Peptaloid: A Comprehensive Database for Exploring Peptide Alkaloid DOI

Bibhu Prasad Behera,

Himanshu Naik, V. Badireenath Konkimalla

et al.

Journal of Chemical Information and Modeling, Journal Year: 2024, Volume and Issue: 64(22), P. 8387 - 8395

Published: Nov. 1, 2024

Peptaloid is the first dedicated database for peptide alkaloid molecules, a unique class of naturally derived compounds known their structural diversity and significant biological activities. Despite promising potential in drug discovery therapeutic development, research on alkaloids has been limited by absence comprehensive centralized resource. Fragmented data across various sources have posed challenge, underscoring need specialized to facilitate more efficient application. addresses this critical gap providing with over 161,000 entries, each detailed structural, physicochemical, pharmacological properties. By leveraging advanced computational tools machine learning, generates ADMET profiles, aiding identifying optimizing candidates. Designed versatility, supports applications beyond discovery, including ecology material sciences. (as alkaloids) will play crucial role innovation collaboration scientific disciplines. accessible at https://peptaloid.niser.ac.in.

Language: Английский

Bioactive peptides with antioxidant and ACE inhibitory properties in goat milk protein hydrolysates: Peptidomics and molecular docking study DOI
Wenhua Zhang,

Mohamed Aamer Abubaker,

Zekun Li

et al.

International Journal of Biological Macromolecules, Journal Year: 2025, Volume and Issue: 299, P. 140286 - 140286

Published: Jan. 23, 2025

Language: Английский

Citations

2
Exploring biotechnology for plastic recycling, degradation and upcycling for a sustainable future DOI
Xu Liu, Helen Park, Yannic S. Ackermann

et al.

Biotechnology Advances, Journal Year: 2025, Volume and Issue: unknown, P. 108544 - 108544

Published: Feb. 1, 2025

Language: Английский

Citations

2
Selective On-Site Detection and Quantification of Polystyrene Microplastics in Water Using Fluorescence-Tagged Peptides and Electrochemical Impedance Spectroscopy DOI Creative Commons
Abbas Motalebizadeh, Somayeh Fardindoost,

Mina Hoorfar

et al.

Journal of Hazardous Materials, Journal Year: 2024, Volume and Issue: 480, P. 136004 - 136004

Published: Sept. 30, 2024

Language: Английский

Citations

4
SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery for synthetic binding protein innovation DOI Creative Commons
Yanlin Li, Fengcheng Li,

Zixin Duan

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 53(D1), P. D595 - D603

Published: Oct. 16, 2024

Abstract Synthetic binding proteins (SBPs) represent a pivotal class of artificially engineered proteins, meticulously crafted to exhibit targeted properties and specific functions. Here, the SYNBIP database, comprehensive resource for SBPs, has been significantly updated. These enhancements include (i) featuring 3D structures 899 SBP–target complexes illustrate epitopes (ii) using SBPs in monomer or complex forms with target their sequence space expanded five times 12 025 by integrating structure-based protein generation framework property prediction tool, (iii) offering detailed information on 78 473 newly identified SBP-like scaffolds from RCSB Protein Data Bank, an additional 16 401 555 ones AlphaFold Structure Database, (iv) database is regularly updated, incorporating 153 new SBPs. Furthermore, structural models all have enhanced through application AlphaFold2, clinical statuses concurrently refreshed. Additionally, design methods employed each SBP are now prominently featured database. In sum, 2.0 designed provide researchers essential data, facilitating innovation research, diagnosis therapy. freely accessible at https://idrblab.org/synbip/.

Language: Английский

Citations

4
Rational design of peptides to overcome drug resistance by metabolic regulation DOI
Min Sun, Le He, Ran Chen

et al.

Drug Resistance Updates, Journal Year: 2025, Volume and Issue: unknown, P. 101208 - 101208

Published: Jan. 1, 2025

Language: Английский

Citations

0
Engineered material-binding peptide empowers biocatalysis in stainless steel flow reactors for phosphate recovery DOI Creative Commons
Yi Lu,

Florian Bourdeaux,

Binbin Nian

et al.

Chem, Journal Year: 2025, Volume and Issue: unknown, P. 102395 - 102395

Published: Jan. 1, 2025

Language: Английский

Citations

0
Peptide-Based Strategies for Detecting Microplastics in Aquatic Systems: A Review DOI Creative Commons
Abbas Motalebizadeh, Somayeh Fardindoost, Mina Hoorfar

et al.

Trends in Environmental Analytical Chemistry, Journal Year: 2025, Volume and Issue: 46, P. e00265 - e00265

Published: April 23, 2025

Language: Английский

Citations

0
Multistep Self-Assembly of the Gold-Binding Peptide AuBP1 DOI

Chris Johnson,

Taylor Bader, Kyle Boone

et al.

The Journal of Physical Chemistry B, Journal Year: 2025, Volume and Issue: unknown

Published: April 14, 2025

Solid-binding peptides have emerged as a distinct class of peptides, offering significant potential for biohybrid materials technologies due to their ability bind selectively specific target material and integrate different with bioactive molecules ease biochemical genetic conjugation proteins. Their vast applications span health nonmedical including biocatalysis, biosensing, agriculture, well sustainable engineering platforms. As these continue expand, it is critical understand the optimal performance conditions develop fundamental understanding factors controlling binding surface organization that lead self-assembled properties at interfaces. In this work, self-assembly one such peptide, AuBP1 (WAGAKRLVLRRE), was revisited through atomic force microscopy (AFM) studies conducted on Au(111) gain further insight into assembly process. Peptide film coverage monitored function adsorption time (seconds hours) concentration peptide (1 fM 10 μM). Our analysis reveals initial isolated followed by large-scale network clustered slower filling remaining sites uniform film, finally reorganization film. observations suggest multistep process involving both peptide-peptide peptide-surface interactions cooperatively influence transitions. We compared noncooperative semicooperative models, which provided additional growth phase Understanding real-time kinetics boundary robust films could extend utilization material-binding future technologies.

Language: Английский

Citations

0
Development of a Finishing Process for Imbuing Flame Retardancy into Materials Using Biohybrid Anchor Peptides DOI Creative Commons
Rahel Heesemann,

M.M. Sanders,

Roshan Paul

et al.

Applied Sciences, Journal Year: 2024, Volume and Issue: 14(14), P. 6107 - 6107

Published: July 12, 2024

Flame retardants are commonly used to reduce fire risk in various products and environments, including textiles. While many of these additives contain harmful substances, efforts underway their usage. Current research aims minimize flame-retardant quantities enhance durability against external factors. This involves utilizing anchor peptides or material-binding (MBPs), which versatile molecules that bind strongly surfaces like MBPs can be equipped with functional molecules, e.g., additives, by chemical enzymatic bioconjugation. In this research, biohybrid flame an adapted finishing process developed. Specifically, biobased adhesion promoters, the so-called MBPs, finish textiles additives. To date, there is no for treating so a laboratory-scale based on foulard was Necessary parameters, such as take-off speed contact pressure squeezing rollers, determined experimentally. order develop process, trials designed carried out. Part testing comparison different (e.g., glass woven fabrics aramid fabrics) under conditions ratios retardants). The finished then analysed validated regarding flammability amount adhered retardants.

Language: Английский

Citations

1
The spatial separation of basic amino acids is similar in RHAMM and hyaluronan binding peptide P15‐1 despite different sequences and conformations DOI Creative Commons
Mehmet Emre Erkanli, Ted Keunsil Kang,

Thorsten Kirsch

et al.

Proteoglycan Research, Journal Year: 2024, Volume and Issue: 2(3)

Published: July 1, 2024

Abstract Peptides that increase pro‐reparative responses to injury and disease by modulating the functional organization of hyaluronan (HA) with its cell surface binding proteins (e.g., soluble receptor for hyaluronan‐mediated motility [RHAMM] integral membrane CD44) have potential therapeutic value. The RHAMM HA is an attractive target, since normally absent or expressed at low levels in homeostatic conditions, but expression significantly elevated extracellular matrix during tissue stress, response‐to‐injury, cancers inflammation‐based diseases. HA‐binding site contains two closely spaced sequences clustered basic amino acids, alpha‐helical conformation. In present communication, we test whether conformation required effective peptide HA, competitive disruption HA–RHAMM interaction. RHAMM‐competitive P15‐1, identified using unbiased approach phage display, was examined circular dichroism spectroscopy conformation‐predictive AI‐based AlphaFold2 algorithm. Unlike RHAMM, P15‐1 found adopt irregular conformations solution rather than alpha helices. Instead, our structural analysis suggests primary determinant peptide‐HA associated a specific clustering spacing pattern allowing favorable electrostatic interaction carboxylate groups on HA.

Language: Английский

Citations

0