journal article·2023-09-12Open access

Endoproteolysis of Oligopeptide-Based Coacervates for Enzymatic Modeling

Zhicheng Jin, Chuxuan Ling, Wonjun Yim, Yu-Ci Chang, Tengyu He, Ke Li, Jiajing Zhou, Yong Cheng, Yi Li, Justin Yeung, Ruijia Wang, Pavla Fajtová, Lubna Amer, Hedi Mattoussi, Anthony J. O’Donoghue, Jesse V. Jokerst

ACS Nano· Volume 17· Issue 17

Abstract

Better insights into the fate of membraneless organelles could strengthen the understanding of the transition from prebiotic components to multicellular organisms. Compartmentalized enzyme reactions in a synthetic coacervate have been investigated, yet there remains a gap in understanding the enzyme interactions with coacervate as a substrate hub. Here, we study how the molecularly crowded nature of the coacervate affects the interactions of the embedded substrate with a protease. We design oligopeptide-based coacervates that comprise an anionic Asp-peptide (D 10 ) and a cationic Arg-peptide (R 5 R 5 ) with a proteolytic cleavage site. The coacervates dissolve in the presence of the main protease (M pro ) implicated in the coronavirus lifecycle. We capitalize on the condensed structure, introduce a self-quenching mechanism, and model the enzyme kinetics by using Cy5.5-labeled peptides. The determined specificity constant ( k cat /K M ) is 5817 M –1 s –1 and is similar to that of the free substrate. We further show that the enzyme kinetics depend on the type and quantity of dye incorporated into the coacervates. Our work presents a simple design for enzyme-responsive coacervates and provides insights into the interactions between the enzyme and coacervates as a whole.
Source: openalex_inverted_index · Quality: baseline

Research context

OpenAlex topics: Protein Structure and Dynamics · RNA and protein synthesis mechanisms · RNA modifications and cancer

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

Department of NanoEngineering, University of California, San Diego, La Jolla 92093, California, United States

Materials Science and Engineering Program, University of California, San Diego, La Jolla 92093, California, United States

Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore 138634, Republic of Singapore

Department of Bioengineering, University of California, San Diego, La Jolla 92093, California, United States

Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla 92093, California, United States

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla 92093, California, United States

Department of Chemistry and Biochemistry, Florida State University, Tallahassee 32306, Florida, United States

Department of Radiology, University of California, San Diego, La Jolla 92093, California, United States

Funding

National Institute of Dental and Craniofacial Research · National Institute of Allergy and Infectious Diseases · National Institute on Aging · Division of Materials Research

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