Energetic and structural basis for the preferential formation of the native disulfide loop involving Cys-65 and Cys-72 in synthetic peptide fragments derived from the sequence of ribonuclease A

Talluri, Sekhar; Falcomer, C. M.; Scheraga, Harold A.

doi:10.1021/ja00061a001

Cited by 23 publications

(38 citation statements)

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“…Such a structure (Figure B) resembles the intermediate state found in the most common folding pathway of RNase A observed by Li et al , Using peptide mapping, another intermediate structure, lacking the Cys65-Cys72 disulfide bond, was observed by Rothwarf et al, which is also present in molecular dynamics simulations (Figure D). However, in general, the Cys65-Cys72 disulfide bond was found to be very stable in the simulations performed in this work and was also determined experimentally to be the most populated disulfide bond in one- and two-disulfide-bond intermediates. − The flexible region of residues 16–25, which is the loop between the first and second α-helix, is stabilized by the Cys26-Cys84 disulfide bond at all investigated temperatures, keeping fluctuations on the same level in the 278–308 K temperature range. Also, the last loop in RNase A (residues 111–116) is greatly stabilized by the presence of the Cys58-Cys110 disulfide bond up to T = 308 K.…”

Section: Resultssupporting

confidence: 59%

Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A

Krupa

Sieradzan

Mozolewska

et al. 2017

J. Chem. Theory Comput.

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Ribonuclease A (RNase A) is the most studied member of ribonucleases − a group of enzymes responsible for catalyzing RNA degradation. RNase A contains four disulfide bonds, which were found to be necessary for the native structure of the protein to form. In this work the kinetics and thermodynamics of RNase unfolding were studied by means of a series of coarse-grained canonical molecular-dynamics simulations, run at various temperatures, and replica-exchange molecular dynamics simulations with the UNRES force field, which is capable of dynamic formation and breaking the disulfide bonds during the course of the simulations. It was found that the Cys40-Cys95 bond was the first to break, while the Cys26-Cys84 bond was the last to break, independent of temperature, in agreement with available experimental data. Except for the Cys40-Cys95 bond, all disulfide bonds were relatively stable during the simulations. The formation/disruption of disulfide bonds was found to be temperature dependent for three out of four disulfide bonds in RNase A, except for the most stable disulfide bond between Cys65 and Cys72. A stable intermediate without the Cys40-Cys95 disulfide bond, with structure similar to that of the most common folding intermediate observed experimentally, was found in simulated unfolding. In agreement with experiment, non-native disulfide bonds were also observed. By analyzing residue-position fluctuations, it was found that native disulfide bonds are located in the highly flexible regions of the protein, which is probably why their presence is necessary for the stability of RNase A.

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Section: Resultssupporting

confidence: 59%

Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A

Krupa

Sieradzan

Mozolewska

et al. 2017

J. Chem. Theory Comput.

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“…The preference of the 4:1 ratio for the native 65–72 disulfide bond relative to the non‐native 58–65 disulfide bond is the same in the 1S folding stage of both the native protein and of an isolated 58–72 fragment 109, 110. Since both possible loops, 58–65 and 65–72, have the same number of residues and, hence, involve the same entropy of loop closure, this 4:1 ratio indicates that specific local interactions lead to the preference for formation of the 65–72 loop; such preferential interactions in this loop have been identified by NMR111 and MM112 computations.…”

Section: Experimental Determination Of Folding Pathwaysmentioning

confidence: 76%

A proposal for a dynamic h‐type index

Rousseau

2008

J. Am. Soc. Inf. Sci.

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“…Scheraga and collaborators (Talluri et al, 1993) investigated fragments from RNAse A that encompassed residues 61 -74 and 65-72. In native RNAse A and in the peptide molecules, disulfide bonds were formed between Cys65 and Cys72.…”

Section: Discussionmentioning

confidence: 99%

The Solution Structure of the Synthetic Circular Peptide

Rietman¹,

Folkers²,

Folmer³

et al. 1996

European Journal of Biochemistry

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The cyclic disulfide peptide CGVSRQGKPYC was prepared to obtain a constrained analogue of residues 17-27 of the DNA-binding loop of the gene-V-encoded ssDNA-binding protein of filamentous bacteriophage MI 3. Amino acid sequences very similar to that of this P-loop have been found in various phage-encoded ssDNA-binding proteins, and it has been proposed that such a loop may occur as a common motif in this class of proteins. The conformation, in aqueous solution, of the synthetic gene-Vprotein binding-loop analogue has been investigated by means of two-dimensional-' H-NMR techniques.Subsequent structure calculations show that the molecule forms a P-loop that includes a turn formed by three residues. This structure, very unusually for a cyclic disulfide peptide, is highly similar to that of the analogous part of the binding loop of the native protein.Comparison with experiments on other cyclic disulfide peptides indicates that the formation, of the /I-sheet (P-hairpin) secondary structure is essentially governed by the amino acid composition of the 11-residue sequence. The disulfide bridge in the 1 1 -residue sequence is essential for conformational stability, as indicated by the finding that the open peptide analogue that encompasses residues Serl7FSer27 does not adopt a detectable secondary structure in water. The bridge replaces the role of the loop formed by residues 49-58 in the protein, which act as a scaffold to hold the N-terminal and C-terminal ends of the DNA-binding loop together.

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Energetic and structural basis for the preferential formation of the native disulfide loop involving Cys-65 and Cys-72 in synthetic peptide fragments derived from the sequence of ribonuclease A

Cited by 23 publications

References 0 publications

Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A

Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A

A proposal for a dynamic h‐type index

The Solution Structure of the Synthetic Circular Peptide

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