A Short Aib/Ala-Based Peptide Helix Is as Stable as an Ala-Based Peptide Helix Double Its Length

Banerjee, Raja; Basu, Gautam

doi:10.1002/1439-7633(20021202)3:12<1263::aid-cbic1263>3.0.co;2-o

Cited by 41 publications

(28 citation statements)

References 28 publications

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“…Leu- Gly-Lys-Gln from protein DNA-glycosylase (1MUG, residues 107–110) for CPS224Ac; Gly- Ser-Ala-Lys from protein Cytochrome C (1YCC, residues 1–4) for CPS226; Leu- Gly-Gly-Leu from protein Activating enzymes of the ubiquitin-like proteins (1JW9, residues 39–42) for CPS228] [13] have been appended at the N-terminus of a designed context free model anchoring helix (ABGY) [27], [28] that contained the helicogenenic Aib residue [29], [30] (Table 1). Another series of 5-residue short sequences (SCPS224Ac, SCPS226, and SCPS228) have also been designed where the anchoring helix (ABGY), after the ‘C α NN’ motif containing residues, has been replaced by ‘Ala’ residue only (Table 1).…”

Section: Resultsmentioning

confidence: 99%

Conformational Preference of ‘CαNN’ Short Peptide Motif towards Recognition of Anions

2013

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Among several ‘anion binding motifs’, the recently described ‘CαNN’ motif occurring in the loop regions preceding a helix, is conserved through evolution both in sequence and its conformation. To establish the significance of the conserved sequence and their intrinsic affinity for anions, a series of peptides containing the naturally occurring ‘CαNN’ motif at the N-terminus of a designed helix, have been modeled and studied in a context free system using computational techniques. Appearance of a single interacting site with negative binding free-energy for both the sulfate and phosphate ions, as evidenced in docking experiments, establishes that the ‘CαNN’ segment has an intrinsic affinity for anions. Molecular Dynamics (MD) simulation studies reveal that interaction with anion triggers a conformational switch from non-helical to helical state at the ‘CαNN’ segment, which extends the length of the anchoring-helix by one turn at the N-terminus. Computational experiments substantiate the significance of sequence/structural context and justify the conserved nature of the ‘CαNN’ sequence for anion recognition through “local” interaction.

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Section: Resultsmentioning

confidence: 99%

Conformational Preference of ‘CαNN’ Short Peptide Motif towards Recognition of Anions

2013

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“…The sequence Leu-Gly-Lys-Gln, a C a NN structural motif appeared in protein DNA-glycosylase, was attached at the N-terminus of a model anchor helix: Ala-Aib-Ala-Lys-Ala-Aib-Lys-AlaLys-Ala-Aib-Gly-Gly-Tyr-NH 2 (ABGY) (Banerjee and Basu, 2002;Banerjee et al, 2009) using solid phase fmoc protocol. The overall sequence of the chimeric peptide: Ac-Leu-Gly-Lys-Gln-Ala-AibAla-Lys-Ala-Aib-Lys-Ala-Lys-Ala-Aib-Gly-Gly-Tyr-NH 2 (CPS224Ac, MW 1757) would be an ideal candidate for exhibiting 'anion recognition' in isolated condition pertaining a conformational switching from the non-helical to helix conformation at the anion binding site, as observed in crystal structure (Denessiouk et al, 2005).…”

Section: Peptide Designmentioning

confidence: 99%

“…This might be either due to stabilization of helical conformation with change in helix-coil equilibrium towards helix or participation of non-helical residues in helix formation along with the stabilization of the existing helix. CD spectra of the model anchor helix (peptide ABGY in Banerjee and Basu (2002) and Banerjee et al (2009)) present at the C-terminus of the chimeric polypeptide CPS224Ac were also obtained in absence as well as in presence of sulfate ion separately. However, no appreciable change in CD spectra of ABGY were observed upon addition of sulfate ion ( Fig.…”

Section: Circular Dichroism and Ir Spectroscopymentioning

confidence: 99%

“…The underlined segment in the sequence was found to be attached with sulfate (SO 2À 4 ) ion in the reported crystal structure (Barrett et al, 1998). The segment was appended at the N-terminus of a designed model helix (Ala-Aib-Ala-Lys-Ala-Aib-Lys-Ala-Lys-Ala-AibGly-Gly-Tyr-NH 2 ) (Banerjee and Basu, 2002;Banerjee et al, 2009) whose backbone conformation was attained without any tertiary interaction. Complementary spectroscopic techniques were used to characterize the conformational landscape of this short chimeric peptide (CPS224Ac) in a context free environment in absence as well as in presence of sulfate ion.…”

Section: Introductionmentioning

confidence: 99%

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Sulfate ion interaction with ‘anion recognition’ short peptide motif at the N-terminus of an isolated helix: A conformational landscape

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Banerjee

2010

Journal of Structural Biology

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“…The efficacy of the pentameric EPYAS sequence to act as a helix N‐cap motif (in the cis Pro conformation) in short peptides was also tested by attaching the sequence motif onto the N‐termini of two helical peptides containing Ala (helix preferred), Lys (for water solubility) and Aib (B; strong helix inducer) . The shapes of the CD spectra of the peptides (Supporting Information Fig.…”

Section: Resultsmentioning

confidence: 99%

Type VIa β‐turn‐fused helix N‐termini: A novel helix N‐cap motif containing cis proline

et al. 2017

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Helix N-capping motifs often form hydrogen bonds with terminal amide groups which otherwise would be free. Also, without an amide hydrogen, proline (trans) is over-represented at helix N-termini (N1 position) because this naturally removes the need to hydrogen bond one terminal amide. However, the preference of cisPro, vis-à-vis helix N-termini, is not known. We show that cisPro (α or PP ) often appears at the N-cap position (N0) of helices. The N-cap cisPro(α ) is associated with a six-residue sequence motif - X -X -cisPro-X -X -X - with preference for Glu/Gln at X , Phe/Tyr/Trp at X and Ser/Thr at X . The motif, formed by the fusion of a helix and a type VIa β-turn, contains a hydrogen bond between the side chain of X and the side chain/backbone of X , a α-helical hydrogen bond between X and X and stacking interaction between cisPro and an aromatic residue at X . NMR experiments on peptides containing the motif and its variants showed that local interactions associated with the motif, as found in folded proteins, were not enough to significantly tilt the cis/trans equilibrium towards cisPro. This suggests that some other evolutionary pressure must select the cisPro motif (over transPro) at helix N-termini. Database analysis showed that >C = O of the pre-cisPro(α ) residue at the helix N-cap, directed opposite to the N→C helical axis, participates in long-range interactions. We hypothesize that the cisPro(α ) motif is preferred at helix N-termini because it allows the helix to participate in long-range interactions that may be structurally and functionally important.

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A Short Aib/Ala-Based Peptide Helix Is as Stable as an Ala-Based Peptide Helix Double Its Length

Cited by 41 publications

References 28 publications

Conformational Preference of ‘CαNN’ Short Peptide Motif towards Recognition of Anions

Conformational Preference of ‘CαNN’ Short Peptide Motif towards Recognition of Anions

Sulfate ion interaction with ‘anion recognition’ short peptide motif at the N-terminus of an isolated helix: A conformational landscape

Type VIa β‐turn‐fused helix N‐termini: A novel helix N‐cap motif containing cis proline

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