MOHD ATHAR^1,*, ANU MANHAS², NISARG RANA², AHMAD IRFAN³

BIOCELL, Vol.48, No.6, pp. 935-944, 2024, DOI:10.32604/biocell.2024.049891

Abstract Computational methods have significantly transformed biomedical research, offering a comprehensive exploration of disease mechanisms and molecular protein functions. This article reviews a spectrum of computational tools and network analysis databases that play a crucial role in identifying potential interactions and signaling networks contributing to the onset of disease states. The utilization of protein/gene interaction and genetic variation databases, coupled with pathway analysis can facilitate the identification of potential drug targets. By bridging the gap between molecular-level information and disease understanding, this review contributes insights into the impactful utilization of computational methods, paving the way for More >

RYAN STARK^*

BIOCELL, Vol.47, No.6, pp. 1191-1198, 2023, DOI:10.32604/biocell.2023.027838

Abstract Protein-mediated interactions are the fundamental mechanism through which cells regulate health and disease. These interactions require physical contact between proteins and their respective targets of interest. These targets include not only other proteins but also nucleic acids and other important molecules as well. These proteins are often involved in multibody complexes that work dynamically to regulate cellular health and function. Various techniques have been adapted to study these important interactions, such as affinity-based assays, mass spectrometry, and fluorescent detection. The application of these techniques has led to a greater understanding of how protein interactions are More >

DIEGO MASONE^1,2,*

BIOCELL, Vol.47, No.1, pp. 1-14, 2023, DOI:10.32604/biocell.2023.024146

Abstract The inflexible concept of membrane curvature as an independent property of lipid structures is today obsolete. Lipid bilayers behave as many-body entities with emergent properties that depend on their interactions with the environment. In particular, proteins exert crucial actions on lipid molecules that ultimately condition the collective properties of the membranes. In this review, the potential of enhanced molecular dynamics to address cell-biology problems is discussed. The cases of membrane deformation, membrane fusion, and the fusion pore are analyzed from the perspective of the dimensionality reduction by collective variables. Coupled lipid-protein interactions as fundamental determinants More >

Yao SUN, Yao LI, Xin SUN, Qiong WU, Lei WANG^*

BIOCELL, Vol.44, No.1, pp. 117-126, 2020, DOI:10.32604/biocell.2020.08242

Abstract Phosphorylation is a common type of post-translational modification (PTM). It plays a vital role in many cellular processes. The reversible phosphorylation and dephosphorylation affect protein structures and proteinprotein interactions. Previously, we obtained five proteins that interact with ethylene-responsive factor (ERF) from the cDNA library of Populus simonii x Populus nigra. To further investigate the effect of dephosphorylation of PsnERF on its protein binding ability, we generated different phosphorylation states of PsnERF and demonstrated their protein binding capacity by the yeast two-hybrid assay (Y2H). The secondary structures and 3D structures of PsnERF, ERFm, TrunERF, and psnerf^197/198/202a were predicted More >

Chenyi An¹, Wei Chen^2,*

Molecular & Cellular Biomechanics, Vol.16, Suppl.2, pp. 109-110, 2019, DOI:10.32604/mcb.2019.07634

Abstract Biomembrane force probe (BFP) is a single-molecule biomechanical technique that has been widely used to characterize protein dynamics (e.g., protein-protein interactions and protein conformational changes), especially suitable for measuring force-regulated receptor-ligand binding kinetics in situ[1-4]. Integrated with various force spectroscopies, such as lifetime assay, it has become a powerful platform to systematically characterize many force-regulated receptor-ligand dissociation of great biological significance, which cannot be done with traditional solution based assays (e.g., surface plasma resonance) [5].
Even though the BFP has been quite successful in characterizing binding kinetics of weak and transient molecular interactions, it is… More >