Cited by 355Protein Structure and DynamicsChemical Synthesis and AnalysisRNA and protein synthesis mechanisms

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Elucidating the Folding Problem of Helical Peptides using Empirical Parameters. II†. Helix Macrodipole Effects and Rational Modification of the Helical Content of Natural Peptides

Muñoz, Victor, Serrano, Luis·1995·Journal of Molecular Biology

DOI 10.1006/jmbi.1994.0023

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Abstract

Explaining the helical behaviour of amino acid sequences in solution could be one of the first steps in solving the protein folding problem in a rational way. The information about the conformational behaviour of helical peptides in solution, as well as the alpha-helix stability in proteins, has been utilised to derive a database with the energy contributions for various interaction taking place in an alpha-helix: intrinsic helical propensities, side-chain to side-chain interactions, main-chain to main-chain hydrogen bonds, and capping effects. This database was implemented in a algorithm based on the helix-coil transition theory (AGADIR). Here, the effects on helix stability due to interactions between charged groups and the helix macrodipole are described, quantified and implemented in AGADIR. The algorithm correctly calculates the average helical behaviour in solution of 423 peptides analysed by circular dichroism and it describes the helicity at a residue level, as found when comparing the prediction for each amino acid residue with the data derived from nuclear magnetic resonance studies. Using AGADIR we have done a rational modification of peptides corresponding to protein secondary structure elements in order to increase their helical content. The circular dichroism analysis of the mutant peptides showed a very good agreement between the experimental and calculated helical content. Moreover, in certain specific cases in which strong tertiary contacts in folded proteins do not exist, the algorithm successfully predicts the length of mutagenised alpha-helices. It is interesting to note that the final values of the parameters used do not significantly differ in absolute terms from those extracted from mutagenesis studies in proteins. This indicates that the same physico-chemical principles stand for both systems.

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“Support for this hypothesis is provided by calculations with a program developed by Serrano and co-workers, AGADIR1s, which explicitly includes energies for side-chain ‐side-chain interactions and side-chain ‐helix macrodipole interactions ( Munoz & Serrano, 1994, 1995, 1997 ).”
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Background
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Background
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MethodSelf-citation
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Method
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“es/ developed by the Serrano’s group [55-59] was used to predict the cementoin secondary structures.”
Method
The Solution Structure of a Chimeric LEKTI Domain Reveals a Chameleon Sequence
Tidow, H., Lauber, T., Vitzithum, K., Sommerhoff, C. P., ROSCH, P. J., & Marx, U. C. (2004) · Biochemistry · doi:10.1021/bi0492399 · Cited by 24
“This hypothesis is confirmed by the helix propensity prediction algorithm AGADIR ( 54 ), resulting in helical propensities of <2% for both the 310-helix of domain 1 and the chameleon sequence (Leu32-Ile38).”
Background
Helix propensities of conformationally restricted amino acids. Non-natural substitutes for helix breaking proline and helix forming alanine
Alı́as, M., Ayuso-Tejedor, S., Fernández‐Recio, J., Cativiela, C., & Sancho, J. (2010) · Organic & Biomolecular Chemistry · doi:10.1039/b919671d · Cited by 23
Understanding the α‐helix to coil transition in polypeptides using network rigidity: Predicting heat and cold denaturation in mixed solvent conditions
Jacobs, D. J., & Wood, G. G. (2004) · Biopolymers · doi:10.1002/bip.20102 · Cited by 23
Conformations of peptide fragments from the FK506 binding protein: comparison with the native and urea-unfolded states.
Callihan, D. E., & Logan, T. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2440 · Cited by 23
Low-Level Expression of a Folding-Incompetent Protein in Escherichia coli: Search for the Molecular Determinants of Protein Aggregation In Vivo
Winkelmann, J., Calloni, G., Campioni, S., Mannini, B., Taddei, N., & Chiti, F. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.03.030 · Cited by 22
Cellular Chaperone Function of Intrinsically Disordered Dehydrin ERD14
Murvai, N., Kalmár, L., Szabó, B., Schád, É., Micsonai, A., Kardos, J., Buday, L., Han, K., Tompa, P., & Tantos, Á. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22126190 · Cited by 23
Spectroscopic studies of the C-terminal secretion signal of the Serratia marcescens haem acquisition protein (HasA) in various membrane-mimetic environments.
Wolff, N., Delepelaire, P., Ghigo, J., & Delepierre, M. (1997) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1997.0400a.x · Cited by 23
The N-Terminal Peptides of the Three Human Isoforms of the Mitochondrial Voltage-Dependent Anion Channel Have Different Helical Propensities.
Guardiani, C., Scorciapino, M. A., Amodeo, G., Grdadolnik, J., Pappalardo, G., Pinto, V. D., Ceccarelli, M., & Casu, M. (2015) · Biochemistry · doi:10.1021/acs.biochem.5b00469 · Cited by 20
Application of modern reversed-phase peptide retention prediction algorithms to the Houghten and DeGraw dataset: Peptide helicity and its effect on prediction accuracy
Reimer, J. M., Spicer, V., & Krokhin, O. V. (2012) · Journal of Chromatography A · doi:10.1016/j.chroma.2012.07.092 · Cited by 21
Sequence and structural diversity in endotoxin-binding dodecapeptides.
Zhu, Y., Ho, B., & Ding, J. (2003) · Biochimica et Biophysica Acta · doi:10.1016/s0005-2736(03)00060-9 · Cited by 17
Stability and Design of α‐Helices
Doig, A. J., Errington, N., & Iqbalsyah, T. M. (2005) · doi:10.1002/9783527619498.ch9 · Cited by 21
Direct Ubiquitin Independent Recognition and Degradation of a Folded Protein by the Eukaryotic Proteasomes-Origin of Intrinsic Degradation Signals
Gautam, A. K. S., Balakrishnan, S., & Venkatraman, P. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034864 · Cited by 22
“Two mutants that could enhance the secondary structure in the F-helix were designed using AGADIR.”
Method
Using NMR Chemical Shifts to Determine Residue-Specific Secondary Structure Populations for Intrinsically Disordered Proteins
Borcherds, W. M., & Daughdrill, G. W. (2018) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2018.09.011 · Cited by 20
“…each method described in Section 4 for a series of six c-Myb TAD constructs: WT, P289A, P289/316A, E292D, L300G, and L300P with circular dichroism (CD) data where the percent helicity was estimated using the molar residual ellipticity at 222nm (Munoz & Serrano, 1994, 1995; Poosapati et al., 2018).”
Method
Empirical Correction for Differences in Chemical Exchange Rates in Hydrogen Exchange-Mass Spectrometry Measurements
Toth, R. T., Mills, B. J., Joshi, S. B., Esfandiary, R., Bishop, S. M., Middaugh, C. R., Volkin, D. B., & Weis, D. D. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b01396 · Cited by 20
Analysis of electrostatic interactions in the denatured state ensemble of the N‐terminal domain of L9 under native conditions
Meng, W., & Raleigh, D. (2011) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.23145 · Cited by 19
Attractive Sulfur...π Interaction between Fluorinated Dimethyl Sulfur (FDMS) and Benzene
Yan, S. (2007) · Bulletin of the Korean Chemical Society · doi:10.5012/bkcs.2007.28.6.959 · Cited by 19
Protein secondary structure and stability determined by combining exoproteolysis and matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry
Villanueva, J., Villegas, S., Querol, E., Avilés, F. X., & Serrano, L. G. (2002) · Journal of Mass Spectrometry · doi:10.1002/jms.356 · Cited by 19
Self-citation
Sequence analysis of an artificial family of RNA‐binding peptides
Barrick, J. E., & Roberts, R. W. (2002) · Protein Science · doi:10.1110/ps.0208902 · Cited by 19
Promiscuous and Selective: How Intrinsically Disordered BH3 Proteins Interact with Their Pro-survival Partner MCL-1
Dahal, L., Kwan, T. O. C., Hollins, J. J., & Clarke, J. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.04.004 · Cited by 18
NMR evidence for forming highly populated helical conformations in the partially folded hNck2 SH3 domain.
Liu, J., & Song, J.-X. (2008) · Biophysical Journal · doi:10.1529/biophysj.107.125641 · Cited by 16
“However, the prediction by AGADIR (32,33) only yielded 2.2% and 1.1% helix fractions at pH 6.5 and 2.0, respectively.”
BackgroundInfluential
Design of stable α‐helices using global sequence optimization
Petukhov, M., Tatsu, Y., Tamaki, K., Murase, S., Uekawa, H., Yoshikawa, S., Serrano, L., & Yumoto, N. (2009) · Journal of Peptide Science · doi:10.1002/psc.1122 · Cited by 18
Self-citation

Authors: Muñoz, V., & Serrano, L.
Affiliations: European Molecular Biology Laboratory (DE)
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 1995-01
Volume: 245
Issue: 3
Pages: 275-296
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1006/jmbi.1994.0023
OpenAlex: W2039104547
Cited by: 354
References: 0
Citations by year: 2026: 5 · 2025: 3 · 2024: 7 · 2023: 6 · 2022: 9 · 2021: 11 · 2020: 9 · 2019: 5 · 2018: 7 · 2017: 7 · 2016: 5 · 2015: 4 · 2014: 11 · 2013: 8 · 2012: 12
FWCI: 7.32
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Journal of Molecular Biology (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Physical Sciences › Chemistry › Organic Chemistry › Chemical Synthesis and Analysis
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords: helical peptides, protein folding, alpha-helix stability, helical propensity, side-chain interactions, hydrogen bonding, peptide modification, circular dichroism
MeSH terms: Methyl-Accepting Chemotaxis Proteins, Algorithms, Amino Acid Sequence, Bacterial Proteins, Circular Dichroism, Membrane Proteins, Models, Chemical, Molecular Sequence Data, Peptides, Recombinant Proteins, Spectrin, Protein Structure, Secondary, Protein Folding

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Elucidating the Folding Problem of Helical Peptides using Empirical Parameters. II†. Helix Macrodipole Effects and Rational Modification of the Helical Content of Natural Peptides

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