相关论文: Amino Acids and Their Biological Derivatives Modul…

Proteins are macromolecules which hardly act alone; they need to make interactions with some other proteins to do so. Numerous factors are there which can regulate the interactions between proteins [4]. Here in this present study we aim to…

Despite being used for decades as stabilizers, amino acids (AAs) remain mysterious components of many medical and biological formulations. Hypotheses on their role vary ranging from hydrotropic to protein-specific effects (stabilization…

Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays require computational methods for efficient PPI prediction.…

Liquid liquid phase separation (LLPS) of proteins is an intracellular process that is widely used by cells for many purposes. In living cells (in vivo), LLPS occurs in complex and crowded environments. Amino acids (AAs) are vital components…

How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…

The protein-protein interactions (PPIs) of 14-3-3 proteins are a model system for studying PPI stabilization. The complex natural product Fusicoccin A stabilizes many 14-3-3 PPIs but is not amenable for use in SAR studies, motivating the…

Proteins congregate into complexes to perform fundamental cellular functions. Phenotypic outcomes, in health and disease, are often mechanistically driven by the remodeling of protein complexes by protein coding mutations or cellular…

Aligning protein interaction networks (PPI) of two or more organisms consists of finding a mapping of the nodes (proteins) of the networks that captures important structural and functional associations (similarity). It is a well studied but…

The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…

In this paper, we quantify weak protein protein interactions in solution using Cross-Interaction Chromatography (CIC) and Surface Plasmon Resonance (SPR) and demonstrate that they can be modulated by the addition of free amino acids. With…

We model the evolution of eukaryotic protein-protein interaction (PPI) networks. In our model, PPI networks evolve by two known biological mechanisms: (1) Gene duplication, which is followed by rapid diversification of duplicate…

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…

We demonstrate that Protein-Protein Interaction (PPI) networks in several eucaryotic organisms contain significantly more self-interacting proteins than expected if such homodimers randomly appeared in the course of the evolution. We also…

Protein-protein interactions (PPIs) are of fundamental importance for the human body, and the knowledge of their existence can facilitate very important tasks like drug target developing and therapy design. The high-throughput experiments…

Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the…

We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…

The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been…

Many protein-protein interaction (PPI) networks take place in the fluid yet structured plasma membrane. Lipid domains, sometimes termed rafts, have been implicated in the functioning of various membrane-bound signaling processes. Here, we…

Protein phase transitions govern numerous diseases, including neurodegenerative disorders such as Parkinson's and Alzheimer's. In Parkinson's disease, distinct species of the protein alpha-synuclein undergo phase transitions from highly…

Protein-protein interactions (PPIs) are fundamental to cellular function and disease mechanisms. Current learning-based PPI predictors focus on learning powerful protein representations but neglect designing specialized classification…