Protein design: From the aspect of water solubility and stability

R Qing, S Hao, E Smorodina, D Jin, A Zalevsky… - Chemical …, 2022 - ACS Publications
Water solubility and structural stability are key merits for proteins defined by the primary
sequence and 3D-conformation. Their manipulation represents important aspects of the …

Nonspecific binding—fundamental concepts and consequences for biosensing applications

A Frutiger, A Tanno, S Hwu, RF Tiefenauer… - Chemical …, 2021 - ACS Publications
Nature achieves differentiation of specific and nonspecific binding in molecular interactions
through precise control of biomolecules in space and time. Artificial systems such as …

Inference of macromolecular assemblies from crystalline state

E Krissinel, K Henrick - Journal of molecular biology, 2007 - Elsevier
We discuss basic physical–chemical principles underlying the formation of stable
macromolecular complexes, which in many cases are likely to be the biological units …

The atomic structure of protein-protein recognition sites

LL Conte, C Chothia, J Janin - Journal of molecular biology, 1999 - Elsevier
The non-covalent assembly of proteins that fold separately is central to many biological
processes, and differs from the permanent macromolecular assembly of protein subunits in …

[HTML][HTML] Conceptual evolution of cell signaling

A Nair, P Chauhan, B Saha, KF Kubatzky - International journal of …, 2019 - mdpi.com
During the last 100 years, cell signaling has evolved into a common mechanism for most
physiological processes across systems. Although the majority of cell signaling principles …

Water mediation in protein folding and molecular recognition

Y Levy, JN Onuchic - Annu. Rev. Biophys. Biomol. Struct., 2006 - annualreviews.org
Water is essential for life in many ways, and without it biomolecules might no longer truly be
biomolecules. In particular, water is important to the structure, stability, dynamics, and …

De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity

SE Boyken, Z Chen, B Groves, RA Langan… - Science, 2016 - science.org
In nature, structural specificity in DNA and proteins is encoded differently: In DNA, specificity
arises from modular hydrogen bonds in the core of the double helix, whereas in proteins …

Hot spots—A review of the protein–protein interface determinant amino‐acid residues

IS Moreira, PA Fernandes… - … : Structure, Function, and …, 2007 - Wiley Online Library
Proteins tendency to bind to one another in a highly specific manner forming stable
complexes is fundamental to all biological processes. A better understanding of complex …

[HTML][HTML] Computational design of novel protein–protein interactions–An overview on methodological approaches and applications

A Marchand, AK Van Hall-Beauvais… - Current Opinion in …, 2022 - Elsevier
Protein–protein interactions (PPIs) govern numerous cellular functions in terms of signaling,
transport, defense and many others. Designing novel PPIs poses a fundamental challenge …

[HTML][HTML] Classification and prediction of protein–protein interaction interface using machine learning algorithm

S Das, S Chakrabarti - Scientific reports, 2021 - nature.com
Structural insight of the protein–protein interaction (PPI) interface can provide knowledge
about the kinetics, thermodynamics and molecular functions of the complex while …