scholarly journals Controllability of protein-protein interaction phosphorylation-based networks: Participation of the hub 14-3-3 protein family

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Marina Uhart ◽  
Gabriel Flores ◽  
Diego M. Bustos
Keyword(s):  
Protein Interaction ◽  
Protein Family ◽  
Protein Protein Interaction

scholarly journals In silico analyses of human collagen protein function prediction

2018 ◽  
Vol 24 ◽  
pp. 55-65
Author(s):  
MS Ahmed ◽  
M Kamruzzaman ◽  
MM Rana ◽  
Z Akond ◽  
MNH Mollah
Keyword(s):  
Protein Interaction ◽  
Human Body ◽  
Protein Function ◽  
Protein Sequences ◽  
Protein Family ◽  
Functional Domain ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Collagen Protein ◽  
Human Collagen

Collagen is the extracellular matrix protein in the several connective tissues in the human body. It is an important component for mediating cell-cell interactions and pathological conditions in human body. In this study we perform the analysis of physiochemical properties and investigate the functional characteristics of human collagen proteins. Also investigate the functional protein groups by the statistical analysis. The collagen protein family consisting 28 members in human which are involving in the complex structure of protein. The protein function, protein sequence properties, domain composition, phylogenetic and protein-protein interaction (PPI) networks analysis of human collagen alpha-1 protein sequences are implemented by the online bioinformatics tools which are currently available. Based on the PCA analysis amino acid composition, features of collagen protein sequences are divided into two supreme influential functional groups such as collagen 12, 14, 20 formed one group and the rest of others formed another group. The protein-protein interaction network study using STRING showed that top interacting score of functional group proteins 0.952, 0.939 and 0.929. The most common functional domain of collagen proteins are VWC, C4, LamG, VWA, KU, C1Q, TSPN and FN3. Physicochemical, functional and phylogenetic classification can give extensive information of protein’s structure and function. The depiction of alpha-1 chains of collagen protein family in human collagen 12, 14 and 20 as a prospective protein cluster. These three proteins are possess, low glycine and proline, very high aliphatic index and a close evolutionary relation in the human skin.J. bio-sci. 24: 55-65, 2016

scholarly journals Fe65L2: a new member of the Fe65 protein family interacting with the intracellular domain of the Alzheimer's β-amyloid precursor protein

1998 ◽  
Vol 330 (1) ◽  
pp. 513-519 ◽  
Author(s):  
Angela DUILIO ◽  
Raffaella FARAONIO ◽  
Giuseppina MINOPOLI ◽  
Nicola ZAMBRANO ◽  
Tommaso RUSSO
Keyword(s):  
Amyloid Precursor Protein ◽  
Protein Interaction ◽  
Protein Family ◽  
Precursor Protein ◽  
Protein Isoforms ◽  
Rat Tissues ◽  
Interaction Domain ◽  
Intracellular Domain ◽  
Protein Protein Interaction ◽  
Β Amyloid

We previously demonstrated that Fe65 protein is one of the ligands of the cytoplasmic domain of β-amyloid precursor protein (APP). Another ligand of this molecule was recently identified; it is similar to Fe65, so it was named Fe65-like (Fe65L1). Herein we describe the cloning of another Fe65-like cDNA (Fe65L2), similar to Fe65 and to Fe65L1, which encodes a protein of approx. 50 kDa. Its cognate mRNA is expressed in various rat tissues, particularly in brain and testis. The three members of the Fe65 protein family share several structural and functional characteristics. The primary structures of the three proteins can be aligned in three regions corresponding to the protein-protein interaction domains of Fe65 [the protein-protein interaction domain containing two conserved tryptophan residues and the two phosphotyrosine interaction domain/phosphotyrosine binding (PID/PTB) domains], whereas the remaining sequences are poorly related. Like Fe65, Fe65L1 and Fe65L2 genes encode two different protein isoforms, derived from the alternative splicing of a very small exon of only six nucleotides, which results, within the N-terminal PID/PTB domain, in the presence or absence of two acidic/basic amino acids. Fe65L2 is able to interact, both in vitro and in vivo, with the intracellular domain of APP. Also, in the case of APP, another two closely related proteins exist, named β-amyloid precursor-like protein (APLP)1 and APLP2: by using the interaction trap procedure we observed that both Fe65 and Fe65L2 interact with APP, APLP1 or APLP2, although with different efficiencies.

An efficient transient assays system using Agrobacterium-mediated transformation of onion (Allium cepa) epidermal cells

2020 ◽  
Vol 80 (03) ◽  
Author(s):  
Yu-Miao Zhang ◽  
Jun Wang ◽  
Tao Wu
Keyword(s):  
Subcellular Localization ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Epidermal Cells ◽  
Cyclin Dependent Kinase ◽  
Protein Subcellular Localization ◽  
Protein Protein Interactions ◽  
Efficient System ◽  
Protein Protein Interaction ◽  
Onion Epidermal Cells

In this study, the Agrobacterium infection medium, infection duration, detergent, and cell density were optimized. The sorghum-based infection medium (SbIM), 10-20 min infection time, addition of 0.01% Silwet L-77, and Agrobacterium optical density at 600 nm (OD600), improved the competence of onion epidermal cells to support Agrobacterium infection at >90% efficiency. Cyclin-dependent kinase D-2 (CDKD-2) and cytochrome c-type biogenesis protein (CYCH), protein-protein interactions were localized. The optimized procedure is a quick and efficient system for examining protein subcellular localization and protein-protein interaction.

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