Progress in the prediction of pKa values in proteins

E Alexov, EL Mehler, N Baker… - Proteins: structure …, 2011 - Wiley Online Library
The pKa‐cooperative aims to provide a forum for experimental and theoretical researchers
interested in protein pKa values and protein electrostatics in general. The first round of the …

Encapsulation of drug molecules by cucurbiturils: effects on their chemical properties in aqueous solution

DH Macartney - Israel Journal of Chemistry, 2011 - Wiley Online Library
The effects of the encapsulation of drugs and other molecules of biomedical interest by
cucurbit [n] uril (n= 5–8, 10) host molecules on the chemical properties of the drugs in …

Very fast empirical prediction and rationalization of protein pKa values

H Li, AD Robertson, JH Jensen - Proteins: Structure, Function …, 2005 - Wiley Online Library
A very fast empirical method is presented for structure‐based protein pKa prediction and
rationalization. The desolvation effects and intra‐protein interactions, which cause variations …

Structural changes of region 1-16 of the Alzheimer disease amyloid β-peptide upon zinc binding and in vitro aging

S Zirah, SA Kozin, AK Mazur, A Blond… - Journal of Biological …, 2006 - ASBMB
Amyloid deposits within the cerebral tissue constitute a characteristic lesion associated with
Alzheimer disease. They mainly consist of the amyloid peptide Aβ and display an abnormal …

MCCE2: Improving protein pKa calculations with extensive side chain rotamer sampling

Y Song, J Mao, MR Gunner - Journal of computational …, 2009 - Wiley Online Library
Multiconformation continuum electrostatics (MCCE) explores different conformational
degrees of freedom in Monte Carlo calculations of protein residue and ligand pKas. Explicit …

Empirical relationships between protein structure and carboxyl pKa values in proteins

WR Forsyth, JM Antosiewicz… - … Structure, Function, and …, 2002 - Wiley Online Library
Relationships between protein structure and ionization of carboxyl groups were investigated
in 24 proteins of known structure and for which 115 aspartate and 97 glutamate pKa values …

Molecular determinants of the pKa values of Asp and Glu residues in staphylococcal nuclease

CA Castaneda, CA Fitch, A Majumdar… - Proteins: Structure …, 2009 - Wiley Online Library
Prior computational studies of the acid‐unfolding behavior of staphylococcal nuclease
(SNase) suggest that the pKa values of its carboxylic groups are difficult to reproduce with …

Fungal ribotoxins: molecular dissection of a family of natural killers

J Lacadena, E Álvarez-García… - FEMS microbiology …, 2007 - academic.oup.com
RNase T1 is the best known representative of a large family of ribonucleolytic proteins
secreted by fungi, mostly Aspergillus and Penicillium species. Ribotoxins stand out among …

Benchmarking pKa prediction

MN Davies, CP Toseland, DS Moss, DR Flower - BMC biochemistry, 2006 - Springer
Background pK a values are a measure of the protonation of ionizable groups in proteins.
Ionizable groups are involved in intra-protein, protein-solvent and protein-ligand interactions …

The role of hydrophobic microenvironments in modulating pKa shifts in proteins

EL Mehler, M Fuxreiter, I Simon… - Proteins: Structure …, 2002 - Wiley Online Library
The screened Coulomb potential (SCP) method, combined with a quantitative description of
the microenvironments around titratable groups, based on the Hydrophobic Fragmental …