Biomedical subjects

C Anders Olson

Publications and source records attributed to C Anders Olson.

7 recordsLinked to original sources

PubMed2004

Crystal structures of the ADP and ATP bound forms of the Bacillus anti-sigma factor SpoIIAB in complex with the anti-anti-sigma SpoIIAA.

Cell type-specific transcription during Bacillus sporulation is established by sigma(F), the activity of which is controlled by a regulatory circuit involving the anti-sigma factor and serine kinase SpoIIAB, and the anti-anti-sigma SpoIIAA. When ATP is present in the nucleotide-binding site of SpoIIAB, SpoIIAA is phosphorylated, followed by dissociation. The nucleotide-binding site of SpoIIAB is left bound to ADP. SpoIIAB(ADP) can bind an unphosphorylated molecule of SpoIIAA as a stable binding partner. Thus, in this circuit, SpoIIAA plays a dual role as a substrate of the SpoIIAB kinase activity, as well as a tight binding inhibitor. Crystal structures of both the pre-phosphorylation complex and the inhibitory complex, SpoIIAB(ATP) and SpoIIAB(ADP) bound to SpoIIAA, respectively, have been determined. The structural differences between the two forms are subtle and confined to interactions with the phosphoryl groups of the nucleotides. The structures reveal details of the SpoIIAA:SpoIIAB interactions and how phosphorylated SpoIIAA dissociates from SpoIIAB(ADP). Finally, the results confirm and expand upon the docking model for SpoIIAA function as an anti-anti-sigma in releasing sigma(F) from SpoIIAB.

Adenosine Diphosphate↗

PubMed2002

Non-classical helix-stabilizing interactions: C-H...O H-bonding between Phe and Glu side chains in alpha-helical peptides.

The classical picture of H-bonds has evolved considerably. In contrast to earlier expectations, C-H...O H-bonds are now known to be prevalent in both small organic and large biological systems. However, there are few reports on the energetic contribution of C-H...O H-bonds in protein or polypeptide systems and we do not know whether such interactions are stabilizing. Here we investigate C-H...O H-bonding interactions between Phe and Glu side chains by determining their effects on the helicity of model alpha-helical peptides using a combination of CD and NMR spectroscopy. The results suggest that Glu/Phe C-H...O H-bonding interactions stabilize helical structure, but only in the orientation Glu --> Phe (N --> C). Each Glu --> Phe (N --> C) interaction can contribute approximately -0.5 kcal mol(-1) to the stability of helical peptide. In the reverse orientation, Phe --> Glu (N --> C) appears to contribute negligibly. pH titrations provide further evidence for the existence of C-H...O H-bonds. The C-H...O H-bonding interactions in these peptides are insensitive to the screening effect of added neutral salt. Our results provide quantitative energetic information on C-H...O H-bonds that should be useful for empirical force-field calibration.

Amino Acid Sequence↗

PubMed2002

D/H amide isotope effect in model alpha-helical peptides.

The contribution of amide related hydrogen bonds to protein stability has recently been evaluated using the "Cm experiment", which measures the D/H amide isotope effect in proteins. We show here using isolated alpha-helical peptides that there is a significant effect of denaturant concentration on the measured D/H isotope effect, and that valid comparison of different proteins requires correcting for differences in denaturant (GdmHCl) concentration. Finally our results suggest that H-bonds in an isolated alpha-helix may contribute more to helix stability because of less strain compared to those in helical proteins and that the buried helical H-bonds in helical proteins are not necessarily energetically more favorable than solvent exposed H-bonds in isolated helices.

Alanine↗

PubMed2002

Polyproline II structure in a sequence of seven alanine residues.

A sequence of seven alanine residues-too short to form an alpha-helix and whose side chains do not interact with each other-is a particularly simple model for testing the common description of denatured proteins as structureless random coils. The (3)J(HN alpha) coupling constants of individual alanine residues have been measured from 2 to 56 degrees C by using isotopically labeled samples. The results display a thermal transition between different backbone conformations, which is confirmed by CD spectra. The NMR results suggest that polyproline II is the dominant conformation at 2 degrees C and the content of beta strand is increased by approximately 10% at 55 degrees C relative to that at 2 degrees C. The polyproline II conformation is consistent with recent studies of short alanine peptides, including structure prediction by ab initio quantum mechanics and solution structures for both a blocked alanine dipeptide and an alanine tripeptide. CD and other optical spectroscopies have found structure in longer "random coil" peptides and have implicated polyproline II, which is a major backbone conformation in residues within loop regions of protein structures. Our result suggests that the backbone conformational entropy in alanine peptides is considerably smaller than estimated by the random coil model. New thermodynamic data confirm this suggestion: the entropy loss on alanine helix formation is only 2.2 entropy units per residue.

Alanine↗

PubMed2002

Cation-pi interaction in model alpha-helical peptides.

Cation-pi interactions are increasingly recognized as important in chemistry and biology. Here we investigate the cation-pi interaction by determining its effect on the helicity of model peptides using a combination of CD and NMR spectroscopy. The data show that a single Trp/Arg interaction on the surface of a peptide can make a significant net favorable free energy contribution to helix stability if the two residues are positioned with appropriate spacing and orientation. The solvent-exposed Trp-->Arg (i, i + 4) interaction in helices can contribute -0.4 kcal/mol to the helix stability, while no free energy gain is detected if the two residues have the reversed orientation, Arg-->Trp (i, i + 4). The derived free energy is consistent with other experimental results studied in proteins or model peptides on cation-pi interactions. However in the same system the postulated Phe/Arg (i, i + 4) cation-pi interaction provides no net free energy to helix stability. Thus the Trp-->Arg interaction is stronger than Phe-->Arg. The cation-pi interactions are not sensitive to the screening effect by adding neutral salt as indicated by salt titration. Our results are in qualitative agreement with theoretical calculations emphasizing that cation-pi interactions can contribute significantly to protein stability with the order Trp > Phe. However, our and other experimental values are significantly smaller than estimates from theoretical calculations.

Amino Acid Sequence↗

PubMed2002

Crystal structure of the Bacillus stearothermophilus anti-sigma factor SpoIIAB with the sporulation sigma factor sigmaF.

Cell type-specific transcription during Bacillus sporulation is established by sigmaF. SpoIIAB is an anti-sigma that binds and negatively regulates sigmaF, as well as a serine kinase that phosphorylates and inactivates the anti-anti-sigma SpoIIAA. The crystal structure of sigmaF bound to the SpoIIAB dimer in the low-affinity, ADP form has been determined at 2.9 A resolution. SpoIIAB adopts the GHKL superfamily fold of ATPases and histidine kinases. A domain of sigmaF contacts both SpoIIAB monomers, while 80% of the sigma factor is disordered. The interaction occludes an RNA polymerase binding surface of sigmaF, explaining the SpoIIAB anti-sigma activity. The structure also explains the specificity of SpoIIAB for its target sigma factors and, in combination with genetic and biochemical data, provides insight into the mechanism of SpoIIAA anti-anti-sigma activity.

Adenosine Triphosphate↗

PubMed2002

Structure of the bacterial RNA polymerase promoter specificity sigma subunit.

The sigma subunit is the key regulator of bacterial transcription. Proteolysis of Thermus aquaticus sigma(A), which occurred in situ during crystallization, reveals three domains, sigma(2), sigma(3), and sigma(4), connected by flexible linkers. Crystal structures of each domain were determined, as well as of sigma(4) complexed with -35 element DNA. Exposed surfaces of each domain are important for RNA polymerase binding. Universally conserved residues important for -10 element recognition and melting lie on one face of sigma(2), while residues important for extended -10 recognition lie on sigma(3). Genetic studies correctly predicted that a helix-turn-helix motif in sigma(4) recognizes the -35 element but not the details of the protein-DNA interactions. Positive control mutants in sigma(4) cluster in two regions, positioned to interact with activators bound just upstream or downstream of the -35 element.

Bacterial Proteins↗