Energetics of Polar Side-Chain Interactions in Helical Peptides:  Salt Effects on Ion Pairs and Hydrogen Bonds

Js, Smith; Jm, Scholtz

doi:10.1021/bi972026h

Cited by 99 publications

(130 citation statements)

References 40 publications

(74 reference statements)

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“…For example, the change 0.08 kcal/mol as compared to AAA. If propensities are taken into account, the salt bridge is stabilizing by 0.73 kcal/mol and slightly greater than the stabilization observed by introducing simple salt bridges in helical peptides (Lyu et al, 1992;Smith & Scholtz, 1998). This implies residual interactions, possibly electrostatic in origin, as shown at the bottom of the panel.…”

Section: Resultsmentioning

confidence: 91%

“…The strength of a salt bridge can be estimated by different experimental methodologies: changes in the helicity of model peptides (Merutka & Stellwagen, 1990;Lyu et al, 1992;Scholtz et al, 1993), shifts in pK, of interacting side chains (Anderson et al, 1990;, or T, differences in model proteins Dao-Pin et al, 1991). Using the first method, Smith and Scholtz (1998) report that simple salt bridges stabilize helical peptides by free energies ranging from 120 cal/mol for DK in an i, i + 3 spacing to 650 kcal/mol for HE with an i, i + 4 spacing. In a helices, the i, i + 4 spacing is a stronger stabilizing interaction than the i, i + 3 spacing (Huyghues-Despointes et al, 1993a).…”

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confidence: 99%

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Surface salt bridges stabilize the GCN4 leucine zipper

Spek

Bui

et al. 1998

Protein Science

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We present a study of the role of salt bridges in stabilizing a simplified tertiary structural motif, the coiled-coil. Changes in GCN4 sequence have been engineered that introduce trial patterns of single and multiple salt bridges at solvent exposed sites. At the same sites, a set of alanine mutants was generated to provide a reference for thermodynamic analysis of the salt bridges. Introduction of three alanines stabilizes the dimer by 1.1 kcal/mol relative to the wild-type. An arrangement corresponding to a complex type of salt bridge involving three groups stabilizes the dimer by 1.7 kcall mol, an apparent elevation of the melting temperature relative to wild type of about 22 "C. While identifying local from nonlocal contributions to protein stability is difficult, stabilizing interactions can be identified by use of cycles. Introduction of alanines for side chains of lower helix propensity and complex salt bridges both stabilize the coiled-coil, so that combining the two should yield melting temperatures substantially higher than the starting species, approaching those of thermophilic sequences. Keywords: GCN4; leucine zipper; salt bridge; thermal stabilityInteractions that stabilize the native state of proteins include the hydrophobic effect, van der Waals interactions, hydrogen bonds and ionic effects, including dipole interactions and salt bridges (Creighton, 1993). The question of which of these are most important in protein stabilization has been debated since the review by Kauzmann (1959). One aspect of the problem concerns how to account for the additional stabilization of proteins from thermophiles, which can have very high thermal stabilities (see Hiller et al., 1997). Since the pioneering work of Matthews et al. (1974) on thermolysin, structures of thermophilic and mesophilic proteins have been compared in a search for clues to what accounts for the higher stability of the former (Korndorfer et al., 1995;Yip et al., 1995;Hatanaka et al., 1997;Robb & Maeder, 1998). In 1978, Perutz (1978 observed that the main discernible difference between a thermophilic and mesophilic version of ferrodoxin lay in the greater number of salt bridges on the surface of the thermophile. As more crystal structures of thermophilic proteins have become available, other mechanisms have been proposed to explain their stability (Vogt & Argos, 1997): improved internal packing, burial of a greater hydrophobic area (Chan et al., 1995; Delboni et al., 1995), and networks of complex salt bridges (Yip et al., 1995;Pappenberger et al., 1997 Yip et al., 1995;Robb & Maeder, 1998).Here, we consider the role of complex salt bridges in stabilizing a simplified model protein structure. The strength of a salt bridge can be estimated by different experimental methodologies: changes in the helicity of model peptides (Merutka & Stellwagen, 1990;Lyu et al., 1992;Scholtz et al., 1993), shifts in pK, of interacting side chains (Anderson et al., 1990;, or T, differences in model proteins Dao-Pin et al., 1991). Using the first method, Smi...

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Section: Resultsmentioning

confidence: 91%

mentioning

confidence: 99%

Surface salt bridges stabilize the GCN4 leucine zipper

Spek

Bui

et al. 1998

Protein Science

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“…Indeed, the R-helical fold is highly dependent on salt concentration ( Figure 1A). These results are reminiscent of those from peptides containing tandem salt bridges that are quite sensitive to charge screening due to many interacting charged groups in proximity (21,23). The radixin 311-469 R-domain structure is furthermore responsive to pH titration, as the state of ionization of side chains clearly controls the ability to form ion pairs ( Figure 1B).…”

Section: Structuralmentioning

confidence: 82%

Insights into a Single Rod-like Helix in Activated Radixin Required for Membrane−Cytoskeletal Cross-Linking

et al. 2003

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The members of the ezrin-radixin-moesin (ERM) family of proteins function as membranecytoskeletal cross-linkers in actin-rich cell surface structures. ERM proteins are thereby thought to be essential for cortical cytoskeleton organization, cell motility, adhesion, and proliferation. These modular polypeptides consist of a central helix-rich region, termed the R-domain, that connects an N-terminal FERM domain required for membrane binding and a C-terminal region which contains a major actinbinding motif. Conformational regulation of ERM protein function occurs by association of the FERM and C-terminal domains, whereby the membrane-and actin-binding activities are mutually suppressed and the protein is thought to take an inactive "closed" form. Here we report in Vitro and in ViVo studies of radixin to address the role of the R-domain in conformational activation of ERM proteins. Remarkably, an isolated R-domain comprised of radixin 311-469 forms a monomeric, stable helical rod that spans 240 Å in length from the N-terminus to the C-terminus, most likely stabilized by extensive salt bridge interactions. By fusing green fluorescent protein variants to the FERM and C-terminal domains, we probed in Vitro conformational changes impacted by the presence of the R-domain using fluorescence resonance energy transfer (FRET). Furthermore, deletion of this unusually long R-helical structure (radixin residues 314-411) prevents ERM membrane targeting in ViVo.

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“…The few ΔG measurements available for these cases seem to be in agreement with our observations. (HuyghuesDespointes and Baldwin, 1997;HuyghuesDespointes et al, 1995;Scholtz et al, 1993;Smith and Scholtz, 1998;Taylor, 2002) A comparison of the propensities determined for the (i, i + 4) combinations and the experimentally determined free energies of several (i, i + 4) amino acid sidechain interactions indicates a reasonable correlation between these two sets of values.…”

Section: Pair Propensity and δG For Helix Stabilizationmentioning

confidence: 84%