4.6 Article

Expanding the Database of Signal-Anchor-Release Domain Endolysins Through Metagenomics

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biotechnology & Applied Microbiology

Cloning, Characterization, and Antibacterial Properties of Endolysin LysE Against Planktonic Cells and Biofilms of Aeromonas hydrophila

Pallavi Baliga et al.

Summary: Multidrug-resistant bacteria pose a major threat to public health worldwide, and bacteriophage endolysin LysE shows potential as an alternative antibiotic candidate. This study demonstrates that recombinant LysE protein, when combined with outer membrane permeabilizers, exhibits strong antibacterial activity against Gram-negative bacteria. The enzyme remains active at different pH levels and even at high temperatures. Furthermore, LysE shows antibiofilm capabilities when combined with EDTA and synergistic effects when combined with lower concentrations of colistin against Aeromonas hydrophila.

PROBIOTICS AND ANTIMICROBIAL PROTEINS (2023)

Editorial Material Biochemical Research Methods

Deep learning and protein structure modeling

Minkyung Baek et al.

NATURE METHODS (2022)

Article Biochemistry & Molecular Biology

Structural and biochemical characterization of the Clostridium perfringens-specific Zn2+-dependent amidase endolysin, Psa, catalytic domain

Hiroshi Sekiya et al.

Summary: Phage-derived endolysins like Psa have the potential to serve as alternative antimicrobial agents by specifically lysing bacteria. The X-ray structure of the Psa catalytic domain reveals a unique substrate-binding groove important for amidase activity, suggesting a potential catalytic reaction mechanism mediated by Zn2+ in the Amidase_2 family.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2021)

Article Microbiology

Bacteriophages that infect Gram-negative bacteria as source of signal-arrest-release motif lysins

Marco Tulio Pardini Gontijo et al.

Summary: The study focused on investigating the evolutionary markers of signal peptide-containing lysins to penetrate the outer membrane of Gram-negative bacteria, identifying potential candidates for the treatment of MDR bacteria.

RESEARCH IN MICROBIOLOGY (2021)

Article Biochemistry & Molecular Biology

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

David Sehnal et al.

Summary: Large biomolecular structures are being determined experimentally using established techniques such as crystallography and electron microscopy, with performance requirements for visualization and analysis tools increasing rapidly. The Mol* Viewer is an advanced online web-native 3D visualization tool that allows visualization of complex structures, and is the primary tool used by PDBe and RCSB PDB.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

Accurate prediction of protein structures and interactions using a three-track neural network

Minkyung Baek et al.

Summary: Through the three-track network, we achieved accuracies approaching those of DeepMind in CASP14, enabling rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and providing insights into the functions of proteins with currently unknown structure.

SCIENCE (2021)

Review Infectious Diseases

Current Status of Endolysin-Based Treatments against Gram-Negative Bacteria

Marco Tulio Pardini Gontijo et al.

Summary: The heterologous expression of endolysin can be optimized to reduce toxicity and improve antimicrobial activity, while polyhistidine tags aid in purification and could enhance permeation when used with outer membrane permeabilizers.

ANTIBIOTICS-BASEL (2021)

Article Biochemistry & Molecular Biology

IPC 2.0: prediction of isoelectric point and pKa dissociation constants

Lukasz Pawel Kozlowski

Summary: The isoelectric point is the pH at which a molecule is electrically neutral, dependent on factors like charged groups from amino acids in proteins and peptides, and is used in experiments like 2D gel electrophoresis and computational predictions. IPC 2.0, utilizing a mix of deep learning and support vector regression models, outperforms previous algorithms in predicting proteins and peptides' isoelectric points with higher accuracy. Additionally, the web server's prediction of pK(a) values using sequence data alone is better and faster than structure-based methods.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

Pfam: The protein families database in 2021

Jaina Mistry et al.

Summary: The Pfam database has recently added a large number of protein families and domains, made revisions for COVID-19 research, and introduced Pfam-B as a supplement. These updates and improvements can help researchers classify protein sequences more effectively and conduct related studies.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

FATCAT 2.0: towards a better understanding of the structural diversity of proteins

Zhanwen Li et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemistry & Molecular Biology

Phylogenetic origin and sequence features of MreB from the wall-less swimming bacteria Spiroplasma

Daichi Takahashi et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2020)

Review Pharmacology & Pharmacy

Advantages and Limitations of Bacteriophages for the Treatment of Bacterial Infections

Nicola Principi et al.

FRONTIERS IN PHARMACOLOGY (2019)

Article Biochemical Research Methods

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

Kazutaka Katoh et al.

BRIEFINGS IN BIOINFORMATICS (2019)

Article Biochemistry & Molecular Biology

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

Lukas Zimmermann et al.

JOURNAL OF MOLECULAR BIOLOGY (2018)

Article Microbiology

Thousands of Novel Endolysins Discovered in Uncultured Phage Genomes

Iris Fernandez-Ruiz et al.

FRONTIERS IN MICROBIOLOGY (2018)

Editorial Material Microbiology

The language of phages

Andrea Du Toit

NATURE REVIEWS MICROBIOLOGY (2017)

Article Multidisciplinary Sciences

Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans

Felipe H. Coutinho et al.

NATURE COMMUNICATIONS (2017)

Article Multidisciplinary Sciences

Uncovering Earth's virome

David Paez-Espino et al.

NATURE (2016)

Article Microbiology

Genomes of Abundant and Widespread Viruses from the Deep Ocean

Carolina Megumi Mizuno et al.

Article Biotechnology & Applied Microbiology

Purification of Antibacterial CHAPK Protein Using a Self-Cleaving Fusion Tag and Its Activity Against Methicillin-Resistant Staphylococcus aureus

Elahe Seyed Hosseini et al.

PROBIOTICS AND ANTIMICROBIAL PROTEINS (2016)

Article Biochemistry & Molecular Biology

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

Tauno Metsalu et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Pharmacology & Pharmacy

Bacteriophages and their Enzymes in Biofilm Control

Benjamin Chan et al.

CURRENT PHARMACEUTICAL DESIGN (2014)

Review Microbiology

Phage Lysis: Three Steps, Three Choices, One Outcome

Ryland Young

JOURNAL OF MICROBIOLOGY (2014)

Article Biotechnology & Applied Microbiology

Exogenous Lytic Adivity of SPN9CC Endolysin Against Gram-Negative Bacteria

Jeong-A Lim et al.

JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY (2014)

Article Virology

Molecular Aspects and Comparative Genomics of Bacteriophage Endolysins

Hugo Oliveira et al.

JOURNAL OF VIROLOGY (2013)

Article Genetics & Heredity

Expanding the Marine Virosphere Using Metagenomics

Carolina Megumi Mizuno et al.

PLOS GENETICS (2013)

Article Biochemical Research Methods

Rapid membrane protein topology prediction

Aron Hennerdal et al.

BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

The high-affinity peptidoglycan binding domain of Pseudomonas phage endolysin KZ144

Yves Briers et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2009)

Article Biochemical Research Methods

phyloXML: XML for evolutionary biology and comparative genomics

Mira V. Han et al.

BMC BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Regulation of a muralytic enzyme by dynamic membrane topology

Qingan Sun et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)

Article Microbiology

The pinholin of lambdoid phage 21: Control of lysis by membrane depolarization

Taehyun Park et al.

JOURNAL OF BACTERIOLOGY (2007)

Article Multidisciplinary Sciences

A signal-arrest-release sequence mediates export and control of the phage P1 endolysin

M Xu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Biochemistry & Molecular Biology

WebLogo: A sequence logo generator

GE Crooks et al.

GENOME RESEARCH (2004)

Article Biochemistry & Molecular Biology

A combined transmembrane topology and signal peptide prediction method

L Käll et al.

JOURNAL OF MOLECULAR BIOLOGY (2004)

Article Biochemistry & Molecular Biology

Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes

A Krogh et al.

JOURNAL OF MOLECULAR BIOLOGY (2001)