Protein design

Transcription factors (TFs) are proteins essential for regulating genetic transcriptions by binding to transcription factor binding sites (TFBSs) in DNA sequences. Accurate predictions of TFBSs can contribute to the design and construction of metabolic regulatory systems based on TFs. Although various deep-learning algorithms have been developed for predicting TFBSs, the prediction performance needs to be improved. This paper proposes a bidirectional encoder representations from transformers (BERT)-based model, called BERT-TFBS, to predict TFBSs solely based on DNA sequences...

BACKGROUND: Dementia is a major public health challenge for aging societies worldwide. Neuroinflammation is thought to be a key factor in dementia development. The aim of this study was to comprehensively assess translocator protein (TSPO) expression by positron emission tomography (PET) imaging to reveal the characteristics of neuroinflammation in dementia. METHODS: We used a meta-analysis to retrieve literature on TSPO expression in dementia using PET imaging technology, including but not limited to the quality of the study design, sample size, and the type of TSPO ligand used in the study...

The microbial enzyme diaminopimelate epimerase (DapF), a vital enzyme in the lysine biosynthetic pathway, catalyzes the conversion of L, L-diaminopimelate (L, L-DAP) to D, L-diaminopimelate (D, L-DAP) using a catalytic cysteine dyad with one cysteine in thiol state and another in thiolate. Under oxidizing conditions, the catalytic cysteines of apo DapF form a disulfide bond that alters the structure and function of DapF. Given its potential as a target for antimicrobial resistance treatments, understanding DapF's functional dynamics is imperative...

Given continued failure of BACE1 inhibitor programs at symptomatic and prodromal stages of Alzheimer's disease (AD), clinical trials need to target the earlier preclinical stage. However, trial design is complex in this population with negative diagnosis of classical hippocampal amnesia on standard memory tests. Besides recent advances in brain imaging, electroencephalogram, and fluid-based biomarkers, new cognitive markers should be established for earlier diagnosis that can optimize recruitment to BACE1 inhibitor trials in presymptomatic AD...

INTRODUCTION: Immunotherapy has shown encouraging outcomes in breast cancer (BC) treatment in recent years. The programmed cell death ligand 1 (PD-L1) transmembrane protein is suggested to function as a co-inhibitory factor in the immune response, where it collaborates with programmed cell death protein 1 (PD-1) to stimulate apoptosis, suppress cytokine release from PD-1 positive cells, and limit the growth of PD-1 positive cells. Furthermore, in many malignancies, PD-L1 reduces the immune system's response to neoplastic cells...

BACKGROUND: Breast cancer (BC) cases in Makassar, Indonesia, are on the rise, with 2723 cases recorded in 2018. Tumor cells in the blood indicate metastasis, emphasizing the need for early diagnosis and monitoring. Pleiotrophin (PTN) is associated with various human malignancies, and recent studies suggest a correlation between PTN expression and advanced BC stages; therefore, PTN could serve as an independent predictor of metastasis. This study aimed to determine the correlation between serum PTN level, histopathological grading, and metastasis occurrence in BC patients in Makassar, Indonesia...

The hydrogen bonding interaction between an amide N-H and the amide N of the preceding residue is prevalent in proline-containing proteins and peptides. However, the N-H···N hydrogen bonding interaction is rare in non-prolyl natural peptides due to restricted dihedral angles. Herein, we stabilize this type of interaction in 8-aminoquinoline appended non-prolyl peptides through bifurcated N···H···N hydrogen bond. The 8-aminoquinoline-incorporated model peptides 2a-i were designed, synthesized, and the crystal structures of 2a-c and 2i were solved...

As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues its global spread, the exploration of novel therapeutic and diagnostic strategies is still needed. The virus enters host cells by binding the angiotensin-converting enzyme 2 (ACE2) receptor through the spike protein. Here, we develop an engineered, small, stable, and catalytically inactive version of ACE2, termed miniature ACE2 (mACE2), designed to bind the spike protein with high affinity. Employing a magnetic nanoparticle-based assay, we harnessed the strong binding affinity of mACE2 to develop a sensitive and specific platform for the detection or neutralization of SARS-CoV-2...

Antibiotics are designed to effectively treat bacterial infections while minimizing harm to the human body. They work by targeting specific components of bacteria or by disrupting essential processes such as cell wall synthesis, membrane function, protein production, and metabolic pathways. However, the misuse and overuse of antibiotics have led to the emergence of drug resistance in humans, animals, and agriculture, contributing to the global spread of this problem. Drug resistance can be either innate or acquired, with acquired resistance involving changes in the bacterial chromosomes or transferable elements...

BACKGROUND: Ferritin is an iron deposition protein and a commonly ordered clinical test. While high levels may signify iron deposition, the majority are due to metabolic, inflammatory, infectious, and malignant disorders. The association between ferritin elevations < 1000 μg/L and long-term mortality is well demonstrated. The association between extreme ferritin elevations, namely ferritin levels over 10,000 μg/L, and short-term mortality, as well as predictors of mortality, has not been defined...

This study aimed to develop synthetic Claudin18.2 (CLDN18.2) chimeric antigen receptor (CAR)-T (CAR-T) cells as a treatment for advanced gastric cancer using lentiviral vector genetic engineering technology that targets the CLDN18.2 antigen and simultaneously overcomes the immunosuppressive environment caused by programmed cell death protein 1 (PD-1). Synthetic CAR T cells are a promising approach in cancer immunotherapy but face many challenges in solid tumors. One of the major problems is immunosuppression caused by PD-1...

The development of oligomeric glucagon-like peptide-1 (GLP-1) and GLP-1-containing coagonists holds promise for enhancing the therapeutic potential of the GLP-1-based drugs for treating type 2 diabetes mellitus (T2DM). Here, we report a facile, efficient, and customizable strategy based on genetically encoded SpyCatcher-SpyTag chemistry and an inducible, cleavable self-aggregating tag (icSAT) scheme. icSAT-tagged SpyTag-fused GLP-1 and the dimeric or trimeric SpyCatcher scaffold were designed for dimeric or trimeric GLP-1, while icSAT-tagged SpyCatcher-fused GLP-1 and the icSAT-tagged SpyTag-fused GIP were designed for dual GLP-1/GIP (glucose-dependent insulinotropic polypeptide) receptor agonist...

Constructing antifouling surfaces is a crucial technique for optimizing the performance of devices such as water treatment membranes and medical devices in practical environments. These surfaces are achieved by modification with hydrophilic polymers. Notably, zwitterionic (ZI) polymers have attracted considerable interest because of their ability to form a robust hydration layer and inhibit the adsorption of foulants. However, the importance of the molecular weight and density of the ZI polymer on the antifouling property is partially understood, and the surface design still retains an empirical flavor...

Peripheral surgery-induced neural inflammation is a key pathogenic mechanism of postoperative cognitive dysfunction (POCD). However, the mechanism underlying neuroinflammation and associated neural injury remains elusive. Surgery itself can lead to gut damage, and the occurrence of POCD is accompanied by high levels of TNF-α in the serum and blood‒brain barrier (BBB) damage. Reductions in stress, inflammation and protein loss have been emphasized as strategies for enhanced recovery after surgery (ERAS)...

UNLABELLED: Smallpox is a highly contagious human disease caused by the variola virus. Although the disease was eliminated in 1979 due to its highly contagious nature and historical pathogenicity, with a mortality rate of up to 30%, this virus is an important candidate for biological weapons. Currently, vaccines are the critical measures to prevent this virus infection and spread. In this study, we designed a peptide vaccine using immunoinformatics tools, which have the potential to activate human immunity against variola virus infection efficiently...

UNLABELLED: A US collection of invasive Escherichia coli serotype O1 bloodstream infection (BSI) isolates were assessed for genotypic and phenotypic diversity as the basis for designing a broadly protective O-antigen vaccine. Eighty percent of the BSI isolate serotype O1 strains were genotypically ST95 O1:K1:H7. The carbohydrate repeat unit structure of the O1a subtype was conserved in the three strains tested representing core genome multi-locus sequence types (MLST) sequence types ST95, ST38, and ST59...

This paper presents interdisciplinary research exploring the development of inclusive multisensory science books, communicating immunology data for blind, low-vision and diverse needs audiences. The research adopted an inductive theory-building approach, practice-based art methods and music and design methods, leveraging the lived experience of a legally blind artist. The research also involved designers and scientists in a cocreation process, producing books that incorporate tactile artworks, Braille-inspired protein models, image sonification and interaction...

UNLABELLED: Depression is a common psychiatric comorbidity among patients with epilepsy (PWE), affecting more than a third of PWE. Management of depression may improve quality of life of epileptic patients. Unfortunately, available antidepressants worsen epilepsy by reducing the seizure threshold. This situation demands search of new safer target for combined directorate of epilepsy and comorbid depression. A system biology approach may be useful to find novel pathways/markers for the cure of both epilepsy and associated depression via analyzing available genomic and proteomic information...

Pancreatic adenocarcinoma (PDAC) is one of the most deadly cancers, characterized by extremely limited therapeutic options and a poor prognosis, as it is often diagnosed during late disease stages. Innovative and selective treatments are urgently needed, since current therapies have limited efficacy and significant side effects. Through proteomics analysis of extracellular vesicles, we discovered an imbalanced distribution of amino acids secreted by PDAC tumor cells. Our findings revealed that PDAC cells preferentially excrete proteins with certain preferential amino acids, including isoleucine and histidine, via extracellular vesicles...

OBJECTIVE: At present, there remains controversy regarding the clinical efficacy of Corbrin (Bailing) capsules in the treatment of renal insufficiency (RI). A meta-analytic approach was adopted in this study to assess the clinical efficacy of Corbrin capsules for treating RI, aiming to provide a certain level of clinical evidence to guide the selection of RI therapeutic interventions. METHODS: The meta-analysis was conducted on databases containing PubMed, CNKI, Weipu Database, Cochrane Library and Wanfang until January 2023...