Biology subjects

Fernandez-Quintero, M. L.

Publications and source records attributed to Fernandez-Quintero, M. L..

21 records · Page 2Linked to original sources

bioRxiv2022

Challenges in antibody structure prediction

The tremendous advances in structural biology and the exponential increase of high-quality experimental structures available in the PDB motivated numerous studies to tackle the grand challenge of predicting protein structures. AlphaFold2 revolutionized the field of protein structure prediction, by combining artificial intelligence with evolutionary information. Antibodies are one of the most important classes of biotherapeutic proteins. Accurate structure models are a prerequisite to advance biophysical property predictions and consequently antibody design. Various specialized tools are available to predict antibody structures based on different principles and profiting from current advances in protein structure prediction based on artificial intelligence. Here, we want to emphasize the importance of reliable protein structure models and highlight the enormous advances in the field. At the same time, we want to raise the awareness that protein structure models--and in particular antibody models--may suffer from structural inaccuracies, namely incorrect cis-amid bonds, wrong stereochemistry or clashes. We show that these inaccuracies affect biophysical property predictions such as surface hydrophobicity. Thus, we stress the significance of carefully reviewing protein structure models before investing further computing power and setting up experiments. To facilitate the assessment of model quality, we provide a tool "TopModel" to validate structure models.

bioinformatics↗

bioRxiv2021

Calcium current modulation by the γ1 subunit depends on alternative splicing of CaV1.1

The skeletal muscle voltage-gated calcium channel (CaV1.1) primarily functions as voltage sensor for excitation-contraction coupling. Conversely, its ion-conducting function is modulated by multiple mechanisms within the pore-forming 1S subunit and the auxiliary 2{delta}-1 and {gamma}1 subunits. Particularly, developmentally regulated alternative splicing of exon 29, which inserts 19 amino acids in the extracellular IVS3-S4 loop of CaV1.1a, greatly reduces the current density and shifts the voltage-dependence of activation to positive potentials outside the physiological range. We generated a new HEK293-cell line stably expressing 2{delta}-1, {beta}3, and STAC3. When the adult (CaV1.1a) and the embryonic (CaV1.1e) splice variants were expressed in these cells, the difference in the voltage-dependence of activation observed in muscle cells was reproduced, but not the reduced current density of CaV1.1a. Only when we further co-expressed the {gamma}1 subunit, the current density of CaV1.1a, but not of CaV1.1e, was reduced by >50 %. In addition, {gamma}1 caused a shift of the voltage-dependence of inactivation to negative voltages in both variants. Thus, the current-reducing effect of {gamma}1, but not its effect on inactivation, is specifically dependent on the inclusion of exon 29 in CaV1.1a. Molecular structure modeling revealed several direct ionic interactions between oppositely charged residues in the IVS3-S4 loop and the {gamma}1 subunit. However, substitution of these residues by alanine, individually or in combination, did not abolish the {gamma}1-dependent reduction of current density, suggesting that structural rearrangements of CaV1.1a induced by inclusion of exon 29 allosterically empower the {gamma}1 subunit to exert its inhibitory action on CaV1.1 calcium currents. SummaryEl Ghaleb et al. analyzed the effects of the {gamma}1 subunit on current properties and expression of the adult (CaV1.1a) and embryonic (CaV1.1e) calcium channel splice variants, demonstrating that {gamma}1 reduces the current amplitude in a splicing-dependent manner.

physiology↗

bioRxiv2021

OCD.py - Characterizing immunoglobulin inter-domain orientations

SummaryInter-domain orientations between immunoglobulin domains are important for the modeling and engineering of novel antibody therapeutics. Previous tools to describe these orientations are applicable only to the variable domains of antibodies and T-cell receptors. We present the "Orientation of Cylindrical Domains (OCD)" tool, which employs a transferable approach to calculate inter-domain orientations for all immunoglobulin domains. Based on a reference structure, the OCD tool automatically builds a suitable reference coordinate system for each domain. Through alignment, the reference coordinate systems are transferred onto the sample to calculate six measures which fully characterize the inter-domain orientation. Availability and implementationThe OCD approach is implemented as a stand-alone Python script, OCD.py, which can handle multiple types of data input for the analysis of single structures and molecular dynamics trajectories alike. OCD.py is available at https://github.com/liedllab/OCD under MIT license. Supplementary InformationSupplementary information and data are available at Bioinformatics online.

bioinformatics↗