Current Proteomics - Volume 18, Issue 5, 2021

The biomedical network is becoming a fundamental tool to represent sophisticated biosystems, while Random Walk (RW) models on it are becoming a sharp sword to address such challenging issues as gene function annotation, drug target identification, and disease biomarker recognition. Recently, numerous random walk models have been proposed and applied to biomedical networks. Due to good performan Read More

With the rapid development of high-throughput techniques, mass spectrometry has been widely used for large-scale protein analysis. To search for the existing proteins, discover biomarkers, and diagnose and prognose diseases, machine learning methods are applied in mass spectrometry data analysis. This paper reviews the applications of five kinds of machine learning methods to mass spectrometry data analysis from an algo Read More

The fast growth of protein sequencing and protein structure data has promoted the development of the protein structural class prediction. Several prediction methods have been proposed to study protein folding rate, DNA binding sites, as well as reducing the search of conformational space and realizing the prediction of tertiary structure. This paper introduces the current approaches of protein structural class prediction and Read More

Background: Identification of protein subcellular location is an important problem because the subcellular location is highly related to protein function. It is fundamental to determine the locations with biology experiments. However, these experiments are of high costs and time-consuming. The alternative way to address such a problem is to design effective computational methods. Objective: To date, several computational Read More

Background: DNA and protein are important components of living organisms. DNA binding protein is a helicase, which is a protein specifically responsible for binding to DNA single- stranded regions. It is a necessary component for DNA replication, recombination and repair, and plays a key role in the function of various biomolecules. Although there are already some classification prediction methods for this protein, the use Read More

Background: Nitration is an important Post-Translational Modification (PTM) occurring on the tyrosine residues of proteins. The occurrence of protein tyrosine nitration under disease conditions is inevitable and represents a shift from the signal transducing physiological actions of - NO to oxidative and potentially pathogenic pathways. Abnormal protein nitration modification can lead to serious human diseases, including ne Read More

Background: Streptococcus pneumoniaeis a leading cause of human respiratory tract infection. Despite the lack of activities of antioxidative enzymes, including cytochromes, hemoproteins, and peroxidases/catalases, traits conferring the aerotolerant-anaerobic growth of this bacterium are conserved, with the high efficacy of antioxidative actions, in an oxygen-rich environment. Objective: Through proteome analysis, this Read More

Background: Angiotensin-converting enzyme 2 (ACE2) is primarily involved in the maturation of angiotensin. It also represents the main receptor for the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) that caused a serious epidemic COVID-19. Available evidence indicates that at the cell membrane, ACE2 can form heteromeric complexes with other membrane proteins, including the amino acid transporter B0 A Read More

Background: Talin-1 is involved in the invasion and synapse development of the Human Immunodeficiency Virus (HIV). We found that talin-1 was cleaved into a 38 KDa fragment (talin-C) in the Peripheral Blood Mononuclear Cells (PBMCs) of HIV patients; however, the underlying mechanisms remain unknown. Objective: This study aimed to determine the relationship between talin-C and HIV infection and to identify the mecha Read More

Objective: Extensive retinal ischemia caused by proliferative diabetic retinopathy (PDR) may develop into neovascular glaucoma (NVG). We searched for the proteins which might participate in neovascularization through the analysis of aqueous humor (AH) proteomics in patients with NVG secondary to PDR to increasing the understanding of the possible mechanism of neovascularization. Methods: We collected 12 sam Read More

Background: Multiple myeloma (MM) is characterized by infiltration of bone marrow (BM) with clonal malignant plasma cells. The percentage of plasma cells in the BM is required for both diagnosis and prognosis. Objective: Intracellular protein screening and quantitative proteomic analysis were performed in myeloma plasma cells with an aim to compare expressions between low (0-9%), intermediate (10-20%) and high (>2 Read More

Aims: This study aimed to generate an improved method of protein extraction and purification from plant tissues containing very high amounts of phenolic compounds and other interfering biomolecules. Background: Protein extraction at proteomic studies on some plant species, including conifers, is challenging, and the yield and quality are unpredictable. Objective: Two popular protocols were combined with each other to Read More

Background: P-21 activating kinase 4 (PAK4) is implicated in the poor prognosis of many cancers, especially in the progression of Triple Negative Breast Cancer (TNBC). The present study was aimed at designing some potential drug candidates as PAK4 inhibitors for breast cancer therapy. Objective: This study aimed to finding novel inhibitors of PAK4 from natural compounds using computational approach. Methods: An e-p Read More