RESEARCH: CANCER
FOLDING PROJECT #15316 PROFILE

This project relates to graspetides, a type of molecule with unique ring structures that give them special powers like fighting infections. Scientists will use computer simulations to study how these rings form in different graspetide groups and see if there are specific patterns or rules.

Note: This TLDR is a simplication and may not be 100% accurate.

Graspetides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by the ATP-grasp ligase–catalyzed macrolactam or macrolactone linkages in their structure.

These macrocycles impart structural stability and diverse bioactivities, including antimicrobial, antiviral, and enzyme inhibitory effects.

Graspetides are classified into distinct groups based on sequence motifs, cyclization patterns, and biosynthetic machinery.

While each group exhibits characteristic ring topologies, the molecular basis by which core peptide sequence and folding pathways dictate the order of ring formation remains poorly understood. In this study, we will investigate model species from multiple graspetide groups using atomic-level molecular dynamics (MD) simulations.

By comparing folding trajectories across these representative systems, we aim to identify conserved and group-specific determinants of ring pattern formation, and to assess whether distinct biosynthetic groups exhibit preferences for particular ring closure orders.

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Graspetides

A class of ribosomally synthesized and post-translationally modified peptides (RiPPs).

Graspetides are a special type of molecule made up of amino acids. They are created by cells through a complex process and have unique ring structures that give them important abilities. These abilities include fighting infections, blocking viruses, and interfering with the activity of enzymes.

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Ribosomally synthesized and post-translationally modified peptides (RiPPs)

Ribosomally synthesized and post-translationally modified peptides (RiPPs)

RiPPs are a diverse group of peptides made by ribosomes (the cellular machinery that builds proteins). After being made, these peptides undergo further modifications to become functional molecules with various roles in biological processes.

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ATP-grasp ligase

An enzyme that uses ATP to form bonds between molecules.

ATP-grasp ligases are enzymes that play a crucial role in building complex molecules. They use the energy from ATP (the cell's energy currency) to join different parts together, creating new chemical structures.

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Macrolactam

A cyclic amide containing a large ring structure.

Macrolactam is a type of molecule with a large ring-like structure formed by linking an amine group to a carbonyl group. These structures are often found in natural products and have important roles in biological processes.

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Macrolactone

A cyclic ester containing a large ring structure.

Macrolactone is another type of molecule with a large ring-like structure formed by linking a hydroxyl group to a carbonyl group. These structures are also found in natural products and have diverse biological activities.

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Molecular dynamics (MD) simulations

Molecular dynamics (MD) simulations

MD simulations are computer-based methods used to study the movement and interactions of atoms and molecules. These simulations allow scientists to understand how molecules behave over time and predict their structures and properties.