Effect of proline residues on protein folding

doi:10.1016/0022-2836(81)90342-9

Journal of Molecular Biology

Volume 145, Issue 1, 5 January 1981, Pages 251-263

https://doi.org/10.1016/0022-2836(81)90342-9 Get rights and content

Abstract

Conformational energy calculations have been used to study the role of the proline residues in the folding of bovine pancreatic trypsin inhibitor. In the calculation, each of the four proline residues of this small protein is forced from the trans to cis peptide isomer while still part of the native folded structure. The cis proline residue can always be accommodated by small changes of the native conformation (< 1 Å root-mean-square deviation). For three of the four proline residues, Pro2, Pro9 and Pro 13, being in the cis form is calculated to destabilize the folded conformation by less than 11 kcal/mol, suggesting that rapid folding to a stable native-like conformation can occur with either isomeric form. For one of these three, Pro13, the destabilization is only 1 kcal/mol, suggesting the existence of an alternative folded native conformation with Pro13 cis. The fourth proline residue, Pro8, is calculated to destabilize the native conformation by so much (33 kcal/mol) that it will block folding in the manner proposed by Brandts et al. (1975).

References (29)

R.L. Baldwin
Trends Biochem. Sci
(1978)
T.E. Creighton
J. Mol. Biol
(1977)
T.E. Creighton
J. Mol. Biol
(1978)
T.E. Creighton
J. Mol. Biol
(1980)
J.-R. Garel et al.
J. Mol. Biol
(1975)
M. Levitt
J. Mol. Biol
(1974)
M. Levitt et al.
J. Mol. Biol
(1969)
S. Lifson et al.
Comp. Chem
(1979)
F.M. Pohl
FEBS Letters
(1976)
G.N. Ramachandran et al.
J. Mol. Biol
(1976)

A. Warshel et al.

J. Mol. Biol

(1976)

J.F. Brandts et al.

Biochemistry

(1975)

J.F. Brandts et al.

K.H. Cook et al.

Cited by (141)

Efficient and accurate calculation of proline cis/trans isomerization free energies from Hamiltonian replica exchange molecular dynamics simulations
2023, Structure
Proline cis/trans isomerization plays an important role in many biological processes but occurs on time scales not accessible to brute-force molecular dynamics (MD) simulations. We have designed a new Hamiltonian replica exchange scheme, ω-bias potential replica exchange molecular dynamics (ωBP-REMD), to efficiently and accurately calculate proline cis/trans isomerization free energies. ωBP-REMD is applied to various proline-containing tripeptides and a biologically important proline residue in the N2-domain of the gene-3-protein of phage fd in the wildtype and mutant variants of the protein. Excellent cis/trans transition rates are obtained. Reweighting of the sampled probability distribution along the peptide bond dihedral angle allows construction of the corresponding free-energy profile and calculation of the cis/trans isomerization free energy with high statistical precision. Very good agreement with experimental data is obtained. ωBP-REMD outperforms standard umbrella sampling in terms of convergence and agreement with experiment and strongly reduces perturbation of the local structure near the proline residue.
Evolutionarily Conserved Proline Residues Impede the Misfolding of the Mouse Prion Protein by Destabilizing an Aggregation-competent Partially Unfolded Form
2022, Journal of Molecular Biology
The misfolding of the prion protein has been linked to several neurodegenerative diseases. Despite extensive studies, the mechanism of the misfolding process remains poorly understood. The present study structurally delineates the role of the conserved proline residues present in the structured C-terminal domain of the mouse prion protein (moPrP) in the misfolding process. It is shown that mutation of these Pro residues to Ala leads to destabilization of the native (N) state, and also to rapid misfolding. Using hydrogen–deuterium exchange (HDX) studies coupled with mass spectrometry (MS), it has been shown that the N state of moPrP is in rapid equilibrium with a partially unfolded form (PUF2*) at pH 4. It has been shown that the Pro to Ala mutations make PUF2* energetically more accessible from the N state by stabilizing it relative to the unfolded (U) state. The apparent rate constant of misfolding is found to be linearly proportional to the extent to which PUF2* is populated in equilibrium with the N state, strongly indicating that misfolding commences from PUF2*. It has also been shown that the Pro residues restrict the boundary of the structural core of the misfolded oligomers. Overall, this study highlights how the conserved proline residues control misfolding of the prion protein by modulating the stability of the partially unfolded form from which misfolding commences.
Pro5 is not essential for the formation of ‘Ni-hook’ in nickel superoxide dismutase
2022, Journal of Inorganic Biochemistry
The N-terminus of nickel-dependent superoxide dismutase (NiSOD) forms a structural motif known as the “Ni-hook,” where the peptide wraps around the metal to bring cysteine-2 and cysteine-6 into spatial proximity, allowing these residues to coordinate in a cis-geometry. A highly conserved proline-5 residue in the Ni-hook adopts a cis-conformation that is widely considered important for its formation. Herein, we investigate this role by point mutation of Pro5 to alanine. The results obtained show that the variant exhibits wild-type-like redox catalysis and features a Ni(III) center very similar to that found in enzyme. Structural analysis using X-ray absorption spectroscopy of the nickel sites in as-isolated P5A-NiSOD reveals changes in the variant and are consistent with a six-coordinate Ni site with (N/O)₄S₂ coordination. These changes are attributed to changes in the Ni(II) site structure. Nickel-binding studies using isothermal titration calorimetry reveal two binding events with K_d = 25(20) nM, and 250(60) nM. These events are attributed to i) Ni(II) binding to a preformed Ni-hook containing cis-Pro5 and ii) the combination of trans- to cis- isomerization upon Ni(II) binding, respectively. The higher-affinity binding event is absent in P5A-NiSOD, an observation attributed to the low abundance of the cis-Ala5 isomer in the apo-protein.
Mutational analysis in patients with neuromuscular disorders: Detection of mitochondrial deletion and double mutations in the MT-ATP6 gene
2016, Biochemical and Biophysical Research Communications
Citation Excerpt :
Since the functionality of a protein is dependent upon its ability to fold into a precise three-dimensional shape, proline's linkage to other amino acids through the amino group contributes to various bends and links in the shape of the protein, without which the protein could not function properly. Thus, proteins made up of hundreds of amino acids are able to configure themselves into the correct shape, and then carry out vital functions [21]. Consequently, the substitution of the Proline residue at position 136 could probably affect the folding of the ATP6 protein structure.
Mitochondrial diseases encompass a wide variety of pathologies characterized by a dysfunction of the mitochondrial respiratory chain resulting in an energy deficiency. The respiratory chain consists of five multi-protein complexes providing coupling between nutrient oxidation and phosphorylation of ADP to ATP. In the present report, we studied mitochondrial genes of complex I, III, IV and V in 2 Tunisian patients with mitochondrial neuromuscular disorders. In the first patient, we detected the m.8392C>T variation (P136S) in the mitochondrial ATPase6 gene and the m.8527A>G transition at the junction MT-ATP6/MT-ATP8 which change the initiation codon AUG to GUG. The presence of these two variations in such an important gene could probably affect the ATP synthesis in the studied patient. In the second patient, we detected several known variations in addition to a mitochondrial deletion in the major arc of the mtDNA eliminating tRNA and respiratory chain protein genes. This deletion could be responsible of an inefficient translation leading to an inefficient mitochondrial protein synthesis in P2.
The cis conformation of proline leads to weaker binding of a p53 peptide to MDM2 compared to trans
2015, Archives of Biochemistry and Biophysics
The cis and trans conformations of the Xaa–Pro (Xaa: any amino acid) peptide bond are thermodynamically stable while other peptide bonds strongly prefer trans. The effect of proline cis–trans isomerization on protein binding has not been thoroughly investigated. In this study, computer simulations were used to calculate the absolute binding affinity for a p53 peptide (residues 17–29) to MDM2 for both cis and trans isomers of the p53 proline in position 27. Results show that the cis isomer of p53(17–29) binds more weakly to MDM2 than the trans isomer, and that this is primarily due to the difference in the free energy cost associated with the loss of conformational entropy of p53(17–29) when it binds to MDM2. The population of cis p53(17–29) was estimated to be 0.8% of the total population in the bound state. The stronger binding of trans p53(17–29) to MDM2 compared to cis may leave a minimal level of p53 available to respond to cellular stress. This study demonstrates that it is feasible to estimate the absolute binding affinity for an intrinsically disordered protein fragment binding to an ordered protein that are in good agreement with experimental results.
Conserved proline residues prevent dimerization and aggregation in the β-lactamase BlaC
2024, Protein Science

View all citing articles on Scopus

^☆: This research was supported by a National Science Foundation award (PCM-7808029).

^†: Author's permanent address.

View full text

Journal of Molecular Biology

Effect of proline residues on protein folding☆

Abstract

Trends Biochem. Sci

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

J. Mol. Biol

Comp. Chem

FEBS Letters

J. Mol. Biol

J. Mol. Biol

Biochemistry