scholarly journals Computational investigation of protein surface polarity and pH-dependence: application to antibodies shows that antibody-antigen interfaces tend to be relatively polar

2018 ◽  
Author(s):  
Max Hebditch ◽  
Jim Warwicker
Keyword(s):  
Ionic Strength ◽  
Ph Dependence ◽  
Protein Solubility ◽  
Solubility Prediction ◽  
Surface Polarity ◽  
Protein Surface ◽  
Ionic Strength Dependence ◽  
Surface Patches ◽  
Self Association ◽  
Protein Biophysics

AbstractProtein instability leads to reversible self-association and irreversible aggregation which is a major concern for developing new biopharmaceutical leads. Protein solution behaviour is dictated by the physicochemical properties of the protein and the solution. Optimising protein solutions through experimental screens and targeted protein engineering can be a difficult and time consuming process. Here, we describe development of the protein-sol web server, which was previously restricted to protein solubility prediction from amino acid sequence. Tools are presented for calculating and mapping patches of hydrophobicity and charge on the protein surface. In addition, predictions of folded state stability and net charge are displayed as a heatmap for a range of pH and ionic strength conditions. Tools are evaluated in the context of antibodies, their fragments and interactions. Surprisingly, antibody-antigen interfaces are, on average, at least as polar as Fab surfaces. This benchmarking process provides the user with thresholds with which to assess non-polar surface patches, and possible solubility implications, in proteins of interest. Stability heatmaps compare favourably with experimental data for CH2 and CH3 domains. Display and quantification of surface polarity and pH / ionic strength dependence will be useful generally for investigation of protein biophysics.

scholarly journals Local pH-dependent conformational changes leading to proteolytic susceptibility of cystatin C

1994 ◽  
Vol 302 (2) ◽  
pp. 411-416 ◽  
Author(s):  
P J Berti ◽  
A C Storer
Keyword(s):  
Ionic Strength ◽  
Conformational Change ◽  
Cystatin C ◽  
Conformational Changes ◽  
Ph Dependence ◽  
Significant Proportion ◽  
Cysteine Protease Inhibitor ◽  
Ionic Strength Dependence ◽  
Ph Dependent ◽  
Ph Range

Cystatin C, a cysteine protease inhibitor, was subject to hydrolysis at two sites when complexed with papain and in the presence of excess papain. A pH-dependent cleavage at His-86 increases Asp-87 was observed, as well as a pH-independent one at Gly-4 increases Lys-5. His-86 increases Asp-87 hydrolysis increased with decreasing pH and was characterized kinetically. It could be described by a single ionization with pKa = 3.4 +/- 0.2 and (kcat./Km)max. = 1.4 (+/- 0.4) x 10(4) M-1.s-1 at I = 0.3 M. C.d. spectroscopy, also at I = 0.3 M, demonstrated a conformational change with pKa = 3.2 +/- 0.2, indicating that the pH-dependence of hydrolysis was due to a conformational change in cystatin C. At I = 0.15 M, the pKa of the conformational change observed by c.d. shifted to 4.1 +/- 0.1. This indicates that at physiological ionic strength of 0.15 M, a significant proportion of cystatin C complexed with protease would be in a proteolytically labile conformation over the pH range 4.5 to 5, which is encountered in lysosomes. This may constitute a mechanism for clearing inappropriately localized cystatins. A pH-dependent conformational variability in this region of the inhibitor could explain the differences in the X-ray crystallographic and n.m.r. structures of the homologous chicken cystatin. The ionic-strength dependence of ionization indicates a hydrophobic stabilization of the ionizable group. The lack of pH-dependence of hydrolysis at Gly-4 increases Lys-5, with kcat./Km = 220 +/- 41 M-1.s-1 in the pH range 3.89 to 7.96 was unexpected in light of the normal, bell-shaped pH-dependence of papain-catalysed hydrolyses. This may reflect a different rate-limiting step of cystatin C hydrolysis.

The ionic strength dependence of chromatin folding

1978 ◽  
Vol 36 (2) ◽  
pp. 220-221
Author(s):  
F. Thoma ◽  
TH. Koller
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
Ionic Strength ◽  
Specimen Preparation ◽  
Preparation Technique ◽  
Carbon Supports ◽  
Ionic Strength Dependence ◽  
Chromatin Folding ◽  
Strength Dependence ◽  
Preparation Techniques

Under a variety of electron microscope specimen preparation techniques different forms of chromatin appearance can be distinguished: beads-on-a-string, a 100 Å nucleofilament, a 250 Å fiber and a compact 300 to 500 Å fiber.Using a standardized specimen preparation technique we wanted to find out whether there is any relation between these different forms of chromatin or not. We show that with increasing ionic strength a chromatin fiber consisting of a row of nucleo- somes progressively folds up into a solenoid-like structure with a diameter of about 300 Å.For the preparation of chromatin for electron microscopy the avoidance of stretching artifacts during adsorption to the carbon supports is of utmost importance. The samples are fixed with 0.1% glutaraldehyde at 4°C for at least 12 hrs. The material was usually examined between 24 and 48 hrs after the onset of fixation.

Self-association of insulin. Its pH dependence and effect of plasma

Diabetes ◽  
1987 ◽  
Vol 36 (3) ◽  
pp. 261-264 ◽  
Author(s):  
E. Helmerhorst ◽  
G. B. Stokes
Keyword(s):  
Ph Dependence ◽  
Self Association

Meso tetrakis ortho-, meta-, and para-N-alkylpyridiniopor-phyrins: kinetics of copper(II) and zinc(II) incorporation and zinc porphyrin demetalation

2003 ◽  
Vol 07 (03) ◽  
pp. 139-146 ◽  
Author(s):  
Peter Hambright ◽  
Ines Batinić-Haberle ◽  
Ivan Spasojević
Keyword(s):  
Aqueous Solution ◽  
Ionic Strength ◽  
Effective Charge ◽  
Methyl Ethyl ◽  
Ionic Strength Dependence ◽  
Zinc Porphyrin ◽  
Cationic Porphyrin ◽  
Strength Dependence ◽  
Acid Catalyzed ◽  
Kinetics Of

The relative reactivities of the tetrakis( N -alkylpyridinium- X - yl )-porphyrins where X = 4 (alkyl = methyl, ethyl, n -propyl) , X = 3 (methyl) , and X = 2 (methyl, ethyl, n -propyl, n -butyl, n -hexyl, n -octyl) were studied in aqueous solution. From the ionic strength dependence of the metalation rate constants, the effective charge of a particular cationic porphyrin was usually larger when copper(II) rather than zinc(II) was the reactant. The kinetics of ZnOH + incorporation and the acid catalyzed removal of zinc from the porphyrins in 1.0 M HCl were also studied. In general, the more basic 4- (para-) and 3- (meta-) isomers were the most reactive, followed by the less basic 2- (ortho-) methyl to n -butyl derivatives, with the lipophilic ortho n -hexyl and n -octyl porphyrins the least reactive.

Ionic Strength Dependence of Protonation Constants ofN-Alkyl Substituted Open Chain Diamines in NaClaq

2004 ◽  
Vol 49 (1) ◽  
pp. 109-115 ◽  
Author(s):  
Francesco Crea ◽  
Concetta De Stefano ◽  
Ottavia Giuffrè ◽  
Silvio Sammartano
Keyword(s):  
Ionic Strength ◽  
Protonation Constants ◽  
Ionic Strength Dependence ◽  
Open Chain ◽  
Strength Dependence
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