Choopanian, P. | Search bioRxiv

bioRxiv2025

A Fast Approach for Structural and Evolutionary Analysis Based on Energetic Profile Protein Comparison

In structural bioinformatics, the efficiency of predicting protein similarity, function, and evolutionary relationships is crucial. Our approach proposed herein leverages protein energy profiles derived from a knowledge-based potential, deviating from traditional methods relying on structural alignment or atomic distances. This method assigns unique energy profiles to individual proteins, facilitating rapid comparative analysis for both structural similarities and evolutionary relationships across various hierarchical levels. Our study demonstrates that energy profiles contain substantial information about protein structure at class, fold, superfamily, and family levels. Notably, these profiles accurately distinguish proteins across species, illustrated by the classification of coronavirus spike glycoproteins and bacteriocin proteins. Introducing a separation measure based on energy profile similarity, our method shows significant correlation with a network-based approach, emphasizing the potential of energy profiles as efficient predictors for drug combinations with faster computational requirements. Our key insight is that the sequence-based energy profile strongly correlates with structure-derived energy, enabling rapid and efficient protein comparisons based solely on sequences.

bioinformatics↗

bioRxiv2021

Metabolomic Signature of Amino Acids in Plasma of Patients with non-segmental Vitiligo

IntroductionVitiligo is an asymptomatic disorder that results from the loss of pigments (melanin), causing skin or mucosal depigmentation and impairs beauty. ObjectiveDue to the complexity of the pathogenesis of this disease and various theories including self-safety theory, oxidative stress, neurological theory and internal defects of melanocytes behind it, and finally, the vast role of amino acids in body metabolism and various activities of the body, amino acids targeted based metabolomics was set up to follow any fluctuation inside this disease. MethodologyThe study of amino acid profiles in plasma of people with non-segmental vitiligo using a liquid chromatography equipped with fluorescent detector was performed to find remarkable biomarkers for the diagnosis and evaluation of disease severity of patients with vitiligo. Twenty-two amino acids derivatized with o-phthalaldehyde (OPA) and fluorylmethyloxycarbonyl chloride (FMOC), were precisely determined. Next, the concentrations of these twenty-two amino acids and their corresponding molar ratios were calculated in 37 patients (including 18 females and 19 males) and corresponding 34 healthy individuals (18 females and 16 males). Using R programing, the data were completely analyzed between the two groups of patients and healthy to find suitable and reliable biomarkers. ResultsInterestingly, comparing the two groups, in the patient group, tyrosine, cysteine, the ratio of tyrosine to lysine and the ratio of cysteine to ornithine were increased while, arginine, lysine, ornithine and glycine ratios to cysteine have been decreased. These amino acids were selected for identification of patients with accuracy of detection of approximately 0.95 using the assessment of logistic regression. ConclusionThese results indicate a disruption of the production of melanin, increased immune activity and oxidative stress, which are also involved in the effects of vitiligo. Therefore, these amino acids can be used as biomarker for the evaluation of risk, prevention of complications in individuals at risk and monitoring of treatment process.

biochemistry↗