8 research outputs found
Secondary structure of Ac-Ala-LysH polyalanine peptides (=5,10,15) in vacuo: Helical or not?
The polyalanine-based peptide series Ac-Ala_n-LysH+ (n=5-20) is a prime
example that a secondary structure motif which is well-known from the solution
phase (here: helices) can be formed in vacuo. We here revisit this conclusion
for n=5,10,15, using density-functional theory (van der Waals corrected
generalized gradient approximation), and gas-phase infrared vibrational
spectroscopy. For the longer molecules (n=10,15) \alpha-helical models provide
good qualitative agreement (theory vs. experiment) already in the harmonic
approximation. For n=5, the lowest energy conformer is not a simple helix, but
competes closely with \alpha-helical motifs at 300K. Close agreement between
infrared spectra from experiment and ab initio molecular dynamics (including
anharmonic effects) supports our findings.Comment: 4 pages, 4 figures, Submitted to JPC Letter
Exploring the conformational preferences of 20-residue peptides in isolation: Ac-Ala 19
Infrarotspektroskopie zur Charakterisierung von Sekundärstrukturelementen von Biomolekülen in der Gasphase
Vibrational spectroscopy is a commonly used method in structural
investigations of biomolecules in the condensed phase. Vibrational modes, such
as C−O stretching vibrations (amide-I) in the range of 1700 cm−1 or N−H
bending vibrations (amide-II) at around 1500 cm−1 , are sensitive to the
three-dimensional arrangement of the atoms in the proteins. Knowledge of the
band positions makes it possible to obtain a global picture of the fundamental
conformation of the molecule. Investigations on gas-phase biomolecules allow
for an insight into the intrinsic intra-molecular interactions, which
determine the molecular structure. Many proteins possess secondary structural
elements, including for instance α-helix and β-sheet, and these motifs often
determine the structure of the entire protein. For this thesis biomolecules in
the gas phase were investigated using infrared spectroscopy, the goal being to
define band positions of significant structural characteristics in the
infrared spectrum. The amide-I band position for the various secondary
structural elements was an area of particular research interest. In the
pursuit of these research aims mass spectrometry, infrared spectroscopy, and
density functional theory methodologies were employed.Schwingungsspektroskopie ist eine gebräuchliche Methode zur Strukturaufklärung
von Biomolekülen in der kondensierten Phase. Schwingungsmoden, wie zum
Beispiel die C−O Streckschwingung (Amid-I Bande) im Bereich von 1700 cm−1 oder
die N−H Biegeschwingung (Amid-II Bande) bei 1500 cm−1 sind empfindlich auf die
dreidimensionale Anordnung der Atome in Proteinen. Die Kenntnis der
Bandenposition kann es ermöglichen, ein umfassendes Bild der zugrundeliegenden
Konformation des Moleküls zu erhalten. Untersuchungen an Biomolekülen in der
Gasphase können einen Einblick in die intrinsischen strukturbestimmenden
Wechselwirkungen des Moleküls liefern. Vielen Proteinen sind
Sekundärstrukturelemente, wie zum Beispiel die α-Helix oder das β-Faltblatt
gemein und deren Motive bestimmen häufig die Struktur des ganzen Proteins. Im
Rahmen dieser Arbeit wurden Biomoleküle in der Gasphase mittels
Infrarotspektroskopie untersucht. Das Ziel war es, strukturcharakteristische
Bandenpositionen im Infrarotspektrum, insbesondere die der Amid-I Bande, von
verschiedenen Sekundärstrukturelementen zu finden. Hierzu wurden Methoden der
Massenspektrometrie mit denen der Infrarotspektroskopie sowie der
Dichtefunktionaltheorie verbunden
Catching proteins in liquid helium droplets
Contains fulltext :
99068.pdf (preprint version ) (Open Access
Amide-I and -II Vibrations of the Cyclic β-Sheet Model Peptide Gramicidin S in the Gas Phase
In the condensed phase, the peptide gramicidin S is often considered
as a model system for a β-sheet structure. Here, we investigate
gramicidin S free of any influences of the environment by measuring
the mid-IR spectra of doubly protonated (deuterated) gramicidin S
in the gas phase. In the amide I (i.e., Cî—»O stretch) region,
the spectra show a broad split peak between 1580 and 1720 cm<sup>−1</sup>. To deduce structural information, the conformational space has
been searched using molecular dynamics methods and several structural
candidates have been further investigated at the density functional
level. The calculations show the importance of the interactions of
the charged side-chains with the backbone, which is responsible for
the lower frequency part of the amide I peak. When this interaction
is inhibited via complexation with two 18-crown-6 molecules, the amide
I peak narrows and shows two maxima at 1653 and 1680 cm<sup>−1</sup>. A comparison to calculations shows that for this complexed ion,
four CO groups are in an antiparallel β-sheet arrangement.
Surprisingly, an analysis of the calculated spectra shows that these
β-sheet CO groups give rise to the vibrations near 1680
cm<sup>−1</sup>. This is in sharp contrast to expectations
based on values for the condensed phase, where resonances of β-sheet
sections are thought to occur near 1630 cm<sup>−1</sup>. The
difference between those values might be caused by interactions with
the environment, as the condensed phase value is mostly deduced for
β-sheet sections that are embedded in larger proteins, that
interact strongly with solvent or that are part of partially aggregated
species
Secondary Structure of Ac-Ala<sub><i>n</i></sub>-LysH<sup>+</sup> Polyalanine Peptides (<i>n</i> = 5,10,15) in Vacuo: Helical or Not?
The polyalanine-based peptide series Ac-Ala<sub><i>n</i></sub>-LysH<sup>+</sup> (<i>n</i> = 5−20) is a prime example that a secondary structure motif that is well-known from the solution phase (here: helices) can be formed in vacuo. Here we revisit the series members <i>n</i> = 5,10,15, using density functional theory (van der Waals corrected generalized gradient approximation) for structure predictions, which are then corroborated by room temperature gas-phase infrared vibrational spectroscopy. We employ a <i>quantitative</i> comparison based on Pendry’s reliability factor (popular in surface crystallography). In particular, including <i>anharmonic</i> effects into calculated spectra by way of ab initio molecular dynamics produces remarkably good experiment−theory agreement. We find the longer molecules (<i>n</i> = 10,15) to be firmly α-helical in character. For <i>n</i> = 5, calculated free-energy differences show different H-bond networks to still compete closely. Vibrational spectroscopy indicates a predominance of α-helical motifs at 300 K, but the lowest-energy conformer is not a simple helix
Ir spectroscopy of gas-phase c(60)(-)
Contains fulltext :
99138.pdf (publisher's version ) (Open Access