Protein–DNA binding: complexities and multi-protein codes

T Siggers, R Gordân - Nucleic acids research, 2014 - academic.oup.com
Binding of proteins to particular DNA sites across the genome is a primary determinant of
specificity in genome maintenance and gene regulation. DNA-binding specificity is encoded …

Polyampholytes

AV Dobrynin, RH Colby… - Journal of Polymer …, 2004 - Wiley Online Library
Polyampholytes are charged polymers with both positively and negatively charged groups.
The conformation of these polymers in solutions strongly depends on the distribution of …

Restructuring the crystalline cellulose hydrogen bond network enhances its depolymerization rate

SPS Chundawat, G Bellesia… - Journal of the …, 2011 - ACS Publications
Conversion of lignocellulose to biofuels is partly inefficient due to the deleterious impact of
cellulose crystallinity on enzymatic saccharification. We demonstrate how the synergistic …

The roles of water in the protein matrix: a largely untapped resource for drug discovery

F Spyrakis, MH Ahmed, AS Bayden… - Journal of medicinal …, 2017 - ACS Publications
The value of thoroughly understanding the thermodynamics specific to a drug
discovery/design study is well known. Over the past decade, the crucial roles of water …

Strong and weak hydrogen bonds in the protein–ligand interface

SK Panigrahi, GR Desiraju - Proteins: Structure, Function, and …, 2007 - Wiley Online Library
The characteristics of N H··· O, O H··· O, and C H··· O hydrogen bonds and other weak
intermolecular interactions are analyzed in a large and diverse group of 251 protein–ligand …

[图书][B] Structure in protein chemistry

J Kyte - 2006 - books.google.com
The second edition of Structure in Protein Chemistry showcases the latest developments
and innovations in the field of protein structure analysis and prediction. The book begins by …

The role of water in protein-DNA recognition

B Jayaram, T Jain - Annu. Rev. Biophys. Biomol. Struct., 2004 - annualreviews.org
▪ Abstract Is it by design or by default that water molecules are observed at the interfaces of
some protein-DNA complexes? Both experimental and theoretical studies on the …

Water at biomolecular binding interfaces

Z Li, T Lazaridis - Physical Chemistry Chemical Physics, 2007 - pubs.rsc.org
Water molecules are often found at the binding interface of biomolecular complexes
mediating the interaction between polar groups viahydrogen bonds, or simply filling space …

Protein-DNA recognition patterns and predictions

A Sarai, H Kono - Annu. Rev. Biophys. Biomol. Struct., 2005 - annualreviews.org
▪ Abstract Structural data on protein-DNA complexes provide clues for understanding the
mechanism of protein-DNA recognition. Although the structures of a large number of protein …

Secondary structure sensitivity of hydrogen bond lifetime dynamics in the protein hydration layer

S Bandyopadhyay, S Chakraborty… - Journal of the American …, 2005 - ACS Publications
The heterogeneous nature of a protein surface plays an essential role in its biological
activity and molecular recognition, and this role is mediated at least partly through the …