Interactions of phosphatidylinositol 3-kinase Src homology 3 domain with its ligand peptide studied by absorption, circular dichroism, and UV resonance Raman spectroscopies

Okishio, Nobuyuki; Nagai, Masako; Fukuda, Ryūji; Nagatomo, Shigenori; Kitagawa, Teizo

doi:10.1002/1097-0282(2000)57:4<208::aid-bip2>3.0.co;2-k

Cited by 8 publications

(28 citation statements)

References 111 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Trp55 was determined to be involved in the structural changes from the negative difference peak at 297 nm (17). However, Tyr residues affected by the D21N mutation could not be assigned because there are seven Tyr residues in the SH3 domain.…”

Section: Discussionmentioning

confidence: 99%

“…As illustrated in Figure 10B, the D21N mutation may break an interaction between Asp21 and Tyr14 (Tyr14 destabilized) or disrupt an association between Asp21 and Glu17 or Arg18 (RT loop deformed). The latter case is more plausible, because a notable difference in hydrogen-bonding state of a Tyr residue was not detected between the wild type and the D21N mutant by UVRR spectroscopy, which is sensitive to formation or loss of a hydrogen bond of a Tyr residue (17). Also, the significant decrements of NH chemical shift values of Glu17 and Arg18 (-1.6 and -0.9 ppm, respectively) by introducing the D21N mutation ( Figure 7A) imply that the hydrogen bonds between their amide protons and the O δ atoms of Asp21 are disrupted in the D21N mutant.…”

Section: Discussionmentioning

confidence: 99%

“…Other CD spectra were acquired at the same condition as that used in the previous study (17): Sample concentration was 0.05 or 0.2 mM in 50 mM Tris-HCl (pH 7.2) containing 0.1 M sodium sulfate for a light path of 1 mm at a scan speed of 50 nm min -1 with a 1 nm slit width and 1 s response time, and 20 scans were averaged. CD data were expressed in terms of mean residue molar ellipticity (θ) (deg cm 2 dmol -1 ).…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Role of the Conserved Acidic Residue Asp21 in the Structure of Phosphatidylinositol 3-Kinase Src Homology 3 Domain: Circular Dichroism and Nuclear Magnetic Resonance Studies

et al. 2000

Self Cite

View full text Add to dashboard Cite

To elucidate a role of the Src homology 3 (SH3)-conserved acidic residue Asp21 of the phosphatidylinositol 3-kinase (PI3K) SH3 domain, structural changes induced by the D21N mutation (Asp21 --> Asn) were examined by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopies. In the previous study, we demonstrated that environmental alterations occurred at the side chains of Trp55 and some Tyr residues from the comparison of the near-UV CD spectra of the PI3K SH3 domain with or without a D21N mutation [Okishio, N., et al. (2000) Biopolymers 57, 208-217]. In this work, the affected Tyr residues were identified as Tyr14 and Tyr73 by the CD analysis of a series of mutants, in which every single Tyr residue was replaced by a Phe residue with or without a D21N mutation. The (1)H and (15)N resonance assignments of the PI3K SH3 domain and its D21N mutant revealed that significant chemical shift changes occurred to the aromatic side-chain protons of Trp55 and Tyr14 upon the D21N mutation. All these aromatic residues are implicated in ligand recognition. In addition, the NMR analysis showed that the backbone conformations of Lys15-Asp23, Gly54-Trp55, Asn57-Gly58, and Gly67-Pro70 were affected by the D21N mutation. Furthermore, the (15)N[(1)H] nuclear Overhauser effect values of Tyr14, Glu19, and Glu20 were remarkably changed by the mutation. These results show that the D21N mutation causes structural deformation of more than half of the ligand binding cleft of the domain and provide evidence that Asp21 plays an important role in forming a well-ordered ligand binding cleft in cooperation with the RT loop (Lys15-Glu20).

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Role of the Conserved Acidic Residue Asp21 in the Structure of Phosphatidylinositol 3-Kinase Src Homology 3 Domain: Circular Dichroism and Nuclear Magnetic Resonance Studies

et al. 2000

Self Cite

View full text Add to dashboard Cite

show abstract

“…These differences might be reflected in the CD spectra near 234 nm, a wavelength indicative of the perturbation of Trp and Tyr environments (Okishio et al 2000(Okishio et al , 2003. Figure 4 illustrates that, at this wavelength, EbE4 has a molar residual ellipticity (MRE) closer to zero than any other member of the EbE family.…”

Section: Kinetic Effectsmentioning

confidence: 99%

“…The apparent rates of EbE4 folding and unfolding as a function of urea concentration were therefore investigated further with a focus on slow processes. CD data were collected at 234 nm as a function of time; this wavelength emphasized changes in aromatic packing (Okishio et al 2000(Okishio et al , 2003. Native EbE4 was manually diluted to final urea concentrations ranging from 8.4 to 9.7 M; alternately, EbE4 in 9.1 M urea was diluted to final conditions between 0.4 and 3.6 M urea.…”

Section: Folding and Unfolding Kinetics Of Ebe4mentioning

confidence: 99%

Loop anchor modification causes the population of an alternative native state in an SH3‐like domain

Knappenberger

Lecomte

2007

Protein Science

View full text Add to dashboard Cite

Many stably folded proteins are proposed to contain long, unstructured loops. A series of hybrid proteins (EbE1-4) containing the folded scaffold of photosystem I accessory protein E (PsaE), an SH3-like protein, and the 40-residue heme-binding loop of cytochrome b 5 was created to inspect the dependence of thermodynamic and kinetic parameters on the residues at the interface of folded and flexible regions. Compared to the simplest hybrid (EbE1), the chimeras differed by Gly insertions (EbE2, EbE3) or an asymmetric four-residue restructuring of loop termini (EbE4). NMR spectroscopy indicated that the chimeras retained the PsaE topology; native and unfolded state solubilities, however, were affected to varying degrees. Thermal and chemical denaturation experiments revealed that the EbE2 and EbE1 constructs resulted in a modest destabilization of the PsaE core, whereas apparent stability was increased by >5 kJ/mol in EbE4. EbE3 aggregated at mM concentrations and was not studied in detail. EbE4 populated two native states (N1 and N2), which differed by hydrophobic core packing and C-terminal interactions. At room temperature, the population ratio (;3-4:1) favored the state whose spectroscopic properties most resembled those of PsaE (N1). EbE4 also demonstrated altered folding kinetics, displaying multiple slow phases related to the population of intermediates and possibly N2. It was concluded that loop anchors can affect protein properties, including stability, via short-range effects on local structure and long-range communication with the packed hydrophobic core. Modification of the attachment points appears to be a possible stepping stone in the transition from one three-dimensional structure to another.

show abstract

Modulation of protein–ligand interactions by photocleavage of a cyclic peptide using phosphatidylinositol 3‐kinase SH3 domain as model system

Takahashi

Kuroiwa

Lindfors

et al. 2009

Journal of Peptide Science

Self Cite

View full text Add to dashboard Cite

To photomodulate the interaction of the phosphatidylinositol 3-kinase SH3 domain with a peptide ligand, a cyclic peptide (cyclic-1) with a photolabile side chain-to-side chain linker was synthesized. The conformation of cyclic-1 differs from that of the parent linear peptide, but becomes identical by UV-irradiation. Accordingly, the binding affinity of cyclic-1 to the SH3 domain increased upon conversion of the cyclic to a linear flexible structure by irradiation (K(d): 3.4 +/- 1.7 and 0.9 +/- 0.3 mM, respectively). These results confirm the usefulness of a photocleavable peptide for photocontrol of peptide-protein interactions.

show abstract

Interactions of phosphatidylinositol 3-kinase Src homology 3 domain with its ligand peptide studied by absorption, circular dichroism, and UV resonance Raman spectroscopies

Cited by 8 publications

References 111 publications

Role of the Conserved Acidic Residue Asp21 in the Structure of Phosphatidylinositol 3-Kinase Src Homology 3 Domain: Circular Dichroism and Nuclear Magnetic Resonance Studies

Role of the Conserved Acidic Residue Asp21 in the Structure of Phosphatidylinositol 3-Kinase Src Homology 3 Domain: Circular Dichroism and Nuclear Magnetic Resonance Studies

Loop anchor modification causes the population of an alternative native state in an SH3‐like domain

Modulation of protein–ligand interactions by photocleavage of a cyclic peptide using phosphatidylinositol 3‐kinase SH3 domain as model system

Contact Info

Product

Resources

About