Helical preferences of alanine, glycine, and aminoisobutyric homopeptides

Alemán, Carlos; Roca, Ramón; Luque, F. Javier; Orozco, Modesto

doi:10.1002/(sici)1097-0134(199705)28:1<83::aid-prot8>3.0.co;2-k

Cited by 43 publications

(37 citation statements)

References 57 publications

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“…According to the criteria defined in Eqns (1)-(3), CE is negative or positive in the presence of cooperative or anti-cooperative effects, respectively. It should be noted that CE represents a valuable parameter, which has already been used to study the intrinsic tendency of both coded and non-coded amino acid residues to adopt regular conformations [83][84][85]. Our results, displayed in Figure 15, reveal unfavorable CE values, independently of n. Moreover, CE grows linearly with the number of Adm residues.…”

Section: Conformational Energy Calculationsmentioning

confidence: 65%

En route towards the peptide γ‐helix: X‐ray diffraction analyses and conformational energy calculations of Adm‐rich short peptides

Mazzier

Grassi

Moretto

et al. 2016

Journal of Peptide Science

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We performed the solution-phase synthesis of a set of model peptides, including homo-oligomers, based on the 2-aminoadamantane-2-carboxylic acid (Adm) residue, an extremely bulky, highly lipophilic, tricyclic, achiral, C -tetrasubstituted α-amino acid. In particular, for the difficult peptide coupling reaction between two Adm residues, we took advantage of the Meldal's α-azidoacyl chloride approach. Most of the synthesized Adm peptides were characterized by single-crystal X-ray diffraction analyses. The results indicate a significant propensity for the Adm residue to adopt γ-turn and γ-turn-like conformations. Interestingly, we found that a -CO-(Adm) -NH- sequence is folded in the crystal state into a regular, incipient γ-helix, at variance with the behavior of all of the homo-dipeptides from C -tetrasubstituted α-amino acids already investigated, which tend to adopt either the β-turn or the fully extended conformation. Our density functional theory conformational energy calculations on the terminally blocked homo-peptides (n = 2-8) fully confirmed the crystal-state data, strongly supporting the view that this rigid C -tetrasubstituted α-amino acid residue is largely the most effective building block for γ-helix induction, although to a limited length (anti-cooperative effect). Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

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Section: Conformational Energy Calculationsmentioning

confidence: 65%

En route towards the peptide γ‐helix: X‐ray diffraction analyses and conformational energy calculations of Adm‐rich short peptides

Mazzier

Grassi

Moretto

et al. 2016

Journal of Peptide Science

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“…The cooling system may be an essential condition to obtain unstable glycine polymers. We speculated that alanine polymers were stable due to the formation of helix forms [24,25], but glycine polymers were unstable due to the large flexibility of the residues under CO 2 conditions, like in the aqueous model [25]. …”

Section: Resultsmentioning

confidence: 99%

Amino Acid Synthesis in a Supercritical Carbon Dioxide - Water System

Fujioka

Futamura

Shiohara

et al. 2009

IJMS

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Mars is a CO2-abundant planet, whereas early Earth is thought to be also CO2-abundant. In addition, water was also discovered on Mars in 2008. From the facts and theory, we assumed that soda fountains were present on both planets, and this affected amino acid synthesis. Here, using a supercritical CO2/liquid H2O (10:1) system which mimicked crust soda fountains, we demonstrate production of amino acids from hydroxylamine (nitrogen source) and keto acids (oxylic acid sources). In this research, several amino acids were detected with an amino acid analyzer. Moreover, alanine polymers were detected with LC-MS. Our research lights up a new pathway in the study of life’s origin.

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“…Baldwin et al used a sequence of experimental approaches on this type of polymers [19][20][21][22] which have been complemented by an array of theoretical methods including Molecular Dynamics [23][24][25] (MD) and various types of conformational sampling and Monte Carlo algorithms [26][27][28][29][30][31][32][33] . In helix-coil theory, forming the first helical turn stabilized by (i,i+4) backbone hydrogen bonds nucleates a helix, followed by helix propagation.…”

Section: Introductionmentioning

confidence: 99%

Reversible folding/unfolding of small a-helix in explicit solvent investigated by ABEEMσπ/MM

Cui

Zhong‐zhi

2009

Sci. China Ser. B-Chem.

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We have performed molecular dynamics simulations on the reversible folding/unfolding of small α-helix (short Ala based peptide Ala 5 ) in explicit water solvent in terms of ABEEMσπ/MM. A dynamics analysis shows that the α-helical turn can be preserved up to a period of about 2 ns at 300 K, which supports the conclusions of Margulis et al. The time trajectory of the root mean square deviation between the heavy atoms of the backbone and the helical reference structure indicate that "helix melting and formation occurs rapidly on a time scale of 0.1 ns at 300 K" is not a felicitous conclusion. We first quantificationally concluded that the helix nucleation can maintain 2 ns, 1-1.5 ns and 0.8 ns for Ala 5 at 300 K, 400 K and 500 K, respectively. Furthermore, increasing temperature dose not alter the pathway of folding/unfolding, but change the rate. An analysis of structures in a "transition-state ensemble" shows that helix-to-coil transitions occurs predominantly through breaking of hydrogen bonds at the helix ends (92%), particularly at the C-terminus(50%). Hydrogen bonds' breaking and formation occurs on a time scale of 0.1 ns.reversible folding/unfolding of protein, Ala 5 , temperature, hydrogen bond

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Helical preferences of alanine, glycine, and aminoisobutyric homopeptides

Cited by 43 publications

References 57 publications

En route towards the peptide γ‐helix: X‐ray diffraction analyses and conformational energy calculations of Adm‐rich short peptides

En route towards the peptide γ‐helix: X‐ray diffraction analyses and conformational energy calculations of Adm‐rich short peptides

Amino Acid Synthesis in a Supercritical Carbon Dioxide - Water System

Reversible folding/unfolding of small a-helix in explicit solvent investigated by ABEEMσπ/MM

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