Computational design of environmental sensors for the potent opioid fentanyl

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The encoding and evolution of specificity and affinity in protein-protein interactions is poorly understood. Here, we address this question by quantifying how all mutations in one protein, JUN, alter binding to all other members of a protein family, the 54 ...

Copyright © 2024 the Author(s). Published by PNAS.Liquid-liquid phase separation (LLPS) is an intracellular process widely used by cells for many key biological functions. It occurs in complex and crowded environments, where amino acids (AAs) are vital com ...

Redox homeostasis is a key factor in maintaining cellular function and health. The main determinant of the intracellular redox potential is ubiquitous glutathione (GSH) together with its oxidized dimer (GSSG). Importantly, both redox equilibrium and GSH ho ...

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. This k ...

In the last years, it has been demonstrated a link between the overload of metal ions inside nervous system cells and the onset of severe neurodegenerative diseases. This prompted the investigation of the structural and functional properties of transporter ...

The metabolic engineering community relies on computational methods for pathway design to produce important small molecules in microbial hosts. Metabolic network databases are continuously curated and updated with known and novel reactions that expand the ...

A method for determining the presence of a molecule coupled to the cytoplasmic side of a cellular membrane is disclosed. The method is implemented in a microfluidic setting and is particularly suitable for determining the presence and/or the activity of a ...

Knowledge-based approaches use the statistics collected from protein data-bank structures to estimate effective interaction potentials between amino acid pairs. Empirical relations are typically employed that are based on the crucial choice of a reference ...

Macrocycles are an attractive class of molecules due to their good binding properties and yet rather small size that allows, in many cases, crossing membranes to reach intracellular targets. In comparison to classical small molecule drugs, macrocycles are ...

Proteins are fundamental components in biological systems and crucial for a variety of biological functions. Over the last decades, significant progress in structural biology has facilitated the study of proteins and their interactions with molecular partn ...

The rising resistance and the severe side effects associated with classical anticancer drugs such as cisplatin or mercaptopurines has triggered the development of novel antitumourous agents based on transition metal (e.g. ruthenium, osmium, and gold) organ ...

Evolution has created, selected and evolved large repertoires of proteins that operate in various biological systems. Nowadays biotechnological needs are coming up orders of magnitude faster than proteins naturally evolve. The emergence of de novo protein ...

Knowledge of the atomic-level structure is key to understanding and predicting properties of materials. X-ray diffraction (XRD) is the methods of choice for structures containing well-defined long-range order. However, many materials contain various degree ...

Nature has the ability to cope with extreme pH, temperature and pressure, in addition to bestowing a wide array of functionalities to (bio)macromolecules. These specialized skills have attracted the interest of vast scientific communities especially in vie ...

Pyridomycin, a natural product with potent antituberculosis activity, inhibits a major drug target, the InhA enoyl reductase. Here, we unveil the co-crystal structure and unique ability of pyridomycin to block both the NADH cofactor- and lipid substrate-bi ...

We propose an interactive computational design method for deployable auxetic shells. We realize deployable auxetics as triangular linkages that can be actuated with simple expansive mechanisms to assume a desired freeform target shape. The core feature of ...

Recent crystal structures of G-protein-coupled receptors (GPCRs) have revealed ordered internal water molecules, raising questions about the functional role of those waters for receptor activation that could not be answered by the static structures. Here, ...

The synthesis of three potentially tetradentate, N2S2 Schiff-base-ligands, containing a disulfide bond, (LSSLThio)-S-Thio(L1), (LSSLBr)-S-Br(L2) and (LSSLDiMeO)-S-DiMeO (L3) are reported. These ligands undergo reductive disulfide bond scission upon reactio ...

We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant polymorphs. This id ...

Computational design of environmental sensors for the potent opioid fentanyl

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The genetic architecture of protein interaction affinity and specificity

Amino acids modulate liquid-liquid phase separation in vitro and in vivo by regulating protein-protein interactions

HaloTag-Based Tools for Live-Cell Imaging and Elucidation of Organellar Redox Biology

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

De novo design of protein interactions with learned surface fingerprints

Computational Studies of the Proton-Coupled Metal Ion Transport in the SLC11/NRAMP Family of Transporters

Computational tools and resources for designing new pathways to small molecules

Method and system for determining intracellular mediators' activity

Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules

Methods for the generation of large combinatorial macrocycle libraries

On the exploration of novel methodological approaches for immunogen design: case studies in influenza and hepatitis C

Computational characterisation of the selectivity and binding mode of mono- and binuclear transition metal based anticancer compounds

Functional de novo Protein Design for Targeted Vaccines and Synthetic Biology Applications

Advanced Computational Methods for NMR Crystallography

Reprogramming the B1 Domain of Streptococcal Protein G (GB1) : A Joint Theoretical and Experimental Investigation

Pyridomycin bridges the NADH- and substratebinding pockets of the enoyl reductase InhA

Computational Design of Deployable Auxetic Shells

Activation of G-protein-coupled receptors correlates with the formation of a continuous internal water pathway

DNA-BSA interaction, cytotoxicity and molecular docking of mononuclear zinc complexes with reductively cleaved N2S2 Schiff base ligands

Predicting polymorphism in molecular crystals using orientational entropy