibitor 3), we have constructed a complete, energy-minimized, three-dimensional model of PCI by using the structure of homologous alpha 1-antitrypsin as a template. Sequence analysis, hydrogen-bonding environment, and shape complementarity suggested that the N-terminal residues of PCI, which are not homologous to those of alpha 1-antitrypsin, form an amphipathic alpha-helix, here designated A+ since it precedes the alpha 1-antitrypsin A helix. Electrostatic calculations revealed a single, highly positive surface region arising from both the A+ and H helices, suggesting that this two-helix motif is required for GAG binding by PCI. The dominant role of electrostatic interactions in PCI-heparin binding was confirmed by the strong ionic strength dependence of heparin stimulation. The involvement of the A+ helix in heparin binding was verified by demonstrating that an anti-PCI antibody that specifically binds the A+ peptide blocks heparin binding.

Amino Acid Sequence↗
PubMed1985

A statistical technique for predicting membrane protein structure.

A statistical technique has been developed for predicting the transmembrane segments of membrane proteins from their amino acid sequences. A protein's amino acid sequence is represented by a sequence of membrane propensity values derived from the frequency of occurrence of the amino acids in a number of putative transmembrane segments. A running average over this numeric sequence yields a membrane propensity profile from which transmembrane segments may be chosen. When this method is applied to a pool of ten putative membrane proteins, the predicted intra- and extramembrane regions agree 93.6% on a residue-by-residue basis with previously suggested structures. Predictions of transmembrane segments in cytochrome c oxidase subunits I, II and III and cytochrome b from several species are given, and structural homology between species is examined using membrane propensity profiles. Conclusions are then made about the functionality of several regions in these proteins.

Amino Acid Sequence↗
PubMed1976

Diabetic treatment and primary ventricular fibrillation in acute myocardial infarction.

The relation between mode of therapy and mortality rate and incidence of primary ventricular fibrillation was studied in 265 patients with diabetes mellitus and acute myocardial infarction. Sixty patients were being treated with diet only, 54 were receiving insulin and 151 were taking oral hypoglycemic agents. Fourteen patients (5.3 percent) had primary ventricular fibrillation, and all but one died. No statistically significant association was found between the incidence of primary ventricular fibrillation and the type of treatment for diabetes mellitus. Sixty-four (24.2 percent) of the 265 patients died during hospitalization. Mortality was greater among diabetic patients receiving oral therapy. However, after adjusting for age and sex, the difference among these three treatment regimens did not reach the P less than 0.05 level of significance.

Age Factors↗