Geometry and symmetry presculpt the free-energy landscape of proteins
Trinh Xuan Hoang, Antonio Trovato, Flavio Seno, Jayanth R. Banavar, Amos Maritan
Abstract
We present a simple physical model which demonstrates that the native state folds of proteins can emerge on the basis of considerations of geometry and symmetry. We show that the inherent anisotropy of a chain molecule, the geometrical and energetic constraints placed by the hydrogen bonds and sterics, and hydrophobicity are sufficient to yield a free energy landscape with broad minima even for a homopolymer. These minima correspond to marginally compact structures comprising the menu of folds that proteins choose from to house their native-states in. Our results provide a general framework for understanding the common characteristics of globular proteins.
Create a lesson
Related papers
TopoLIA: Topology-Inspired Latent Interaction Attention for Drug Discovery
Xiang Liu, Yiming Ren, Mustafa Hajij et al.
La-Ribo: RNA Co-Design via Geometry-Latent Flow Matching
Runze Ma, Will Hua, Shuangjia Zheng
MD-LLM-2: A Transferable Language Model of Molecular Dynamics with Physical Conditioning and Explicit Path Probabilities
Mhd Hussein Murtada, Z. Faidon Brotzakis, Michele Vendruscolo
De novo design of monoclonal and bispecific antibodies with OFAntibody
Valhalla Team
A Shortcut to Structure in AlphaFold 3
Jonathan Feldman, Jeffrey Skolnick
Mathematical Invariant-Enabled Topological Neural Networks for Molecular and Materials Property Prediction
Yiming Ren, Xiang Liu, Mustafa Hajij et al.