Water mediation in protein folding and molecular recognition

Y Levy, JN Onuchic - Annu. Rev. Biophys. Biomol. Struct., 2006 - annualreviews.org
Water is essential for life in many ways, and without it biomolecules might no longer truly be
biomolecules. In particular, water is important to the structure, stability, dynamics, and …

Evolutionary and biophysical relationships among the papillomavirus E2 proteins

DM Blakaj, N Fernandez-Fuentes… - … in bioscience: a …, 2009 - pmc.ncbi.nlm.nih.gov
Infection by a human papillomavirus (HPV) may result in a variety of clinical conditions
ranging from benign warts to invasive cancer depending on the viral type. The HPV E2 …

Identification and analysis of papillomavirus E2 protein binding sites in the human genome

L Võsa, A Sudakov, M Remm, M Ustav… - Journal of virology, 2012 - journals.asm.org
Papillomavirus E2 protein is required for the replication and maintenance of viral genomes
and transcriptional regulation of viral genes. E2 functions through sequence-specific binding …

Evolutionary variation of papillomavirus E2 protein and E2 binding sites

A Rogers, M Waltke, PC Angeletti - Virology Journal, 2011 - Springer
Background In an effort to identify the evolutionary changes relevant to E2 function, within
and between papillomavirus genera, we evaluated the E2 binding sites (E2BS) s inside the …

Comprehensive comparison of the interaction of the E2 master regulator with its cognate target DNA sites in 73 human papillomavirus types by sequence statistics

IE Sanchez, M Dellarole, K Gaston… - Nucleic acids …, 2008 - academic.oup.com
Mucosal human papillomaviruses (HPVs) are etiological agents of oral, anal and genital
cancer. Properties of high-and low-risk HPV types cannot be reduced to discrete molecular …

Transition state for protein–DNA recognition

DU Ferreiro, IE Sánchez, G de Prat Gay - Proceedings of the National …, 2008 - pnas.org
We describe the formation of protein–DNA contacts in the two-state route for DNA sequence
recognition by a transcriptional regulator. Surprisingly, direct sequence readout establishes …

Probing the role of interfacial waters in protein–DNA recognition using a hybrid implicit/explicit solvation model

S Li, P Bradley - Proteins: Structure, Function, and …, 2013 - Wiley Online Library
When proteins bind to their DNA target sites, ordered water molecules are often present at
the protein–DNA interface bridging protein and DNA through hydrogen bonds. What is the …

Principles of Amino‐Acid‐Nucleotide Interactions Revealed by Binding Affinities between Homogeneous Oligopeptides and Single‐Stranded DNA Molecules

P Wang, X Fang, R Du, J Wang, M Liu, P Xu… - …, 2022 - Wiley Online Library
We have determined the binding strengths between nucleotides of adenine, thymine,
guanine and cytosine in homogeneous single stranded DNAs and homo‐octapeptides …

The recognition of local DNA conformation by the human papillomavirus type 6 E2 protein

E Hooley, V Fairweather, AR Clarke… - Nucleic acids …, 2006 - academic.oup.com
The E2 proteins are transcription/replication factors from papillomaviruses. Human
papillomaviruses (HPVs) can be broadly divided in two groups; low-risk HPV subtypes …

A quasi‐spontaneous amyloid route in a DNA binding gene regulatory domain: the papillomavirus HPV16 E2 protein

DE Wetzler, EM Castaño, G de Prat‐Gay - Protein science, 2007 - Wiley Online Library
The DNA binding domain of papillomavirus E2 proteins is at the center of the regulation of
gene transcription and replication of the virus. Its unique fold consists of a β‐barrel domain …