Helix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. 17. Threonine Parameters from Random Poly(hydroxylbutylglutamine-co-L-threonine)

Hecht, Michael H.; Zweifel, Bernhard O.; Scheraga, Harold A.

doi:10.1021/ma60063a024

Cited by 21 publications

(14 citation statements)

References 8 publications

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“…S11). This observation is consistent with the experimental finding that the side chain of valine has a destabilizing effect on the helical structure30 because of the branching at the C β carbon.…”

Section: Resultssupporting

confidence: 93%

Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single‐point mutation of a β‐sheet miniprotein

2007

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The effects of a single-point mutation on folding thermodynamics and kinetics are usually interpreted by focusing on the native structure and the transition state. Here, the entire conformational spaces of a 20-residue three-stranded antiparallel beta-sheet peptide (double hairpin) and of its single-point mutant W10V are sampled close to the melting temperature by equilibrium folding-unfolding molecular dynamics simulations for a total of 40 micros. The folded state as well as the most populated free energy basins in the denatured state are isolated by grouping conformations according to fast relaxation at equilibrium. Such kinetic analysis provides more detailed and useful information than a simple projection of the free energy. The W10V mutant has the same native structure as the wild type peptide, and similar folding rate and stability. In the denatured state, the N-terminal hairpin is about 20% more structured in W10V than the wild type mainly because of van der Waals interactions. Notably, the W10V mutation influences also the van der Waals energy at the transition state ensemble causing a shift in the ratio of fluxes between two different transition state regions on parallel folding pathways corresponding to nucleation at either of the two beta-hairpins. Previous experimental studies have focused on the effects of denaturant-dependent or temperature-dependent changes in the structure of the denatured state. The atomistic simulations show that a single-point mutation in the central strand of a beta-sheet peptide results in remarkable changes in the topography of the denatured state ensemble. These changes modulate the relative accessibility of parallel folding pathways because of kinetic partitioning of the denatured state. Therefore, the observed dependence of the folding process on the starting ensemble raises questions on the biological significance of in vitro folding studies under strongly denaturing conditions.

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Section: Resultssupporting

confidence: 93%

Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single‐point mutation of a β‐sheet miniprotein

2007

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“…This problem of indeterminancy of has been encountered in earlier papers, viz., for glycine,5 serine,7,15 valine,10 glutamic acid,11 asparagine,14 lysine,13 arginine,17 and threonine. 19 This behavior arises when it becomes very improbable for the guest residue to nucleate a helical segment in a pure-guest region of the random copolymer. Such nucleation becomes more im- probable as the value of $ of the guest amino acid becomes small compared to the value of nBsB of the host amino acid, where a is the (generally small) relative composition of the guest residue (see Appendix B of paper 1 of this series3).…”

Section: Discussionmentioning

confidence: 99%

Helix-coil stability constants for the naturally occurring amino acids in water. 22. Histidine parameters from random poly[(hydroxybutyl)glutamine-co-L-histidine]

Sueki¹,

Lee²,

Powers³

et al. 1984

Macromolecules

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167

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The synthesis and characterization of water-soluble random copolymers containing L-histidine with JVs-(4-hydroxybutyl)-L-glutamine, and the thermally induced helix-coil transitions of these copolymers in water and in aqueous 0.5 N KC1 solution, are described. The incorporation of both charged and uncharged L-histidine was found to decrease the helix content of the polymer in water, even in the presence of 0.5 N KC1, which effectively shields the electrostatic repulsions among charged L-histidine residues in the a-helical and coil conformations. The Zimm-Bragg parameters and s for the thermally induced helix-coil transition of charged and uncharged poly(L-histidine) in water and in 0.5 N KC1 were deduced from an analysis of the melting curves of the copolymers in the manner described in earlier papers. At physiological temperature, 37 °C, the helix-coil stability constants, s, for charged and uncharged L-histidine are similar, viz., 0.66 and 0.70, respectively. This demonstrates that ionization-deionization of histidine residues does not in itself affect the conformational stabilities of proteins. The synthesis of AZ-acetyl-N-methylhistidinamide and its titration, as well as that of the copolymers, in 0.1 N KC1 are described. Finally, the values of and s, determined for 18 amino acids from experiments on host-guest random copolymers, and those obtained for cystine and proline by extrapolation, are summarized here.

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“…Fraction of Random Coils in Terminal Sequences. Defining IVers as the average number of randomly coiled blocks that are located in end random coil sequences, the fraction of blocks both that are randomly coiled and that propagate from an end is /dce = -^ERs/Ab (11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26) The objective of this section is to develop the expression of /dce in the loops-excluded, imperfect-matching model. The general procedure followed is similar to that developed for the calculation of /bd(/)• Namely, we must sum over all out-of-register sequences of both type-"a" and type-"b" sequences.…”

Section: N-2 I=nb-n+2mentioning

confidence: 99%

“…More explicitly, /dce may be obtained from /dce = \ZJface + D " 1)Z.f1 + IVB~Js* Af, Js + i=l Js*rfAbAI + |S? (IVB -1) + Sg(IVB -1) + Sf(NB) + 4(IVb -1) + S%(Nb -1) + S}(NB) + Sfc(IVB)) (11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27) (II-25d) In the above expression /mce is the fraction of random coils in terminal sequences in an isolated single chain. An explicit expression for /roce may be found in eq PM-II-20.…”

Section: N-2 I=nb-n+2mentioning

confidence: 99%

Effect of loop entropy on the helix-coil transition of α-helical, two-chain, coiled coils. 3. Supermatrix formulation of the imperfect-matching model

Skolnick¹

1984

Macromolecules

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Helix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. 17. Threonine Parameters from Random Poly(hydroxylbutylglutamine-co-L-threonine)

Cited by 21 publications

References 8 publications

Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single‐point mutation of a β‐sheet miniprotein

Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single‐point mutation of a β‐sheet miniprotein

Helix-coil stability constants for the naturally occurring amino acids in water. 22. Histidine parameters from random poly[(hydroxybutyl)glutamine-co-L-histidine]

Effect of loop entropy on the helix-coil transition of α-helical, two-chain, coiled coils. 3. Supermatrix formulation of the imperfect-matching model

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