Many amino acid substitution variants identified in DNA repair genes during human population screenings are predicted to impact protein function

T Xi, IM Jones, HW Mohrenweiser - Genomics, 2004 - Elsevier
Over 520 different amino acid substitution variants have been previously identified in the
systematic screening of 91 human DNA repair genes for sequence variation. Two algorithms …

An intragenic suppressor in the cytochrome c oxidase I gene of mouse mitochondrial DNA

R Acín-Pérez, MP Bayona-Bafaluy… - Human molecular …, 2003 - academic.oup.com
We report here the identification of a cell line containing single and double missense
mutations in cytochrome c oxidase (COX) subunit I gene of mouse mitochondrial DNA …

Designing allosteric control into enzymes by chemical rescue of structure

K Deckert, SJ Budiardjo, LC Brunner… - Journal of the …, 2012 - ACS Publications
Ligand-dependent activity has been engineered into enzymes for purposes ranging from
controlling cell morphology to reprogramming cellular signaling pathways. Where these …

The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation

Y Xia, N DiPrimio, TR Keppel, B Vo… - Journal of the …, 2013 - ACS Publications
The ability to selectively activate function of particular proteins via pharmacological agents is
a longstanding goal in chemical biology. Recently, we reported an approach for designing a …

Structure-Based Engineering of Internal Cavities in Coiled-Coil Peptides,

MK Yadav, JE Redman, LJ Leman… - Biochemistry, 2005 - ACS Publications
Cavities and clefts are frequently important sites of interaction between natural enzymes or
receptors and their corresponding substrate or ligand molecules and exemplify the types of …

Filling small, empty protein cavities: structural and energetic consequences

M Bueno, N Cremades, JL Neira, J Sancho - Journal of molecular biology, 2006 - Elsevier
Most proteins contain small cavities that can be filled by replacing cavity-lining residues by
larger ones. Since shortening mutations in hydrophobic cores tend to destabilize proteins, it …

Energetics of aliphatic deletions in protein cores

M Bueno, LA Campos, J Estrada, J Sancho - Protein science, 2006 - Wiley Online Library
Although core residues can sometimes be replaced by shorter ones without introducing
significant changes in protein structure, the energetic consequences are typically large and …

Thermodynamic fidelity of the mammalian cytochrome P450 2B4 active site in binding substrates and inhibitors

BK Muralidhara, L Sun, S Negi, JR Halpert - Journal of molecular biology, 2008 - Elsevier
Structural plasticity of mammalian cytochromes P450 (CYP) has recently been explored in
our laboratory and elsewhere to understand the ligand-binding promiscuity. CYP2B4 …

X‐ray evidence of a native state with increased compactness populated by tryptophan‐less B. licheniformis β‐lactamase

VA Risso, JP Acierno, S Capaldi, HL Monaco… - Protein …, 2012 - Wiley Online Library
Abstract β‐lactamases confer antibiotic resistance, one of the most serious world‐wide
health problems, and are an excellent theoretical and experimental model in the study of …

Design of ligand binding to an engineered protein cavity using virtual screening and thermal up-shift evaluation

C Machicado, J López-Llano, S Cuesta-López… - Journal of computer …, 2005 - Springer
Proteins could be used to carry and deliver small compounds. As a tool for designing ligand
binding sites in protein cores, a three-step virtual screening method is presented that has …