Theory and simulation of the ultrafast double-bond isomerization of biological chromophores

S Gozem, HL Luk, I Schapiro, M Olivucci - Chemical reviews, 2017 - ACS Publications
Ultrafast processes in light-absorbing proteins have been implicated in the primary step in
the light-to-energy conversion and the initialization of photoresponsive biological functions …

AlphaFill: enriching AlphaFold models with ligands and cofactors

ML Hekkelman, I de Vries, RP Joosten, A Perrakis - Nature Methods, 2023 - nature.com
Artificial intelligence-based protein structure prediction approaches have had a
transformative effect on biomolecular sciences. The predicted protein models in the …

NeoR, a near-infrared absorbing rhodopsin

M Broser, A Spreen, PE Konold, E Schiewer… - Nature …, 2020 - nature.com
The Rhizoclosmatium globosum genome encodes three rhodopsin-guanylyl cyclases
(RGCs), which are predicted to facilitate visual orientation of the fungal zoospores. Here, we …

Structural basis of design and engineering for advanced plant optogenetics

S Banerjee, D Mitra - Trends in plant science, 2020 - cell.com
In optogenetics, light-sensitive proteins are specifically expressed in target cells and light is
used to precisely control the activity of these proteins at high spatiotemporal resolution …

Tuning the Electronic Absorption of Protein-Embedded All-trans-Retinal

W Wang, Z Nossoni, T Berbasova, CT Watson, I Yapici… - Science, 2012 - science.org
Protein-chromophore interactions are a central component of a wide variety of critical
biological processes such as color vision and photosynthesis. To understand the …

Mapping the excited state potential energy surface of a retinal chromophore model with multireference and equation-of-motion coupled-cluster methods

S Gozem, F Melaccio, R Lindh, AI Krylov… - Journal of Chemical …, 2013 - ACS Publications
The photoisomerization of the retinal chromophore of visual pigments proceeds along a
complex reaction coordinate on a multidimensional surface that comprises a hydrogen-out …

a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement

L Pedraza-González, L De Vico, MC Marı́n… - Journal of chemical …, 2019 - ACS Publications
The Automatic Rhodopsin Modeling (ARM) protocol has recently been proposed as a tool
for the fast and parallel generation of basic hybrid quantum mechanics/molecular mechanics …

[PDF][PDF] Conformations of c-aminobutyric acid (GABA): the role of the n! p* interaction

S Blanco, JC López, S Mata, JL Alonso - Angew Chem Int Ed, 2010 - academia.edu
Susana Blanco, Juan C. López,* Santiago Mata, and JosØ L. Alonso g-Aminobutyric acid
(GABA) is arguably the most important inhibitory neurotransmitter in the brain and …

Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination

AN Alexandrova, D Röthlisberger… - Journal of the …, 2008 - ACS Publications
A series of enzymes for Kemp elimination of 5-nitrobenzisoxazole has been recently
designed and tested. In conjunction with the design process, extensive computational …

“Turn-on” protein fluorescence: in situ formation of cyanine dyes

I Yapici, KSS Lee, T Berbasova, M Nosrati… - Journal of the …, 2015 - ACS Publications
Protein reengineering of cellular retinoic acid binding protein II (CRABPII) has yielded a
genetically addressable system, capable of binding a profluorophoric chromophore that …