A review of visualisations of protein fold networks and their relationship with sequence and function

Abstract

Proteins form arguably the most significant link between genotype and phenotype. Understanding the relationship between protein sequence and structure, and applying this knowledge to predict function, is difficult. One way to investigate these relationships is by considering the space of protein folds and how one might move from fold to fold through similarity, or potential evolutionary relationships. The many individual characterisations of fold space presented in the literature can tell us a lot about how well the current Protein Data Bank represents protein fold space, how convergence and divergence may affect protein evolution, how proteins affect the whole of which they are part, and how proteins themselves function. A synthesis of these different approaches and viewpoints seems the most likely way to further our knowledge of protein structure evolution and thus, facilitate improved protein structure design and prediction.

Eco-Friendly Electrospun Nanofibers Based on Plant Proteins as Tunable and Sustainable Biomaterials

“…21 The polypeptide chain sequence and environmental conditions are, in turn, determining factors of inter-and intramolecular interactions (electrostatic forces, hydrophobic interactions, hydrogen bonds, and van der Waals forces). 21,22 The possibility of controlling these interactions may render protein-based nanofibers highly tunable materials with different physicochemical stability, mechanical resistance, and encapsulation/release properties. 23 In this work, inspired by the protein structure−function paradigm in biological systems, 22 we hypothesized that the nature of the protein building blocks affects the properties of the final electrospun biomaterial.…”

“…Protein structure dictates the interactions between the protein and its environment, and subsequently affects the properties of functional supramolecular assemblies . The polypeptide chain sequence and environmental conditions are, in turn, determining factors of inter- and intramolecular interactions (electrostatic forces, hydrophobic interactions, hydrogen bonds, and van der Waals forces). , The possibility of controlling these interactions may render protein-based nanofibers highly tunable materials with different physicochemical stability, mechanical resistance, and encapsulation/release properties …”

“…21,22 The possibility of controlling these interactions may render protein-based nanofibers highly tunable materials with different physicochemical stability, mechanical resistance, and encapsulation/release properties. 23 In this work, inspired by the protein structure−function paradigm in biological systems, 22 we hypothesized that the nature of the protein building blocks affects the properties of the final electrospun biomaterial. Our aim was to develop green and sustainable plant protein-based nanofibers and to investigate the relationship between the protein structural elements and the features of the fabricated materials by employing advanced microscopy techniques and biophysical and mechanical analysis.…”

Design and characterization of a protein fold switching network

“…It is also well-established, however, that some proteins have a propensity for two completely different, but well-ordered, conformations [4][5][6][7][8][9][10][11][12] . Better insight into the ambiguity of the protein folding code would lead to a better understanding of how proteins evolve, how mutation is related to disease, and how function can be annotated to sequences of unknown structure [13][14][15][16][17][18][19][20][21][22][23][24][25][26][27] . If the protein folding code were truly understood, it would be possible both to predict and design proteins that undergo profound switches in conformation.…”