New Insights into the Cooperativity and Dynamics of Dimeric Enzymes

KW Chen, TY Sun, YD Wu - Chemical Reviews, 2023 - ACS Publications
A survey of protein databases indicates that the majority of enzymes exist in oligomeric
forms, with about half of those found in the UniProt database being homodimeric …

Solvation free energy as a measure of hydrophobicity: application to serine protease binding interfaces

J Kraml, AS Kamenik, F Waibl… - Journal of chemical …, 2019 - ACS Publications
Solvation and hydrophobicity play a key role in a variety of biological mechanisms. In
substrate binding, but also in structure-based drug design, the thermodynamic properties of …

DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding

L Li, A Chakravorty, E Alexov - Journal of computational …, 2017 - Wiley Online Library
Long‐range electrostatic forces play an important role in molecular biology, particularly in
macromolecular interactions. However, calculating the electrostatic forces for irregularly …

Modeling electrostatic force in protein-protein recognition

HBM Shashikala, A Chakravorty… - Frontiers in Molecular …, 2019 - frontiersin.org
Electrostatic interactions are important for understanding molecular interactions, since they
are long-range interactions and can guide binding partners to their correct binding positions …

Anisotropic distribution of ammonium sulfate ions in protein crystallization

M Kitahara, S Fudo, T Yoneda, M Nukaga… - Crystal Growth & …, 2019 - ACS Publications
Some proteins are easily crystallized by utilizing ammonium sulfate (AS) as a precipitant,
while others are not. To investigate the difference of AS behavior in protein crystallization …

A new DelPhi feature for modeling electrostatic potential around proteins: Role of bound ions and implications for zeta-potential

A Chakravorty, Z Jia, L Li, E Alexov - Langmuir, 2017 - ACS Publications
A new feature of the popular software DelPhi is developed and reported, allowing for
computing the surface averaged electrostatic potential (SAEP) of macromolecules. The user …

Electrostatic recognition in substrate binding to serine proteases

BJ Waldner, J Kraml, U Kahler, A Spinn… - Journal of Molecular …, 2018 - Wiley Online Library
Serine proteases of the Chymotrypsin family are structurally very similar but have very
different substrate preferences. This study investigates a set of 9 different proteases of this …

Crystal structure of chicken γS-crystallin reveals lattice contacts with implications for function in the lens and the evolution of the βγ-crystallins

V Sagar, SK Chaturvedi, P Schuck, G Wistow - Structure, 2017 - cell.com
Previous attempts to crystallize mammalian γS-crystallin were unsuccessful. Native L16
chicken γS crystallized avidly while the Q16 mutant did not. The X-ray structure for chicken …

Computational insights into the molecular mechanism of the high immunomodulatory activity of LZ-8 protein isolated from the Lingzhi or Reishi medicinal mushroom …

DP Bao, R Bai, YN Gao, Y Wu… - International Journal of …, 2018 - dl.begellhouse.com
ABSTRACT Ling zhi-8 (LZ-8) is the first fungal immunomodulatory protein (FIP) isolated from
the lingzhi or reishi medicinal mushroom, Ganoderma lucidum. LZ-8 effectively induces …

In-silico prediction of domain involved in chilli protein interaction with chilli leaf curl virus and associated betasatellite encoded protein

V Pandey, A Srivastava, N Singh, R Gupta, A Ali… - Discover Plants, 2024 - Springer
The begomovirus-caused chilli leaf curl disease (ChiLCD) is a significant hindrance to the
production of chilies (Capsicum annuum) in many chilli-growing regions worldwide …