pIChemiSt ─ Free Tool for the Calculation of Isoelectric Points of Modified Peptides

Abstract

The isoelectric point (pI) is a fundamental physicochemical property of peptides and proteins. It is widely used to steer design away from low solubility and aggregation and guide peptide separation and purification. Experimental measurements of pI can be replaced by calculations knowing the ionizable groups of peptides and their corresponding pK a values. Different pK a sets are published in the literature for natural amino acids, however, they are insufficient to describe synthetically modified peptides, complex peptides of natural origin, and peptides conjugated with structures of other modalities. Noncanonical modifications (nCAAs) are ignored in the conventional sequence-based pI calculations, therefore producing large errors in their pI predictions. In this work, we describe a pI calculation method that uses the chemical structure as an input, automatically identifies ionizable groups of nCAAs and other fragments, and performs pK a predictions for them. The method is validated on a curated set of experimental measures on 29 modified and 119093 natural peptides, providing an improvement of R 2 from 0.74 to 0.95 and 0.96 against the conventional sequence-based approach for modified peptides for the two studied pK a prediction tools, ACDlabs and pKaMatcher, correspondingly. The method is available in the form of an open source Python library at https://github.com/AstraZeneca/peptidetools, which can be integrated into other proprietary and free software packages. We anticipate that the pI calculation tool may facilitate optimization and purification activities across various application domains of peptides, including the development of biopharmaceuticals.

The Molecular Footprint of Peptides on the Surface of Ultrasmall Gold Nanoparticles (2 nm) Is Governed by Steric Demand

“…The isoelectric points of the particle species were between pH 5 and 6 for all particles. This agrees well with the isoelectric point of the free peptides, which are reported between pH 5 and 6, indicating the integrity of the gold-bound peptides.…”

Sequence-based prediction of the solubility of peptides containing non-natural amino acids

“…A linear combination of ALOGPS 95,96 and XLOGP3 99 is employed to determine the hydrophobicity values. pIChemiSt suite 91 is used to predict the pKa values of mAAs. Structural propensities are calculated using a separate predictor that employs a combination of the number of hydrogen donors and acceptors, the number of rotational bonds, molecular weight and the topological polar surface area.…”

“…pKa values. We calculated pKa values of modified side-chains using the recently developed pIChemiSt suite 91 .…”

Proteoform Identification in 2D Electrophoresis Maps by Using Isoelectric Point Prediction

“…При этом табличные значения pK a были рассчитаны на основании данных, полученных для большой выборки пептидов, в том числе и с различными химическими и посттрансляционными модификациями, и программа может предсказывать pI для белков с ПТМ. Существуют и другие программы, позволяющие делать подобные предсказания [8,9], но отличие от них спектр ПТМ в pIPredict 3 охватывает большую часть возможных в физиологических условиях. Важно, что средняя ошибка предсказания pIPredict 3 для пептидов была меньше 0.1 единицы pH.…”