Peptide models XXIV: An ab initio study on N-formyl-L-prolinamide with trans peptide bond. The existence or non-existence of αL and ϵL conformations

Baldoni, Héctor A.; Rodrı́guez, Ana; Zamora, Miguel A.; Zamarbide, Graciela N.; Enriz, Ricardo D.; Farkas, Ödön; Császár, Pál; Torday, Ladislaus L.; Sosa, Carlos; Jákli, Imre; Perzel, Andràs; Papp, Julius Gy.; Hollósi, Miklós; Csizmadia, Imre G.

doi:10.1016/s0166-1280(98)00571-5

Cited by 54 publications

(50 citation statements)

References 19 publications

(19 reference statements)

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“…For a more detailed tabulation of results see ref. 36. Experimentally obtained conformational parameters (Table 8, vide infra) reveal that serine residues are most commonly found either in the ␣ L (␣-helical) or ␤ L (␤-pleated sheet) conformations and that other backbone types occur far less frequently.…”

Section: Structure and Energeticsmentioning

confidence: 97%

“…Geometry optimizations of small fragments provide a relatively small number of low-energy minima on the related potential energy surface that closely resemble experimentally observed structures. 36,37 Ab initio NMR shielding calculations employing such optimized fragments seem to result in reliable chemical shifts. Furthermore, because ab initio NMR calculations can be carried out using any reference structure, chemical shift-structure correlations of all kinds can be investigated.…”

Section: Introductionmentioning

confidence: 97%

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Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N‐formyl‐serinamide, a model for polar side‐chain containing peptides

2003

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Knowledge of chemical shift-structure relationships could greatly facilitate the NMR chemical shift assignment and structure refinement processes that occur during peptide/protein structure determination via NMR spectroscopy. To determine whether such correlations exist for polar side chain containing amino acid residues the serine dipeptide model, For-L-Ser-NH(2), was studied. Using the GIAO-RHF/6-31+G(d) and GIAO-RHF/TZ2P levels of theory the NMR chemical shifts of all hydrogen ((1)H(N), (1)H(alpha), (1)H(beta1), (1)H(beta2)), carbon ((13)C(alpha), (13)C(beta), (13)C') and nitrogen ((15)N) atoms have been computed for all 44 stable conformers of For-L-Ser-NH(2). An attempt was made to establish correlation between chemical shift of each nucleus and the major conformational variables (omega(0), phi, psi, omega(1), chi,(1) and chi(2)). At both levels of theory a linear correlation can be observed between (1)H(alpha)/phi, (13)C(alpha)/phi, and (13)C(alpha)/psi. These results indicate that the backbone and side-chain structures of For-L-Ser-NH(2) have a strong influence on its chemical shifts.

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Section: Structure and Energeticsmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 97%

Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N‐formyl‐serinamide, a model for polar side‐chain containing peptides

2003

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“…In recent years, several theoretical approaches (Baldoni et al, 1999;Head-Gordan et al,1989;McAllister et al, 1998;Perczel et al,1991;Rodrıguez et al, 1998;) have been used to study two-dimensional potential energy surface E(φ ,ψ) of CH3COHN-CHR-CONHCH3 or HCONH-CHR-CONH2. The multi-dimensional conformational analysis process (MDCA) states (Perczel et al, 1991) the existence of nine minimum, designated by Greek letters Chemistry International 5(2) (2019) [132][133][134][135][136][137][138][139][140][141][142] Theoretical study of the potential energy surface of N-formyl-L-cysteine-amide by using a genetic algorithm multi niche crowding Malika…”

Section: Introductionmentioning

confidence: 99%

Theoretical study of the potential energy surface of N-formyl-L-cysteine-amide by using a genetic algorithm multi niche crowding

Int¹

2019

Preprint

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The generation of molecular structures constituting the conformational space of trans-N-For-L-Cys-NH2 was accomplished using the genetic algorithm MNC coupled to the semi-empirical AM1 method, AM1/GA-MNC. The structural and energy analysis of the obtained conformational space E=E(,ψ) locates 7 regions or minima ɣL, ɣD, L, D, L, ɛD and ɛL. The combination of these folds to structuring modes adopted by the side chain CH2-SH has allowed us to identify 27 stable geometric structures. The regions corresponding to helical folds αD and αL are not favorable for the system that is the subject of current study.Capsule Summary: Molecular structure of trans-N-For-L-Cys-NH2 was studied using the genetic algorithm MNC coupled to the semi-empirical AM1 method, AM1/GA-MNC and combination of the folds to structuring modes adopted by the side chain CH2-SH revealed the possibility of 27 stable geometric structures of N-For-L-Cys-NH2. Cite This Article As:

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“…Note that − or + opposes the sign of the phase angle and in most cases agrees with the sign of χ i 1 . Ring pucker − and + are called also Up and Down,45 or anti and syn,37 respectively. G: The 12 ideal conformers of a single L ‐proline residue according to their positions in the conformational space defined by independent variables ω i −1 , P i and ψ i 38,42…”

Section: Introductionmentioning

confidence: 99%

“…N ‐Formyl– L ‐prolinamide with trans peptide bond was studied previously at HF/3‐21G (Hartree‐Fock), HF/6‐31G, and B3LYP/6‐31G levels of theory 37. The global minimum was found to be the inverse γ‐turn ( γ L + ).…”

Section: Introductionmentioning

confidence: 99%

Prolylproline unit in model peptides and in fragments from databases

Hudáky

Perczel

2007

Proteins

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The prolylproline sequence unit is found in several naturally occurring linear and cyclic peptides with immunosuppressive and toxic activity. Furthermore, Pro-Pro units are abundant in collagen, in ligand motifs binding to SH3 or WW domains, as well as in vital enzymes such as DNA glycosylase and thrombin. In all these sequence units a special role is dedicated to conformation in order to successfully fulfill the appropriate biological function. Therefore, a detailed analysis of the basic conformational properties of Pro-Pro is expected to reveal the versatile structural role of this sequence. PCM (polarizable continuum model) calculations on the basis of ab initio and density functional theory investigations using the model peptide HCO-L-Pro-L-Pro-NH2 are presented. Cis-trans isomerism, backbone conformation and ring puckering are studied. A systematic comparison is made to experimental data gained on L-prolyl-L-proline sequence units retrieved from the Protein Data Bank as well as from the Cambridge Structural Database. PCM data are in good agreement with high-resolution X-ray crystallography. Population data derived from energy calculations and those gained directly from statistics predict that 87% of the Pro-Pro sequence units adopt elongated structures, while 13% form beta-turns. Both approaches prefer the same 6 out of the 36 ideally possible backbone folds. Polyproline II unit (t epsilonL t epsilonL), other elongated structures (c epsilonL t epsilonL, t epsilonL t alphaL and t epsilonL t gammaL), type VIa (t epsilonL c alphaL) and type I or III beta-turns (t alphaL t alphaL) altogether describe 96% of the prolylproline sequences. In disordered proteins or domains, Pro-Pro sequence units may sample the various conformers and contribute to the segmental motions.

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Peptide models XXIV: An ab initio study on N-formyl-L-prolinamide with trans peptide bond. The existence or non-existence of αL and ϵL conformations

Cited by 54 publications

References 19 publications

Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N‐formyl‐serinamide, a model for polar side‐chain containing peptides

Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N‐formyl‐serinamide, a model for polar side‐chain containing peptides

Theoretical study of the potential energy surface of N-formyl-L-cysteine-amide by using a genetic algorithm multi niche crowding

Prolylproline unit in model peptides and in fragments from databases

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