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E-selectin ligand complexes adopt an extended high-affinity conformation

Preston, Roland C. ; Jakob, Roman P. ; Binder, Florian P.C. ; Sager, Christoph P. ; Ernst, Beat ; Maier, Timm

In: Journal of Molecular Cell Biology, 2016, vol. 8, no. 1, p. 62-72

NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary

Yilmaz, Emel ; Güntert, Peter

In: Journal of Biomolecular NMR, 2015, vol. 63, no. 1, p. 21-37

A standard numbering scheme for class c β-lactamases

Mack, Andrew R. ; Barnes, Melissa D. ; Taracila, Magdalena A. ; Hujer, Andrea M. ; Hujer, Kristine M. ; Cabot, Gabriel ; Feldgarden, Michael ; Haft, Daniel H. ; Klimke, William ; Akker, Focco van den ; Vila, Alejandro J. ; Smania, Andrea ; Haider, Shozeb ; Papp-Wallace, Krisztina M. ; Bradford, Patricia A. ; Rossolini, Gian Maria ; Docquier, Jean-Denis ; Frère, Jean-Marie ; Galleni, Moreno ; Hanson, Nancy D. ; Oliver, Antonio ; Plésiatyz, Patrick ; Poirel, Laurent ; Nordmann, Patrice ; Palzkill, Timothy G. ; Jacoby, George A. ; Bush, Karen ; Bonomo, Robert A.

In: Antimicrobial Agents and Chemotherapy, 2020, vol. 64, no. 3, p. -

Unlike for classes A and B, a standardized amino acid numbering scheme has not been proposed for the class C (AmpC) β-lactamases, which complicates communication in the field. Here, we propose a scheme developed through a collaborative approach that considers both sequence and structure, preserves traditional numbering of catalytically important residues (Ser64, Lys67, Tyr150, and Lys315),...

Insights into the effect of the G245S single point mutation on the structure of p53 and the binding of the protein to DNA

Lepre, Marco Gaetano ; Omar, Sara Ibrahim ; Grasso, Gianvito ; Morbiducci, Umberto ; Deriu, Marco Agostino ; Tuszynski, Jack A.

In: Molecules, 2017, vol. 22, no. 8, p. 1358

The transcription factor p53 is a potent tumor suppressor dubbed as the “guardian of the genome” because of its ability to orchestrate protective biological outputs in response to a variety of oncogenic stresses. Mutation and thus inactivation of p53 can be found in 50% of human tumors. The majority are missense mutations located in the DNA binding region. Among them, G245S is known to be...

Structure and dynamics of the acyl chains in the membrane trafficking and enzymatic processing of lipids

Vanni, Stefano ; Riccardi, Laura ; Palermo, Giulia ; De Vivo, Marco

In: Accounts of Chemical Research, 2019, vol. 52, no. 11, p. 3087–3096

The regulatory chemical mechanisms of lipid trafficking and degradation are involved in many pathophysiological processes, being implicated in severe pain, inflammation, and cancer. In addition, the processing of lipids is also relevant for industrial and environmental applications. However, there is poor understanding of the chemical features that control lipid membrane trafficking and allow...

Rational modification of estrogen receptor by combination of computational and experimental analysis

Ferrero, Valentina Elisabetta Viviana ; Pedotti, Mattia ; Chiadò, Alessandro ; Simonelli, Luca ; Calzolai, Luigi ; Varani, Luca ; Lettieri, Teresa

In: Plos one, 2014, vol. 9, no. 7, p. e102658

In this manuscript, we modulate the binding properties of estrogen receptor protein by rationally modifying the amino acid composition of its ligand binding domain. By combining sequence alignment and structural analysis of known estrogen receptor- ligand complexes with computational analysis, we were able to predict estrogen receptor mutants with altered binding properties. These predictions...

Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control

Abriata, Luciano ; Vila, Alejandro ; Dal Peraro, Matteo

In: JBIC Journal of Biological Inorganic Chemistry, 2014, vol. 19, no. 4-5, p. 565-575

On the use of one-step perturbation to investigate the dependence of NOE-derived atom-atom distance bound violations of peptides upon a variation of force-field parameters

Lin, Zhixiong ; Oostenbrink, Chris ; van Gunsteren, Wilfred

In: European Biophysics Journal, 2014, vol. 43, no. 2-3, p. 113-119

Lineage-Specific Duplication and Loss of Pepsinogen Genes in Hominoid Evolution

Narita, Yuichi ; Oda, Sen-ichi ; Takenaka, Osamu ; Kageyama, Takashi

In: Journal of Molecular Evolution, 2010, vol. 70, no. 4, p. 313-324

Selection Shapes the Robustness of Ligand-Binding Amino Acids

Bilgin, Tugce ; Kurnaz, Isil ; Wagner, Andreas

In: Journal of Molecular Evolution, 2013, vol. 76, no. 5, p. 343-349