Biomedical subjects

Motoya Kohtani

Publications and source records attributed to Motoya Kohtani.

8 recordsLinked to original sources

PubMed2006

Proton transfer-induced conformational changes and melting in designed peptides in the gas phase.

The conformations of protonated RA15K, RA20K and RA15H (R = arginine, A = alanine, K = lysine, and H = histidine) have been examined in the gas phase as a function of temperature. These peptides were designed so that intramolecular proton transfer will trigger conformational changes between a helix (proton sequestered at the C-terminus) and globule (proton sequestered at the N-terminus). Kinetically controlled structural transitions occur below 400 K (from helix to globule for RA15H, and from globule to helix for RA15K and RA20K). As the temperature is raised, the compact globule found at room temperature expands, accesses more configurations, and becomes entropically favored. At around 500 K, the RA15K and RA20K helices undergo a melting transition. The transition is broad, as expected for a phase transition in a finite system, and becomes narrower as the peptide size increases. In the helical conformation, the two basic residues are well separated; as a result, the proton transfer necessary to drive the melting transition probably involves a mobile proton. For doubly protonated RA15K, a dumbbell-like conformation (resulting from repulsion between the two protonated basic residues) is found at high temperature.

Gases↗

PubMed2005

Non-covalent interactions between unsolvated peptides: helical complexes based on acid-base interactions.

We have used ion-mobility mass spectrometry to examine the conformations of the protonated complex formed between AcA(7)KA(6)KK and AcEA(7)EA(7), helical alanine-based peptides that incorporate glutamic acid (E) and lysine (K). Designed interactions between the acidic E and basic K residues help to stabilize the complex, which is generated by electrospray and studied in the gas phase. There are two main conformations: (1) a coaxial linear arrangement where the helices are tethered together by an EKK interaction between the pair of lysines at the C-terminus of the AcA(7)KA(6)KK peptide and a glutamic acid at the N-terminus of the AcEA(7)EA(7) peptide and (2) a coiled-coil arrangement with side-by-side antiparallel helices where there is an additional EK interaction between the E and K residues in the middle of the helices. The coiled-coil opens up to the coaxial linear structure as the temperature is raised. Entropy and enthalpy changes for the opening of the coiled-coil were derived from the measurements. The enthalpy change indicates that the interaction between the E and K residues in the middle of the helices is a weak neutral hydrogen bond. The EKK interaction is significantly stronger.

Amino Acids, Acidic↗

PubMed2004

The mobile proton in polyalanine peptides.

Ion mobility measurements have been performed for protonated polyalanine peptides (A10 + H+, A15 + H+, A20 + H+, A25 + H+, and A15NH2 + H+) as a function of temperature using a new high-temperature drift tube. Peaks due to helices and globules were found at room temperature for all peptides, except for A10 + H+ (where only the globule is present). As the temperature is increased, the helix and globule peaks broaden and merge to give a single narrow peak. This indicates that the two conformations interconvert rapidly at elevated temperatures. The positions of the merged peaks show that A15 + H+ and A15NH2 + H+ spend most of their time as globules when heated, while A20 + H+ and A25 + H+ spend most of their time as helices. The helix/globule transitions are almost certainly accompanied by intramolecular proton transfer, and so, these results suggest that the proton becomes mobile (able to migrate freely along the backbone) at around 450 K. The peptides dissociate as the temperature is increased further to give predominantly the bn(+), b(n-1)(+), b(n-2)(+), ... series of fragment ions. There is a correlation between the ease of fragmentation and the time spent in the helical conformation for the An + H+ peptides. Helix formation promotes dissociation because it pools the proton at the C-terminus where it is required for dissociation to give the observed products. In addition to the helix and globule, an antiparallel helical dimer is observed for the larger peptides. The dimer can be collisionally dissociated by injection into the drift tube at elevated kinetic energies.

Alanine↗

PubMed2004

Water molecule adsorption on short alanine peptides: how short is the shortest gas-phase alanine-based helix?

Water adsorption measurements have been performed under equilibrium conditions for unsolvated Ac-A(n)K+H(+) and Ac-KA(n)+H(+) peptides with n = 4 - 10. Previous work on larger alanine peptides has shown that two dominant conformations (helices and globules) are present for these peptides and that water adsorbs much more strongly to the globules than to the helices. All the Ac-KA(n)+H(+) peptides studied here (which are expected to be globular) adsorb water strongly, and so do the Ac-A(n)K+H(+) peptides with n < 8. However, for Ac-A(n)K+H(+) with n = 8-10 there is a substantial drop in the propensity to adsorb water. This result suggests that Ac-A(8)K+H(+) is the smallest Ac-A(n)K+H(+) peptide to have a significant helical content in the gas phase. Water adsorption measurements for Ac-V(n)K+H(+) and Ac-L(n)K+H(+) with n = 5-10 suggest that the helix emerges at n = 8 for these peptides as well.

Adsorption↗

PubMed2004

Extreme stability of an unsolvated alpha-helix.

High-temperature ion mobility measurements have been performed for alpha-helical Ac-A15K+H+ and globular Ac-KA15+H+ peptides. The alpha-helical and globular conformations do not melt into random coils as the temperature is raised. Instead, both conformations survive to the point where the peptide signals vanishes due to fragmentation. This occurs at 600 K for the globular Ac-KA15+H+ peptide and at 725 K for the alpha-helical Ac-A15K+H+. For the helical Ac-A15K+H+ peptide it appears that fragmentation is triggered by disruption of the helical conformation.

Alanine↗

PubMed2004

Pi-helix preference in unsolvated peptides.

Ion mobility measurements have been used to examine helix formations in the gas phase for a series of alanine/glycine-based peptides that incorporate a glutamic acid (E) and lysine (K) at various positions along the backbone. Incorporation of an EK pair lowers the percent helix for all positions (presumably because hydrogen bonding between the backbone and the E and K side chains stabilize the nonhelical globular conformations). The largest percent helix is found when the EK pair is in an i,i+5 arrangement, which suggests that the preferred helical conformation for these peptides is a pi-helix. This conclusion is supported by comparison of cross sections deduced from the ion-mobility measurements to average cross sections calculated for conformations obtained from molecular dynamics simulations. The glutamic acid and lysine may form an ion pair that is stabilized by interactions with the helix macro-dipole.

Alanine↗

PubMed2004

Water molecule adsorption on protonated dipeptides.

Equilibrium constants for the adsorption of the first water molecule on six protonated dipeptides (Gly-Gly+H(+), Gly-Ala+H(+), Ala-Gly+H(+), Ala-Ala+H(+), Pro-Gly+H(+), and Gly-Trp+H(+)) have been measured as a function of temperature, and DeltaH(o) and DeltaS(o) determined. Density functional theory calculations were performed for both the unsolvated peptides and the peptide water complexes at the B3LYP/6-311++G level. MP2/6-311++G** calculations were also carried out for Gly/Ala peptides. The calculations suggest that adsorption of a water molecule by these simple dipeptides is a complex process, both the unsolvated peptide and the peptide-water complexes have multiple conformations with similar free energies. Average DeltaH(o) and DeltaS(o) values derived from the calculations are in reasonable agreement with the experimental results. According to the calculations, the dominant water adsorption process involves a significant conformational change to accommodate a bridging water molecule. DeltaH(o) is diminished for Pro-Gly+H(+) mainly because the water interacts with a secondary amine, whereas for Gly-Trp+H(+), DeltaH(o) is significantly decreased by the loss of cation-pi interactions upon water adsorption. For unsolvated peptides the proton affinities of the N-terminus and the backbone carbonyl groups are known to be similar. Addition of a single water molecule causes a significant stabilization of the N-terminus protonation site.

Adsorption↗

PubMed2002

The initial steps in the hydration of unsolvated peptides: water molecule adsorption on alanine-based helices and globules.

Equilibrium constants for the adsorption of the first water molecule onto a variety of unsolvated alanine-based peptides have been measured and Delta H degrees and DeltaS degrees have been determined. The studies were designed to examine the effects of conformation, charge, and composition on the propensity for peptides to bind water. In general, water adsorption occurs significantly more readily on the globular peptides than on helical ones: several of the singly charged helical peptides were not observed to adsorb a water molecule even at -50 degrees C. These results place a limit on the free energy change for interaction between a water molecule and the helical peptide group. Molecular dynamics simulations reproduce most of the main features of the results. The ability to establish a network of hydrogen bonds to several different hydrogen-bonding partners emerges as a critical factor for strong binding of the water molecule. Whether the charge site is involved in water adsorption depends on how well it is shielded. Peptides containing a protonated histidine bind water much more strongly that those containing a protonated lysine because the delocalized charge on histidine is difficult to shield. The entropy change for adsorption of the first water molecule is correlated with the enthalpy change.

Adsorption↗