Secondary Structure of Ac-Alan-LysH+ Polyalanine Peptides (n = 5,10,15) in Vacuo: Helical or Not?

Rossi, Mariana; Blüm, Volker; Kupser, Peter; Helden, Gert von; Bierau, Frauke; Pagel, Kevin; Meijer, Gerard; Scheffler, Matthias

doi:10.1021/jz101394u

Cited by 79 publications

(153 citation statements)

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“…At 800 K the polypeptide is essentially unfolded after 7 ps and remains unfolded up to 30 ps. It is remarkable that our PBE þ vdW results are thus far consistent with the experimental upper limit for helix stability of T % 725 K, while this is not at all the case for plain PBE results, not even for 3 10 instead of . In addition, also the conformational landscapes with and without vdW interactions differ markedly from one another.…”

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confidence: 73%

“…In fact, in vacuo proteins frequently preserve the secondary structure (helices and sheets) observed in solution, and recent results [7] have shown that even tertiary and quaternary structures can be transferred into the gas phase. Joint experimental and ab initio theoretical studies can now successfully determine the geometries of small gas-phase peptides [8][9][10]. Nevertheless, many fundamental questions remain open, such as: (1) How stable is the folded polypeptide helix in comparison to other (meta)-stable structures?…”

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confidence: 99%

“…This allows us to monitor the stabilization of the -helical motif towards the well-defined limit of a perfect infinite alpha helix, and to compare to the direct periodic calculations below. The terminating groups COOH and NH 2 as well as the Ala residues closest to the C terminus are relaxed for n ¼ 5, and then kept at that structure for larger n. For charge-terminated peptides, geometry relaxation does not change the results appreciably, but for neutral peptides short helices are directly unstable [10,24], and would prevent us from comparing charged and neutral systems. The circular symbols in Fig.…”

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Unraveling the Stability of Polypeptide Helices: Critical Role of van der Waals Interactions

et al. 2011

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Folding and unfolding processes are important for the functional capability of polypeptides and proteins. In contrast with a physiological environment (solvated or condensed phases), an in vacuo study provides well-defined ''clean room'' conditions to analyze the intramolecular interactions that largely control the structure, stability, and folding or unfolding dynamics. Here we show that a proper consideration of van der Waals (vdW) dispersion forces in density-functional theory (DFT) is essential, and a recently developed DFT þ vdW approach enables long time-scale ab initio molecular dynamics simulations at an accuracy close to ''gold standard'' quantum-chemical calculations. The results show that the inclusion of vdW interactions qualitatively changes the conformational landscape of alanine polypeptides, and greatly enhances the thermal stability of helical structures, in agreement with gas-phase experiments. The helical motif is a ubiquitous conformation of amino acids in protein structures, and helix formation is a fundamental step of the protein folding process [1][2][3]. Simulations of helix formation and stability are typically carried out in solvent or condensed phases using classical, empirical ''force fields.'' However, different force field parameterizations lead to reliable results only for a narrow class of systems and conditions. A truly bottom-up understanding of polypeptide structure and dynamics would greatly benefit from a first-principles quantum-mechanical treatment, as it becomes increasingly more feasible for large systems and long time scales. In particular, quantum-mechanical simulations in vacuo are invaluable for a quantitative understanding of the intramolecular forces that largely control the structure, stability and (un) folding dynamics of polypeptides.Recent progress in the experimental isolation and spectroscopies of gas-phase biological molecules has lead to increasingly refined vibrational spectra for the structure of peptides and proteins [4][5][6]. In fact, in vacuo proteins frequently preserve the secondary structure (helices and sheets) observed in solution, and recent results [7] have shown that even tertiary and quaternary structures can be transferred into the gas phase. Joint experimental and ab initio theoretical studies can now successfully determine the geometries of small gas-phase peptides [8][9][10]. Nevertheless, many fundamental questions remain open, such as: (1) How stable is the folded polypeptide helix in comparison to other (meta)-stable structures? (2) How important are the different enthalpic and entropic contributions to the stability of helical conformations? Here we provide quantitative insight into the above two questions from first principles for the fundamental case of polyalanine helices in vacuo. Our study reveals the crucial role that van der Waals (vdW) interactions play for the helix stability and dynamics, illustrating how entropy is significantly altered as well. We choose polyalanine as a target for our study due to its high propensity to fo...

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Unraveling the Stability of Polypeptide Helices: Critical Role of van der Waals Interactions

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“…A similar fluxional behavior for Si 6 [31,40] lead to a broadening of the IR absorption bands. We have investigated the possibility that dynamic and anharmonic effects are responsible for the band broadening in the IR-MPD spectrum of Si 16 V þ using a molecular dynamics (MD) simulation performed with the FHI-AIMS program [41,42]. An IR spectrum is obtained from the MD trajectory as the Fourier transform of the autocorrelation function of the time-dependent dipole moment [43].…”

Section: Prl 107 173401 (2011) P H Y S I C a L R E V I E W L E T T Ementioning

confidence: 99%

Structural Identification of Caged Vanadium Doped Silicon Clusters

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The geometry of cationic silicon clusters doped with vanadium, Si n V þ (n ¼ 12-16), is investigated by using infrared multiple photon dissociation of the corresponding rare gas complexes in combination with ab initio calculations. It is shown that the clusters are endohedral cages, and evidence is provided that Si 16 V þ is a fluxional system with a symmetric Frank-Kasper geometry. DOI: 10.1103/PhysRevLett.107.173401 PACS numbers: 36.40.Mr, 33.20.Ea, 61.46.Bc The ongoing trend towards further miniaturization in microelectronics triggers a quest for nanostructured building blocks. Given the importance of silicon in the semiconductor industry, it is straightforward to consider small silicon particles for nanostructuring. The search for silicon building blocks was initiated in the 1990s and revealed strong size dependencies and cluster geometries that do not correspond to bulk fragments [1]. Unfortunately, elemental silicon clusters have dangling bonds, which renders them chemically reactive and therefore not suitable as nanoscale building blocks [2]. In contrast to carbon, silicon prefers the formation of bonds through sp 3 hybridization, resulting in three-dimensional structures [3]. Ion mobility studies demonstrated that silicon structures follow a prolate growth sequence and no fullerenelike caged particles are formed [4,5]. However, incorporating a metal atom or hydrogenation can saturate the dangling bonds and induce the formation of caged silicon clusters [3,6,7].Theoretical investigations of doped silicon clusters have considered dopants from almost every group of the periodic table [6]. Most interestingly, it is predicted that transition-metal atoms possibly stabilize the clusters and induce the formation of symmetric endohedral cages with the dopant atom at the center of the cage, which is of relevance for novel silicon based nanostructured devices [8][9][10][11][12]. For example, fullerenelike cages and Frank-Kasper (FK) polyhedrons, which are tetrahedrally close-packed structures containing interpenetrating polyhedra with coordination numbers 12, 14, 15, or 16 [13], are predicted for Ti and V doped silicon clusters with at least 12 Si atoms [10,14,15]. However, if there are insufficient Si atoms to fully enclose the dopant atom, basketlike structures are formed [11]. Although mass spectrometry and photodissociation experiments [8,[16][17][18][19] show an enhanced stability of specific transition-metal doped silicon clusters, no single experiment has yet provided detailed information on their structure. Up to now, mainly indirect evidence is found for the formation of symmetric species by photoelectron and x-ray spectroscopy studies [20][21][22] and chemical probe methods [20,23].In this Letter, the structure of size selected endohedrally doped silicon clusters is obtained by combining experimental infrared multiple photon dissociation (IR-MPD) spectroscopy with quantum chemical calculations. It will be shown that the V dopant atom in the cationic Si n V þ (n ¼ 12-16) clusters locates at the center ...

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“…1,2,[5][6][7][8][9] For complex molecules, structural assignment by action spectroscopy methods requires comparison with computed spectra. In recent decades, advances in quantum chemistry methods and computer hardware have established density functional theory (DFT) as the framework of choice to compute IR and optical spectra.…”

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Nonlinear effects in infrared action spectroscopy of silicon and vanadium oxide clusters: experiment and kinetic modeling

Calvo

Kiawi

et al. 2015

Phys. Chem. Chem. Phys.

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For structural assignment of gas phase compounds, infrared action spectra are usually compared to computed linear absorption spectra. However, action spectroscopy is highly nonlinear owing to the necessary transfer of the excitation energy and its subsequent redistribution leading to statistical ionization or dissociation. Here, we examine by joint experiment and dedicated modeling how such nonlinear effects affect the spectroscopic features in the case of selected inorganic clusters. Vibrational spectra of neutral silicon clusters are recorded by tunable IR-UV two-color ionization while IR spectra for cationic vanadium oxide clusters are obtained by IR multiphoton absorption followed by dissociation of the bare cluster or of its complex with Xe. Our kinetic modeling accounts for vibrational anharmonicities, for the laser interaction through photon absorption and stimulated emission rates, as well as for the relevant ionization or dissociation rates, all based on input parameters from quantum on the average number of photons absorbed, which is otherwise unaccessible information: several to several tens of photons need to be absorbed to observe a band through dissociation, while three to five photons can be sufficient for detection of a band via IR-UV ionization.

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Secondary Structure of Ac-Ala_n-LysH⁺ Polyalanine Peptides (n = 5,10,15) in Vacuo: Helical or Not?

Cited by 79 publications

References 45 publications

Unraveling the Stability of Polypeptide Helices: Critical Role of van der Waals Interactions

Unraveling the Stability of Polypeptide Helices: Critical Role of van der Waals Interactions

Structural Identification of Caged Vanadium Doped Silicon Clusters

Nonlinear effects in infrared action spectroscopy of silicon and vanadium oxide clusters: experiment and kinetic modeling

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