Satisfiability, sequence niches, and molecular codes in cellular signaling
Christopher R. Myers
Abstract
Biological information processing as implemented by regulatory and signaling networks in living cells requires sufficient specificity of molecular interaction to distinguish signals from one another, but much of regulation and signaling involves somewhat fuzzy and promiscuous recognition of molecular sequences and structures, which can leave systems vulnerable to crosstalk. This paper examines a simple computational model of protein-protein interactions which reveals both a sharp onset of crosstalk and a fragmentation of the neutral network of viable solutions as more proteins compete for regions of sequence space, revealing intrinsic limits to reliable signaling in the face of promiscuity. These results suggest connections to both phase transitions in constraint satisfaction problems and coding theory bounds on the size of communication codes.
Create a lesson
Related papers
SaltyMeta: a curated benchmark and protein language model-informed web tool for salty peptide prediction
Wanchao Chen, Wen Li, Yanan He et al.
Exploring Optimal Parameters for Ligand-Based Virtual Screening in Early Drug Discovery
Temitope Sobodu, Victor Chibuzor Johnson, Ryan Kern et al.
Synthesizing State-of-the-Art Structure Predictions from Soup of Co-folding Models
Hyosoon Jang, Taewon Kim, Sungsoo Ahn
Sequence-Informed Geometric Evaluation of RNA 3D Structures
Andrea Zerio, Yighua Yao, Alessandro Micheli et al.
Multi-ligand simultaneous docking of Carica papaya leaf phytochemicals, Carpaine and Rutin, reveals multi-mechanism inhibition of cancer proteins BCL-2 and WWP1
Merla Sudha, Asmita Saha, Belaguppa Manjunath Ashwin Desai et al.
Predicting directional flexibility in proteins
Vsevolod Viliuga, Leif Seute, Matteo Tadiello et al.