Contribution of hydrophobic interactions to protein stability

Jt, Kellis; Nyberg, Kari; Šali, D.; Ar, Fersht

doi:10.1038/333784a0

Cited by 405 publications

(270 citation statements)

References 26 publications

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“…The V to A substitution removes two carbon atoms; the calculated DDG bind for V654A mutant disfavors the mutant by 1.52 kcal/mol, resulting in a destabilization of approximately 0.8 kcal/mol per carbon atom upon cavity formation. This estimate is in good agreement with the results of earlier experimental studies (Kellis et al, 1988;Eriksson et al, 1992;Pace et al, 1996;Loladze et al, 2002) and theoretical calculations (Nicholls et al, 1991;Lee, 1993;Lazaridis et al, 1995). Replacing V with A at position 654 further reflects only in a slight alteration of some other imatinib contact points (E640, T670, C673 and F811) and some ATP-binding residues (K623 and E671).…”

Section: Molecular Modelingsupporting

confidence: 91%

Functional analyses and molecular modeling of two c-Kit mutations responsible for imatinib secondary resistance in GIST patients

et al. 2006

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Imatinib-acquired resistance related to the presence of secondary point mutations has become a frequent event in gastrointestinal stromal tumors. Here, transient transfection experiments with plasmids carrying two different KIT-acquired point mutations were performed along with immunoprecipitation of total protein extracts, derived from imatinib-treated and untreated cells. The molecular mechanics/Poisson Boltzmann surface area computational techniques were applied to study the interactions of the wild-type and mutated receptors with imatinib at the molecular level. Biochemical analyses showed KIT phosphorylation in cells transfected with vectors carrying the specific mutant genes. Imatinib treatment demonstrated that T670I was insensitive to the drug at all the applied concentrations, whereas V654A was inhibited by 6 lM of imatinib. The modeling of the mutated receptors revealed that both substitutions affect imatinib-binding site, but to a different extent: T670I substantially modifies the binding pocket, whereas V654A induces only relatively confined structural changes. We demonstrated that T670I and V654A cause indeed imatinib-acquired resistance and that the former is more resistant to imatinib than the latter. The application of molecular simulations allowed us to quantify the interactions between the mutated receptors and imatinib, and to propose a molecular rationale for this type of drug resistance.

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Section: Molecular Modelingsupporting

confidence: 91%

Functional analyses and molecular modeling of two c-Kit mutations responsible for imatinib secondary resistance in GIST patients

et al. 2006

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“…Such interactions provide the energy of binding for adsorption of hydrophobic portions of proteins to hydrophobic polystyrene tube walls (Tanford, 1979). They provide the energy to stabilize protein structure through associations of hydrophobic regions within antibody molecules (Miller et al, 1987;Kellis et al, 1988) and for the interactions between hydrophobic surfaces on protein subunits (Janin et al, 1988). For small hydrophobic molecules, such as PCBs, the actual high avidity binding to the antibody active site may be driven by the energy from hydrophobic interactions.…”

Section: Resultsmentioning

confidence: 99%

Comparison of an enzyme-linked immunosorbent assay (ELISA) to gas chromatography (GC) – measurement of polychlorinated biphenyls (PCBs) in selected US fish extracts

et al. 2000

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Robert O., "Comparison of an enzymelinked immunosorbent assay (ELISA) to gas chromatography (GC) -measurement of polychlorinated biphenyls (PCBs) in selected US fish extracts" (1999). USGS Comparison of an enzyme-linked immunosorbent assay (ELISA) to gas chromatography (GC) ± measurement of polychlorinated biphenyls (PCBs) AbstractThe analysis of PCBs in ®sh tissues by immunoassay methods was evaluated using ®sh collected from a US monitoring program, the National Contaminant Biomonitoring Program of the US Department of Interior, Fish and Wildlife Service. Selected composite whole ®sh samples, which represented widely varying concentrations and sources of PCBs, were extracted and subjected to congener PCB analysis by gas chromatography (GC) and total PCB analysis using an ELISA (ePCBs) calibrated against technical Aroclor 1248. PCB congener patterns in these ®shes were di erent from the patterns found in commercial Aroclors or their combinations as demonstrated by principal component analysis of normalized GC congener data. The sum of the PCB congeners measured by GC (total-PCBs) ranged from 37 to 4600 ng/g (wet weight). Concentrations of PCBs as determined by the ELISA method were positively correlated with total-PCBs and the ePCBs/total-PCBs ratios for individual samples ranged from 1 to 6. Ratios of ePCBs/totalPCBs for dilutions of Aroclors 1242, 1254, and 1260 and for matrix spikes range from 0.6 for 1242 to 2.5 for 1254 and 1260. These results suggest that higher chlorinated PCB congeners have higher a nity for the anti-PCB antibodies. Partial least squares with latent variable analysis of GC and ELISA data of selected Aroclors and ®sh samples also support the conclusion that ELISA derived PCB concentrations are dependent on the degree of chlorination. Ó

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“…Although substitutions of aromatic residues with Leu are usually tolerated during evolution (Bordo & Argos, 1991), single replacements of this type have been found to destabilize folded proteins significantly (Kellis et al, 1988;Goldenberg et al, 1989;Coplen et al, 1990;Eriksson et al, 1993). The replacement decreases the size of the side chain and eliminates any interaction specific for aromatic rings.…”

Section: Design and Initial Characterization Of Aromatic + Leu Bpti Vmentioning

confidence: 99%

Mutational analysis of the BPTI folding pathway: I. Effects of aromatic → leucine substitutions on the distribution of folding intermediates

Zhang

Goldenberg

1997

Protein Science

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The roles of aromatic residues in determining the folding pathway of bovine pancreatic trypsin inhibitor (BPTI) were analyzed mutationally by examining the distribution of disulfide-bonded intermediates that accumulated during the refolding of protein variants in which tyrosine or phenylalanine residues were individually replaced with leucine. The eight substitutions examined all caused significant changes in the intermediate distribution. In some cases, the major effect was to decrease the accumulation of intermediates containing two of the three disulfides found in the native protein, without affecting the distribution of earlier intermediates. Other substitutions, however, led to much more random distributions of the intermediates containing only one disulfide. These results indicate that the individual residues making up the hydrophobic core of the native protein make clearly distinguishable contributions to conformation and stability early in folding: The early distribution of intermediates does not appear to be determined by a general hydrophobic collapse. The effects of the substitutions were generally consistent with the structures of the major intermediates determined by NMR studies of analogs, confirming that the distribution of disulfide-bonded species is determined by stabilizing interactions within the ordered regions of the intermediates. The plasticity of the BPTI folding pathway implied by these results can be described using conformational funnels to illustrate the degree to which conformational entropy is lost at different stages in the folding of the wild-type and mutant proteins.Keywords: aromatic residues; bovine pancreatic trypsin inhibitor; conformational funnels; disulfide bonds; hydrophobic residues; protein foldingThe identification and characterization of partially folded intermediate states have historically been major goals in the study of protein folding mechanisms. Early experiments demonstrating the transient accumulation of such species provided important evidence supporting the view that proteins fold via non-random pathReprint requests to: David P. Goldenberg, Department of Biology, University of Utah, Salt Lake City, UT 84112; e-mail: goldenberg@ bioscience.utah.edu.'Current address: Department of Pathology, Harvard University Medical School, Boston, MA 021 15.Abbreviations: BPI?, bovine pancreatic trypsin inhibitor. Amino acid replacements are indicated by the wild-type residue type (using the oneletter code for the 20 standard amino acids), followed by the residue number and the mutant residue type. The disulfides of native BF'TI and folding intermediates are indicated by the residue numbers of the disulfidebonded cysteine residues; N;;, native-like two-disulfide intermediate containing the 30-51 and 5-55 disulfides. Other intermediates are indicated by square brackets enclosing the disulfide bonds they contain; GSSG, oxidized glutathione; DTT:;, the dithiol form of dithiothreitol; GuHCl, guanidinium chloride; IAEDANS, N-iodoacetyl-N"(5-sulfo-l-naphthyl)ethylenediami...

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Contribution of hydrophobic interactions to protein stability

Cited by 405 publications

References 26 publications

Functional analyses and molecular modeling of two c-Kit mutations responsible for imatinib secondary resistance in GIST patients

Functional analyses and molecular modeling of two c-Kit mutations responsible for imatinib secondary resistance in GIST patients

Comparison of an enzyme-linked immunosorbent assay (ELISA) to gas chromatography (GC) – measurement of polychlorinated biphenyls (PCBs) in selected US fish extracts

Mutational analysis of the BPTI folding pathway: I. Effects of aromatic → leucine substitutions on the distribution of folding intermediates

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