Helix compactness and stability: Electron structure calculations of conformer dependent thermodynamic functions

Jákli, Imre; Csizmadia, Imre G.; Fejer, Szilárd N.; Farkas, Ödön; Viskolcz, Béla; Jensen, Svend J. Knak; Perczel, András

doi:10.1016/j.cplett.2013.01.060

Cited by 3 publications

(5 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For a better understanding the site-specific effects on the vibrational spectra, isotopic substitutions were also performed employing the MIM method. An increasing redshift with the number of isotopically labeled 13 C=O functional groups in the peptide molecule was seen. For larger polypeptides, we implemented the two-step-MIM model to circumvent the high computational expense associated with the evaluation of chiroptical spectra at a high level of theory using large basis sets.…”

Section: Introductionmentioning

confidence: 91%

“…Alanine polypeptides are the simplest chiral amino acids, primarily used to model dynamics of secondary structure formation in proteins . Therefore, understanding the balance between various conformational isomers and the associated structural transformations of polyalanine has become an intensely studied research area …”

Section: Introductionmentioning

confidence: 99%

“…In addition, the missing long-range interfragment interactions are accounted at a computationally less expensive level of theory (MIM2). In this work we employed the MIM-VCD and MIM-ROA fragment-based methods to explore the evolution of the chiroptical spectroscopic characteristics of 3 10 -helix, α-helix, β-hairpin, γ-turn, and β-extended conformers of gas phase polyalanine (chain length n = [6][7][8][9][10][11][12][13][14]. The different conformers of polyalanine show distinctive features in the MIM chiroptical spectra and the associated spectral intensities increase with evolution of system size.…”

Section: Introductionmentioning

confidence: 99%

“…[5][6][7][8] Therefore, understanding the balance between various conformational isomers and the associated structural transformations of polyalanine has become an intensely studied research area. [9][10][11][12][13][14] Vibrational circular dichroism 15 (VCD) and Raman optical activity 16 (ROA) are widely used spectroscopic techniques to determine the absolute configurations of polypeptides. [17][18][19][20] Polypeptides show characteristic amide I, II, and III modes in their vibrational spectra.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Molecules‐in‐molecules fragment‐based method for the calculation of chiroptical spectra of large molecules: Vibrational circular dichroism and Raman optical activity spectra of alanine polypeptides

Jose

Raghavachari

2016

Chirality

View full text Add to dashboard Cite

The molecules-in-molecules (MIM) fragment-based method has recently been adapted to evaluate the chiroptical (vibrational circular dichroism [VCD] and Raman optical activity [ROA]) spectra of large molecules such as peptides. In the MIM-VCD and MIM-ROA methods, the relevant higher energy derivatives of the parent molecule are assembled from the corresponding derivatives of smaller fragment subsystems. In addition, the missing long-range interfragment interactions are accounted at a computationally less expensive level of theory (MIM2). In this work we employed the MIM-VCD and MIM-ROA fragment-based methods to explore the evolution of the chiroptical spectroscopic characteristics of 3 -helix, α-helix, β-hairpin, γ-turn, and β-extended conformers of gas phase polyalanine (chain length n = 6-14). The different conformers of polyalanine show distinctive features in the MIM chiroptical spectra and the associated spectral intensities increase with evolution of system size. For a better understanding the site-specific effects on the vibrational spectra, isotopic substitutions were also performed employing the MIM method. An increasing redshift with the number of isotopically labeled C=O functional groups in the peptide molecule was seen. For larger polypeptides, we implemented the two-step-MIM model to circumvent the high computational expense associated with the evaluation of chiroptical spectra at a high level of theory using large basis sets. The chiroptical spectra of α-(alanine) polypeptide obtained using the two-step-MIM model, including continuum solvation effects, show good agreement with the full calculations and experiment. This benchmark study suggests that the MIM-fragment approach can assist in predicting and interpreting chiroptical spectra of large polypeptides.

show abstract

Section: Introductionmentioning

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Molecules‐in‐molecules fragment‐based method for the calculation of chiroptical spectra of large molecules: Vibrational circular dichroism and Raman optical activity spectra of alanine polypeptides

Jose

Raghavachari

2016

Chirality

View full text Add to dashboard Cite

show abstract

“…65 e α-helix, also called 3.6 13 -helix, is the most abundant helical conformation of proteins. 66 e peptide backbone forms a right-handed helical structure via stabilizing intramolecular hydrogen bonds (Figure 3.5b). 18 Each NH group in the backbone forms a hydrogen bond with a backbone C=O four positions earlier in the amino acid sequence.…”

Section: Gibbs Free Energy Entropymentioning

confidence: 99%

Tunable and modular assembly of polypeptides and polypeptide-hybrid biomaterials

Aronsson¹

View full text Add to dashboard Cite

Biomaterials are materials that are speci cally designed to be in contact with biological systems and have for a long time been used in medicine. Examples of biomaterials range from sophisticated prostheses used for replacing outworn body parts to ordinary contact lenses. Currently it is possible to create biomaterials that can e.g. speci cally interact with cells or respond to certain stimuli. Peptides, the shorter version of proteins, are excellent molecules for fabrication of such biomaterials. By following and developing design rules it is possible to obtain peptides that can self-assemble into well-de ned nanostructures and biomaterials. e aim of this thesis is to create "smart" and tunable biomaterials by molecular self-assembly using dimerizing α-helical polypeptides. Two di erent, but structurally related, polypeptide-systems have been used in this thesis. e EKIV-polypeptide system was developed in this thesis and consists of four 28-residue polypeptides that can be mixed-and-matched to self-assemble into four di erent coiled coil heterodimers. e dissociation constant of the di erent heterodimers range from µM to < nM. Due to the large di erence in a nities, the polypeptides are prone to thermodynamic social self-sorting. e JR-polypeptide system, on the other hand, consists of several 42-residue de novo designed helix-loop-helix polypeptides that can dimerize into four-helix bundles. In this work, primarily the glutamic acid-rich polypeptide JR2E has been explored as a component in supramolecular materials. Dimerization was induced by exposing the polypeptide to either Zn 2+ , acidic conditions or the complementary polypeptide JR2K.By conjugating JR2E to hyaluronic acid and the EKIV-polypeptides to star-shaped poly(ethylene glycol), respectively, highly tunable hydrogels that can be self-assembled in a modular fashion have been created. In addition, self-assembly of spherical superstructures has been investigated and were obtained by linking two thiol-modi ed JR2E polypeptides via a disul de bridge in the loop region.e thesis also demonstrates that the polypeptides and the polypeptide-hybrids can be used for encapsulation and release of molecules and nanoparticles. In addition, some of the hydrogels have been explored for 3D cell culture. By using supramolecular interactions combined with bio-orthogonal I covalent crosslinking reactions, hydrogels were obtained that enabled facile encapsulation of cells that retained high viability.e results of the work presented in this thesis show that dimerizing α-helical polypeptides can be used to create modular biomaterials with properties that can be tuned by speci c molecular interactions. e modularity and the tunable properties of these smart biomaterials are conceptually very interesting and make them useful in many emerging biomedical applications, such as 3D cell culture, cell therapy, and drug delivery. II Populärvetenskaplig sammanfattningBiomaterialär material somär designade för a vara i kontakt med biologiskt material och har använts länge inom m...

show abstract

Quantum Chemical Calculations on Small Protein Models

et al. 2014

View full text Add to dashboard Cite

Helix compactness and stability: Electron structure calculations of conformer dependent thermodynamic functions

Cited by 3 publications

References 33 publications

Molecules‐in‐molecules fragment‐based method for the calculation of chiroptical spectra of large molecules: Vibrational circular dichroism and Raman optical activity spectra of alanine polypeptides

Molecules‐in‐molecules fragment‐based method for the calculation of chiroptical spectra of large molecules: Vibrational circular dichroism and Raman optical activity spectra of alanine polypeptides

Tunable and modular assembly of polypeptides and polypeptide-hybrid biomaterials

Quantum Chemical Calculations on Small Protein Models

Contact Info

Product

Resources

About