Aug 2026· Science Technology and Innovation· 0 citations· 27 references
TL;DR
Results highlight tryptophan as a key determinant of ligand recognition and stabilization across both enzymatic and receptor-mediated systems.
Abstract
Tryptophan residues play a critical role in protein-ligand recognition owing to their unique aromatic character, high polarizability, and ability to participate in diverse noncovalent interactions, including π-π stacking, cation-π interactions, hydrogen bonding, and hydrophobic contacts. In this study, a two-stage approach was employed to elucidate the functional significance of tryptophan residues within ligand-binding sites across diverse protein systems. First, a large-scale statistical analysis was performed using a curated dataset of protein-ligand complexes extracted from the BioLiP database. The dataset was analysed with respect to enzymatic classification and Gene Ontology enrichment, revealing a pronounced enrichment of tryptophan residues in the binding sites of hydrolases, oxidoreductases, and transferases, as well as strong associations with metal-ion binding, redox-related functions, and membrane or cytoplasmic localization. Within the G protein-coupled receptor (GPCR) superfamily, rhodopsin-like class A receptors were identified as the most prominently represented group featuring tryptophan-mediated ligand interactions. In the second stage, molecular dynamics simulations were conducted for selected serotonin 5-HT₂ receptor subtypes (5-HT₂A, 5-HT₂B, and 5-HT₂C) to provide atomistic insights into the role of the conserved W6.48 residue. The simulations reveal a stable spatial relationship between the ligand and W6.48, characterized by distances consistent with aromatic anchoring, supporting its role in maintaining ligand orientation and binding pocket organization. Collectively, these results highlight tryptophan as a key determinant of ligand recognition and stabilization across both enzymatic and receptor-mediated systems.
This study illustrates how subtle residue-localized conformational bias can affect the overall protein conformational dynamics influencing protein-protein interactions that are important for cellular functions and related to diseases.
Abir Ben Bouzayene, M. Sai, Alexis Jouin et al.· Angewandte Chemie· 0 citations
Many membrane proteins contain intrinsically disordered regions (IDRs) that play key biological roles by providing structural plasticity, harboring sites for post-translational modifications, and mediating protein clustering and phase separation. Residue-level molecular models parameterized against experimental data have provided insights into how IDR sequence controls conformational properties and phase behavior in soluble proteins. Here, we extend this modeling framework to membrane-associated IDRs. We adapt a coarse-grained lipid model, iSoLFv2, for four phospholipids and combine it with CALVADOS, a residue-level model for IDRs and multi-domain proteins. Protein–lipid cross-interaction parameters are calibrated to reproduce predicted insertion and orientation of transmembrane proteins with diverse architectures. We validate the resulting model against Wimley–White free energies of transfer of hydrophobic peptides and against an experimentally refined conformational ensemble of a flexible membrane receptor. Finally, we show the applicability of the model to a membrane-associated assembly of signaling proteins. The model provides a computationally efficient framework for studying conformational ensembles and assembly of proteins at bilayer–water interfaces.
Whether binding specificity and partner selection in protein-protein interactions (PPIs) can be reliably inferred from static structures or require more dynamic, pathway-resolved energetic analyses remains an open question. To explore this, we focus on the ornithine decarboxylase (ODC)-antizyme isoform 1 (Az1)-antizyme inhibitor (AzIN) system, a well-characterized competitive PPI network that plays a critical role in regulating polyamine homeostasis. By combining extensive all-atom molecular dynamics simulations with biochemical experiments and the development of a new tool, we uncover key dynamic features of the static and recognition pathway interaction. Based on these, we designed novel antizyme isoforms (NAZs). Our analysis, using residue-resolved energetic landscapes, reveals critical determinants of binding specificity and partner selection that static structures alone cannot capture. These insights guide the engineering of NAZs that either directly engage ODC or modulate Az1 availability. This work provides a new perspective, demonstrating that dynamic energetic landscapes, rather than static structures, are key to understanding and modulating competitive protein recognition. Additionally, our DyResEL tool enables broader, more detailed analyses of energetic contributions, offering a versatile approach for exploring PPIs in various biological contexts.
Baolin Guo, Qian Xue, Fan Yang et al.· Journal of Chemical Informat...· 0 citations
Zn-metalloproteins play vital roles in numerous metabolic processes, making them high-value targets for structure-based drug design. To advance these efforts, it is useful to unravel the individual components of the intermolecular interaction energies (DE) that stabilize the Znbinding cavity, both in the absence and presence of bound protein ligands. Here, we utilize quantum chemistry (QC) to decompose DE into distinct physical contributions. The relative magnitudes of these components vary significantly depending on the coordination number (four to six) and the chemical nature ('hard'vs.'soft') of the Zn-coordinating ligands. These high-level QC analyses serve to calibrate and validate polarizable molecular mechanics potentials, effectively extending the accurate description of electronic effects beyond the immediate Zn-binding cavity to enlarged recognition sites and, ultimately, entire protein systems over long molecular dynamics (MD) simulation timescales. Following a concise overview of our QC methodology, we present validation studies on complexes containing up to 300 atoms and discuss the prospects of applying this framework to large-scale simulations of Zn-metalloprotein-ligand complexes. Finally, the structural and energetic role of discrete, highly polarizable water molecules is highlighted.
Kinases are major drug targets especially in cancer therapy. However, the high degree of conservation of their active sites hinders the development of selective inhibitors, motivating a deeper understanding of kinase conformational ensembles and allosteric communication pathways. Here, we use dynamical network analysis to identify key residues involved in a dynamic allostery between the N- and C-lobes that connects the major functional units of the MAP kinase p38α. By combining NMR spectroscopy, activity assays, and in silico analysis of wildtype protein and mutants in the presence or absence of an active-site inhibitor, we experimentally validate the obtained architecture with respect to global protein motion and long-range allosteric modulation. Notably, the identified network highlights communication pathways across several functional sites, prominently involving the allosteric site, the activation loop, and even the lipid-binding domain with its embedded cryptic pocket in the C-lobe. These findings provide mechanistic insight into p38α allostery and suggest viable opportunities for the rational design of allosteric modulators of MAP kinases.
Suchandra Roy Acharyya, J. Weisner, Rafael C. Bernardi et al.· Nature Communications· 0 citations
The folded structure of a protein is understood to be an optimal energy state. However, previous studies have shown that certain amino acid residue positions that play a critical role in protein function are often in a suboptimal energy state or “frustrated”. Here, we leverage over 1200 three-dimensional structures of G protein-coupled receptors (GPCRs) to demonstrate that residues at the interface between GPCR and its ligand or G protein contain a higher density of frustrated residues compared to other structural regions in the receptor. Likewise, the Gα subunit of the trimeric G proteins shows multiple clusters of highly frustrated residues on its surface that overlap with their effector protein (Gbγ, RGS, Adenylyl cyclase, Ric8) binding interfaces. Our study highlights the use of protein frustration as one of the multiple structural properties to identify protein–protein interfaces and for prospective prediction of potential ligand binding sites.
Wenyuan Wei, Roland Del Mundo, Tianyi Yang et al.· Journal of Chemical Informat...· 0 citations