Biology subjects

Nicoludis, J. M.

Publications and source records attributed to Nicoludis, J. M..

4 recordsLinked to original sources

bioRxiv2026

GYDE: A collaborative drug discovery platform for AI-powered protein design and engineering

As computational tools and machine learning models for protein sciences continue to advance and proliferate, bench scientists face increasing technical challenges adopting these tools for specific applications such as drug discovery. Here we present GYDE (Guide Your Design and Engineering), an open-source, versatile, and web-based collaboration platform designed to make computational analyses of proteins and antibodies easily accessible to bench scientists. GYDE enables the exploration of sequence-structure-function relationships through a tightly integrated visual interface, offering researchers a comprehensive exploration of protein functional determinants either via real assay data or computational tools. GYDEs intuitive interface facilitates seamless access to cutting-edge AI models for protein and antibody structure prediction, design, and downstream analyses. The flexible and easy addition of new tools and models is facilitated by the use of the Slivka compute API. The platform supports saved sessions that enable researchers to easily share their findings with other users, fostering a more collaborative scientific community. GYDE is freely available for protein scientists in academia and industry to build drug discovery analytics platforms customized to their needs.

bioinformatics↗

bioRxiv2022

Transient Water Wires Mediate Selective Proton Conduction in Designed Channel Proteins

Summary paragraphSelective proton transport through proteins is essential for forming and utilizing proton gradients in cells. Protons are conducted along hydrogen-bonded "wires" of water molecules and polar sidechains, which, somewhat surprisingly, are often interrupted by dry apolar stretches in the conduction pathways inferred from static protein structures. We hypothesize that protons are conducted through such dry spots by forming transient water wires, often highly correlated with the presence of the excess proton itself in the water wire. To test this hypothesis, we used molecular dynamics simulations to design transmembrane channels with stable water pockets interspersed by apolar segments capable of forming flickering water wires. The minimalist designed channels conduct protons at rates similar to viral proton channels, and they are at least 106-fold more selective for H+ over Na+. These studies inform mechanisms of biological proton conduction and principles for engineering proton-conductive materials.

biophysics↗

bioRxiv2018

Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis

Clustered protocadherins are a large family of paralogous proteins that play important roles in neuronal development. The more than 50 clustered protocadherin isoforms have remarkable homophilic specificity for interactions between cellular surfaces that is controlled by a large antiparallel dimer interface formed by the first four extracellular cadherin (EC) domains. To understand how specificity is achieved between the numerous paralogs, we used a combination of structural and computational approaches. Molecular dynamics simulations revealed that individual EC interactions are weak and go through binding and unbinding events, but together they form a stable complex through polyvalency. Using sequence coevolution, we generated a statistical model of interaction energy for the clustered protocadherin family that measures the contributions of all amino acid pairs in the interface. Our interaction energy model assesses specificity for all possible pairs of isoforms, recapitulating known pairings and predicting the effects of experimental changes in isoform specificity that are consistent with literature results. Our results show that sequence coevolution can be used to understand specificity determinants in a protein family and prioritize interface amino acid substitutions to reprogram specific protein-protein interactions.

biophysics↗

bioRxiv2018

Structures in multiple conformations reveal distinct transition metal and proton pathways in an Nramp transporter

Nramp family transporters--expressed in organisms from bacteria to humans--enable uptake of essential divalent transition metals via an alternating-access mechanism that includes proton co-transport. We present high-resolution structures of Deinococcus radiodurans (Dra)Nramp at complementary stages of its transport cycle to provide a thorough description of the Nramp transport cycle by identifying the key intramolecular rearrangements and changes to the metal coordination sphere. Strikingly, while metal transport requires cycling from outward-to inward-open states, efficient proton transport still occurs in outward-locked (but not inward-locked) DraNramp. We propose a model in which metal and proton enter the transporter via the same external pathway to the binding site, but follow separate routes to the cytoplasm, thus resolving the electrostatic dilemma of using a cation co-substrate to drive a cation primary substrate. Our results illustrate the flexibility of the LeuT fold to support a broad range of co-substrate coupling and conformational change mechanisms.

biochemistry↗