Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization

K Hashimoto, H Nishi, S Bryant… - Physical biology, 2011 - iopscience.iop.org
Many soluble and membrane proteins form homooligomeric complexes in a cell which are
responsible for the diversity and specificity of many pathways, may mediate and regulate …

Prediction of protein–protein interactions: unifying evolution and structure at protein interfaces

N Tuncbag, A Gursoy, O Keskin - Physical biology, 2011 - iopscience.iop.org
The vast majority of the chores in the living cell involve protein–protein interactions.
Providing details of protein interactions at the residue level and incorporating them into …

Exploring Chemical Modifications of Aromatic Amino Acid Residues in Peptides

S Bhunia, M Purushotham, G Karan, B Paul… - Synthesis, 2023 - thieme-connect.com
The chemical diversification of biomolecules set forth a significant area of research that
constitutes an important intersection between chemistry and biology. Amino acids and …

Large-scale evaluation of protein reductive methylation for improving protein crystallization

Y Kim, P Quartey, H Li, L Volkart, C Hatzos, C Chang… - Nature …, 2008 - nature.com
To the editor: Obtaining diffraction-quality crystals is a major bottleneck in protein X-ray
crystallography. For example, the current success rate for protein structure solution at the …

Pie—efficient filters and coarse grained potentials for unbound protein–protein docking

DVS Ravikant, R Elber - Proteins: Structure, Function, and …, 2010 - Wiley Online Library
Identifying correct binding modes in a large set of models is an important step in protein–
protein docking. We identified protein docking filter based on overlap area that significantly …

Thermophilic adaptation of protein complexes inferred from proteomic homology modeling

BG Ma, A Goncearenco, IN Berezovsky - Structure, 2010 - cell.com
As protein complexes must remain in their native conformations at habitat temperatures,
thermal adaptation requires adjustment of their parts and interactions between them. Based …

The Development of a Universal In Silico Predictor of Protein-Protein Interactions

GT Valente, ML Acencio, C Martins, N Lemke - PloS one, 2013 - journals.plos.org
Protein-protein interactions (PPIs) are essential for understanding the function of biological
systems and have been characterized using a vast array of experimental techniques. These …

Analysis and network representation of hotspots in protein interfaces using minimum cut trees

N Tuncbag, FS Salman, O Keskin… - … Structure, Function, and …, 2010 - Wiley Online Library
We propose a novel approach to analyze and visualize residue contact networks of protein
interfaces by graph‐based algorithms using a minimum cut tree (mincut tree). Edges in the …

Quantitative expression of protein heterogeneity: Response of amino acid side chains to their local environment

D Bandyopadhyay, EL Mehler - Proteins: Structure, Function …, 2008 - Wiley Online Library
A general method has been developed to characterize the hydrophobicity or hydrophilicity of
the microenvironment (MENV), in which a given amino acid side chain is immersed, by …

Salvage of failed protein targets by reductive alkylation

K Tan, Y Kim, C Hatzos-Skintges, C Chang… - Structural Genomics and …, 2014 - Springer
The growth of diffraction-quality single crystals is of primary importance in protein X-ray
crystallography. Chemical modification of proteins can alter their surface properties and …