Role of the C-terminal chain in human interferon? stability: An electrostatic study

Altobelli, Gioia; Nacheva, Genoveva; Todorovа, Katerina; Ivanov, Iván; Karshikoff, Andrey

doi:10.1002/1097-0134(20010501)43:2<125::aid-prot1024>3.0.co;2-j

Cited by 8 publications

(5 citation statements)

References 32 publications

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“…1; Zeth et al 2000]). Because the charge status of these residues is of functional significance, we analyzed their electrostatic interactions by means of calculations based on a finite‐difference Poisson‐Boltzmann (FDPB) procedure (Karshikoff 1995; Altobelli et al 2001; Koumanov et al 2001). For our calculations, the truncated trimer model was used (i.e., monomeric structures with the addition of adjacent residues from the neighboring two subunits, including the latching loop L2 in the case of OmpF and PhoE; Karshikoff et al 1994).…”

Section: Resultsmentioning

confidence: 99%

“…All protein partial charges were included in the atomic model. A thorough description of the computation of the protonation/deprotonation equilibrium of titratable sites is given elsewhere (Karshikoff 1995; Altobelli et al 2001; Koumanov et al 2001). In all calculations the bacterial outer membrane was simulated as infinite layer surrounding the porin monomer perpendicular to the longitudinal axis of the pore (Karshikoff et al 1994).…”

Section: Methodsmentioning

confidence: 99%

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Electrostatic properties of the anion selective porin Omp32 from Delftia acidovorans and of the arginine cluster of bacterial porins

et al. 2002

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The functional properties of the anion-selective porin Omp32 from the bacterium Delftia acidovorans, formerly Comamonas acidovorans, are determined by the particularly narrow channel constriction and the electrostatic field inside and outside the pore. A cluster of arginines (Arg 38, Arg 75, and Arg 133) determines the electrostatic field close to the constriction zone. Stacked amino acids carrying charges are prone to drastic pK a shifts. However, optimized calculations of the titration behavior of charged groups, based on the finite-difference Poisson-Boltzmann technique, suggest that all the arginines are charged at physiological pH. Protonation of the clustered arginines is stabilized by one buried glutamate residue (Glu 58), which is strongly interacting with Arg 75 and Arg 38. This functional arrangement of three charged amino acid residues is of general significance because it is found in the constriction zones of all known 16-stranded porins from the ␣-, ␤-, and ␥-proteobacteria.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Electrostatic properties of the anion selective porin Omp32 from Delftia acidovorans and of the arginine cluster of bacterial porins

et al. 2002

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“…Computation of protonation/deprotonation equilibria of titratable groups of Drosophila lebanonensis ADH is based on the theoretical considerations described earlier 11, 12. Here, only some key points relevant for the discussion of the results are presented.…”

Section: Methodsmentioning

confidence: 99%

The catalytic mechanism of Drosophila alcohol dehydrogenase: Evidence for a proton relay modulated by the coupled ionization of the active site Lysine/Tyrosine pair and a NAD⁺ ribose OH switch

et al. 2003

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The ionization properties of the active site residues in Drosophila lebanonensis alcohol dehydrogenase (DADH) were investigated theoretically by using an approach developed to account for multiple locations of the hydrogen atoms of the titratable and polar groups. The electrostatic calculations show that (a) the protonation/deprotonation transition of the binary complex of DADH is related to the coupled ionization of Tyr151 and Lys155 in the active site and (b) the pH dependence of the proton abstraction is correlated with a reorganization of the hydrogen bond network in the active site. On this basis, a proton relay mechanism for substrate dehydrogenation is proposed in which the O2' ribose hydroxyl group from the coenzyme has a key role and acts as a switch. The proton relay chain includes the active site catalytic residues, as well as a chain of eight water molecules that connects the active site with the bulk solvent.

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“…Electrostatic interactions are known to play a dominant role in the early stages of the aggregation . For example, occasionally aggregation may be reduced by introducing point mutations that increase charge repulsion between the protein molecules at low ionic strength . Protein complexes and aggregates stabilized mainly by electrostatic interactions become rapidly weakened with increasing salt concentration because protein charges become neutralized by counterions.…”

Section: Introductionmentioning

confidence: 99%

“…12 For example, occasionally aggregation may be reduced by introducing point mutations that increase charge repulsion between the protein molecules at low ionic strength. 13 Protein complexes and aggregates stabilized mainly by electrostatic interactions become rapidly weakened with increasing salt concentration because protein charges become neutralized by counterions. However, proteins with large net charges may be often stabilized by salts that suppress the intramolecular charge repulsion.…”

Section: ' Introductionmentioning

confidence: 99%

Probing Amyloid-Beta Fibril Stability by Increasing Ionic Strengths

Zidar

Merzel

2011

J. Phys. Chem. B

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Previous experimental studies have demonstrated changing the ionic strength of the solvent to have a great impact on the mechanism of aggregation of amyloid-beta (Aβ) protein leading to distinct fibril morphology at high and low ionic strength. Here, we use molecular dynamics simulations to elucidate the ionic strength-dependent effects on the structure and dynamics of the model Aβ fibril. The change in ionic strength was brought forth by varying the NaCl concentration in the environment surrounding the Aβ fibril. Comparison of the calculated vibrational spectra of Aβ derived from 40 ns all-atom molecular dynamics simulations at different ionic strength reveals the fibril structure to be stiffer with increasing ionic strength. This finding is further corroborated by the calculation of the stretching force constants. Decomposition of binding and dynamical properties into contributions from different structural segments indicates the elongation of the fibril at low ionic strength is most likely promoted by hydrogen bonding between N-terminal parts of the fibril, whereas aggregation at higher ionic strength is suggested to be driven by the hydrophobic interaction.

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Role of the C-terminal chain in human interferon? stability: An electrostatic study

Cited by 8 publications

References 32 publications

Electrostatic properties of the anion selective porin Omp32 from Delftia acidovorans and of the arginine cluster of bacterial porins

Electrostatic properties of the anion selective porin Omp32 from Delftia acidovorans and of the arginine cluster of bacterial porins

The catalytic mechanism of Drosophila alcohol dehydrogenase: Evidence for a proton relay modulated by the coupled ionization of the active site Lysine/Tyrosine pair and a NAD⁺ ribose OH switch

Probing Amyloid-Beta Fibril Stability by Increasing Ionic Strengths

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Role of the C-terminal chain in human interferon? stability: An electrostatic study

Cited by 8 publications

References 32 publications

Electrostatic properties of the anion selective porin Omp32 from Delftia acidovorans and of the arginine cluster of bacterial porins

Electrostatic properties of the anion selective porin Omp32 from Delftia acidovorans and of the arginine cluster of bacterial porins

The catalytic mechanism of Drosophila alcohol dehydrogenase: Evidence for a proton relay modulated by the coupled ionization of the active site Lysine/Tyrosine pair and a NAD+ ribose OH switch

Probing Amyloid-Beta Fibril Stability by Increasing Ionic Strengths

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The catalytic mechanism of Drosophila alcohol dehydrogenase: Evidence for a proton relay modulated by the coupled ionization of the active site Lysine/Tyrosine pair and a NAD⁺ ribose OH switch