Electrostatics in computational protein design

CL Vizcarra, SL Mayo - Current opinion in chemical biology, 2005 - Elsevier
… (CL Vizcarra and SL Mayo, unpublished results). Pokala and Handel [48 • ] have adapted
the GB method of Brooks and co-workers [49] for use in protein design. They overcome the …

Comparison of random mutagenesis and semi-rational designed libraries for improved cytochrome P450 BM3-catalyzed hydroxylation of small alkanes

MMY Chen, CD Snow, CL Vizcarra… - … , Design & Selection, 2012 - academic.oup.com
Three semi-rational approaches, combinatorial site-saturation mutagenesis (CSSM) using a
reduced amino acid set and two libraries based on C orbit and CRAM computational design …

Structure and function of the interacting domains of Spire and Fmn-family formins

CL Vizcarra, B Kreutz, AA Rodal… - Proceedings of the …, 2011 - National Acad Sciences
Evidence for cooperation between actin nucleators is growing. The WH2-containing nucleator
Spire and the formin Cappuccino interact directly, and both are essential for assembly of …

Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function

TP Treynor, CL Vizcarra, D Nedelcu… - Proceedings of the …, 2007 - National Acad Sciences
To determine which of seven library design algorithms best introduces new protein function
without destroying it altogether, seven combinatorial libraries of green fluorescent protein …

[HTML][HTML] Metal binding and interdomain thermodynamics of mammalian metallothionein-3: enthalpically favoured Cu+ supplants entropically favoured Zn 2+ to form Cu …

…, R Lakha, RLE Villones, M Orman, CL Vizcarra… - Chemical …, 2022 - pubs.rsc.org
Metallothioneins (MTs) are a ubiquitous class of small metal-binding proteins involved in
metal homeostasis and detoxification. While known for their high affinity for d10 metal ions, …

[HTML][HTML] The role of formin tails in actin nucleation, processive elongation, and filament bundling

CL Vizcarra, B Bor, ME Quinlan - Journal of Biological Chemistry, 2014 - ASBMB
Formins are multidomain proteins that assemble actin in a wide variety of biological processes.
They both nucleate and remain processively associated with growing filaments, in some …

[HTML][HTML] Interaction between microtubules and the Drosophila formin Cappuccino and its effect on actin assembly

EA Roth-Johnson, CL Vizcarra, JS Bois… - Journal of Biological …, 2014 - ASBMB
Formin family actin nucleators are potential coordinators of the actin and microtubule
cytoskeletons, as they can both nucleate actin filaments and bind microtubules in vitro. To gain a …

One‐and two‐body decomposable Poisson‐Boltzmann methods for protein design calculations

SA Marshall, CL Vizcarra, SL Mayo - Protein Science, 2005 - Wiley Online Library
Successfully modeling electrostatic interactions is one of the key factors required for the
computational design of proteins with desired physical, chemical, and biological properties. In …

Autoinhibition of the formin Cappuccino in the absence of canonical autoinhibitory domains

B Bor, CL Vizcarra, ML Phillips… - Molecular biology of the …, 2012 - Am Soc Cell Biol
Formins are a conserved family of proteins known to enhance actin polymerization. Most
formins are regulated by an intramolecular interaction. The Drosophila formin, Cappuccino (…

Structure of a putative ClpS N‐end rule adaptor protein from the malaria pathogen Plasmodium falciparum

AP AhYoung, A Koehl, CL Vizcarra, D Cascio… - Protein …, 2016 - Wiley Online Library
The N‐end rule pathway uses an evolutionarily conserved mechanism in bacteria and
eukaryotes that marks proteins for degradation by ATP‐dependent chaperones and proteases …