Peptide and protein folding

Chasse, Gregory A.; Rodrı́guez, Ana; Mak, Melody L; Deretey, Eugen; Perczel, András; Sosa, Carlos; Enriz, Ricardo D.; Csizmadia, Imre G.

doi:10.1016/s0166-1280(00)00687-4

Cited by 46 publications

(34 citation statements)

References 168 publications

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“…The large number of conformers is necessary to accurately characterize the topologically probable (stable) set of conformers emerging from the topologically possible set. [1][2][3][4]17,18,40,42,[50][51][52][53][54] Conformational nomenclature follows the rules outlined in the literature. [1][2][3][4]17,18,40,[50][51][52][53][54] The i 2 side chain dihedral angle (phenyl ring rotor) was modeled in the gauche + (g + ), anti (a), and gauche -(g -) conformations.…”

Section: Methodsmentioning

confidence: 99%

Characterization of the Conformational Probability of N-Acetyl-Phenylalanyl-NH₂by RHF, DFT, and MP2 Computation and AIM Analyses, Confirmed by Jet-Cooled Infrared Data

et al. 2005

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Computational and experimental determinations were carried out in parallel on the conformational probability of N-Acetyl-Phenylalanine-NH2 (NAPA). Ab initio computations were completed at the BLYP/6-311G(df,p), B3LYP/6-31G(d), B3LYP/6-31G(d,p), and B3LYP/6-31+G(d) levels of theory, labeled L/61fp, B/6, B/6p, and B/6+, respectively. Three experimentally identified conformers were compared with theoretical data, confirming their identities as the betaLanti, gammaLgauche+, and gammaLgauche- (BACKBONESIDECHAIN) conformers. Evidence comes from matching experimental and theoretical data for all three constituent N-H stretches of NAPA, with a Delta(Experimental-Theoretical) = approximately 1-3 cm(-1), approximately 0-5 cm(-1), and approximately 1-6 cm(-1), at the L/61fp and B/6+ levels, respectively. Corrected-ZPE relative energies were computed to be 0.14, 0.00, 0.26 and 0.00, 0.67, 0.57 (kcal*mol(-1)) for the betaLanti, gammaLgauche+, and gamma(Lgauche- conformers, respectively, at the L/61fp and B/6+ levels, respectively. The MP2/6-31+G(d) level of theory was subsequently found to give similar relative energies. Characterization of the intramolecular interactions responsible for red and blue shifting of the N-H stretches showed the existence of the following intramolecular interactions: C=O[i]- - -HN[i], (Ar[i])-Cgamma- - -HN[i+1], (Ar[i])-Cdelta-H- - -O=C[i-1] for betaLanti; C=O[i-1]- - -HN[i+1], (Ar[i])-Cgamma- - -HN[i+1], (Ar[i])-C-H- - -O=C[i] for gammaLgauche+; and C=O[i-1]- - -HN[i+1] for gammaLgauche-. Each of these interactions were further investigated and subsequently characterized by orbital population and Atoms-In-Molecules (AIM) analyses, with the identity of overlap and bond critical points (BCP) serving as 'scoring criteria', respectively. Experimental and theoretical carbonyl stretches were also compared and showed good agreement, adding further strength to the synergy between experiment and theory.

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Section: Methodsmentioning

confidence: 99%

Characterization of the Conformational Probability of N-Acetyl-Phenylalanyl-NH₂by RHF, DFT, and MP2 Computation and AIM Analyses, Confirmed by Jet-Cooled Infrared Data

et al. 2005

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“…Esterase is including carboxylesterase, thioesterase, lipase, phosphomonoesterase, and phosphodiesterase depends on substrate specificity (Chasse et al, 2001). However carboxylesterase is usually defined as an esterase.…”

Section: (B) (C)mentioning

confidence: 99%

Cloning and characterization of thermostable esterase from Archaeoglobus fulgidus

2008

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Thermostable esterase gene was cloned (Est-AF) from extremophilic microorganisms, Archaeoglobus fulgidus DSM 4304. The protein analysis result showed that Est-AF is monomer with total 247 amino acids and molecular weight of estimated 27.5 kDa. It also showed repeating units G-X-S-X-G (GHSLG) (residues 86 approximately 90) which is reported as active site of known esterases, and the putative catalytic triad composed of Ser88, Asp198 and His226. The esterase activity test with various acyl chain length of rho-nitrophenol resulted that Est-AF showed highest specific activity with rho-nitrophenylbutyrate (pNPC4) and rapidly decrease with rho-nitrophenyl ester contain more than 8 carbon chain. These results represent that cloned enzyme is verified as a carboxylesterase but not a lipase because esterase activity is decreased with rho-nitrophenyl ester contains more than 8 carbon chains but lipase activity does not affected with carbon chain length. Optimum temperature of esterase reaction with rho-nitrophenylbutyrate (pNPC4) was 80 degrees C. When ketoprofen ethyl ester was used as a substrate, activity of Est-AF showed the highest value at 70 degrees C, and 10% of activity still remains after 3 h of incubation at 90 degrees C. This result represents Est-AF has high thermostability with comparison of other esterases that have been reported. However, Est-AF showed low enantioselectivity with ketoprofen ethyl ester. Optimum pH of Est-AF is between pH 7.0 and pH 8.0. Km value of ketoprofen ethyl ester is 1.6 mM and, Vmax is 1.7 micromole/mg protein/min. Est-AF showed similar substrate affinity but slower reaction with ketoprofen ethyl ester compare with esterase from mesophilic strain P. fluorescens.

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“…In a strong polar solvent like water, the interactions among the nearest-neighbor residues of the dipeptides are dramatically modified as compared to those in gas phase, which consequently affect the Ramachandran dihedrals ( ψ , ϕ ) [24, 25] and confer markedly different conformations to the dipeptides in the aqueous phase. Investigations of the numerous parameters involved in dipeptide structure prediction have now been regarded as a pivotal part of the computational studies concerning the structure of protein and energetics of protein folding [26]. …”

Section: Introductionmentioning

confidence: 99%

Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides

Das

Mandal

2013

Biochemistry Research International

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In this theoretical study, the role of the side chain moiety of C-terminal residue in influencing the structural and molecular properties of dipeptides is analyzed by considering a series of seven dipeptides. The C-terminal positions of the dipeptides are varied with seven different amino acid residues, namely. Val, Leu, Asp, Ser, Gln, His, and Pyl while their N-terminal positions are kept constant with Sec residues. Full geometry optimization and vibrational frequency calculations are carried out at B3LYP/6-311++G(d,p) level in gas and aqueous phase. The stereo-electronic effects of the side chain moieties of C-terminal residues are found to influence the values of Φ and Ω dihedrals, planarity of the peptide planes, and geometry around the C7 α-carbon atoms of the dipeptides. The gas phase intramolecular H-bond combinations of the dipeptides are similar to those in aqueous phase. The theoretical vibrational spectra of the dipeptides reflect the nature of intramolecular H-bonds existing in the dipeptide structures. Solvation effects of aqueous environment are evident on the geometrical parameters related to the amide planes, dipole moments, HOMOLUMO energy gaps as well as thermodynamic stability of the dipeptides.

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Peptide and protein folding

Cited by 46 publications

References 168 publications

Characterization of the Conformational Probability of N-Acetyl-Phenylalanyl-NH₂by RHF, DFT, and MP2 Computation and AIM Analyses, Confirmed by Jet-Cooled Infrared Data

Characterization of the Conformational Probability of N-Acetyl-Phenylalanyl-NH₂by RHF, DFT, and MP2 Computation and AIM Analyses, Confirmed by Jet-Cooled Infrared Data

Cloning and characterization of thermostable esterase from Archaeoglobus fulgidus

Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides

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Peptide and protein folding

Cited by 46 publications

References 168 publications

Characterization of the Conformational Probability of N-Acetyl-Phenylalanyl-NH2by RHF, DFT, and MP2 Computation and AIM Analyses, Confirmed by Jet-Cooled Infrared Data

Characterization of the Conformational Probability of N-Acetyl-Phenylalanyl-NH2by RHF, DFT, and MP2 Computation and AIM Analyses, Confirmed by Jet-Cooled Infrared Data

Cloning and characterization of thermostable esterase from Archaeoglobus fulgidus

Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides

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Product

Resources

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Characterization of the Conformational Probability of N-Acetyl-Phenylalanyl-NH₂by RHF, DFT, and MP2 Computation and AIM Analyses, Confirmed by Jet-Cooled Infrared Data

Characterization of the Conformational Probability of N-Acetyl-Phenylalanyl-NH₂by RHF, DFT, and MP2 Computation and AIM Analyses, Confirmed by Jet-Cooled Infrared Data