June 2024 Newsletter

June 27, 2024

High-resolution structures of proteins are critical to understanding molecular mechanisms of biological processes and in the discovery of therapeutic molecules. Cryo-EM has revolutionized structure determination of large proteins and their complexes, but a vast majority of proteins that underlie human diseases are small (< 50 kDa) and usually beyond its reach due to low signal-to-noise images and difficulties in particle alignment. Current strategies to overcome this problem increase the overall size of small protein targets using scaffold proteins that bind to the target, but are limited by inherent flexibility and not being bound to their targets in a rigid manner, resulting in the target being poorly resolved compared to the scaffolds. This paper presents an iteratively engineered molecular design for transforming Fabs (antibody fragments), into conformationally rigid scaffolds (Rigid-Fabs) that, when bound to small proteins (~20 kDa), can enable high-resolution structure determination using cryo-EM. This design introduces multiple disulfide bonds at strategic locations, generates a well-folded Fab constrained into a rigid conformation and can be applied to Fabs from various species, isotypes and chimeric Fabs. This paper presents examples of the Rigid Fab design enabling high-resolution (2.3–2.5 Å) structures of small proteins, Ang2 (26 kDa) and KRAS (21 kDa) by cryo-EM. The strategies for designing disulfide constrained Rigid Fabs in their work thus establish a general approach to overcome the target size limitation of single particle cryo-EM.

Link to the Paper

Employee spotlight

Yu-Chen Yen received training in Structure Biology throughout her graduate and postdoctoral studies. Through this training, she gained experience in protein expression and purification across a range of expression systems, including E. coli, insect cells, and mammalian cells. Additionally, she has developed skills in characterizing purified proteins using biochemical assays and determining protein structures through techniques such as X-ray crystallography and cryo-EM.

Yu-Chen Yen, Ph.D. - Scientist II

Featured Services

Biophysical Characterization ServiceBiophysical characterization plays an essential role in drug discovery R&D. Helix offers biophysical characterization services using key instruments that cover all your research and project needs.We are excited to provide our customers with various biophysical characterization services (ITC, SPR: T200 & 8K, BLI, MST, DLS, TSA, CD, LC/MS, SEC-MALS, Mass Photometry, and more) at affordable prices, with accurate data and fast turnaround time.Contact us today to discuss how we can help you with your biophysical characterization needs.

Helix is hiring!!

Lab Operations Manager: We are looking to add an experienced Lab Operations Manager to our Indianapolis-based team. This role will manage and support the Helix team, planning & tracking all projects to produce high-quality work and support our client’s protein production, biophysical characterization, and structural biology projects.

Senior Scientist - Gene-to-Structure: We are looking to add an experienced senior scientist to join our Indianapolis-based team. This senior-level scientist will support our protein production and structural biology pipelines by producing proteins and setting up crystallization and/or cryo-EM experiments, interfacing with our clients, and writing technical project reports.

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Helix highlights

This month, the Helix team had a cookout day. Yay!! The team and family members got together and enjoyed the beautiful weather outside. We grilled hamburgers and hotdogs, had some snacks and drinks, talked and laughed, and had so much fun.

The team is dedicated to providing the best quality work and services to our customers, also having fun at work, enjoying each other, and maximizing teamwork. :-)

Helix Cookout Day!

Instrument review

Mass photometry is a revolutionary new method of analyzing molecules. It enables the accurate mass measurement of single molecules in solution, in their native state, and without the need for labels. For molecular mass measurements with unmatched sensitivity, speed, and simplicity of use, the TwoMP mass photometer offers a wide mass range and single-molecule resolution.Protein oligomerization: Many proteins adopt a particular oligomeric form under certain conditions. Mass photometry characterizes from purely monomeric to a dynamic equilibrium between multiple states.DNA-protein interactions: Mass photometry can be used to characterize DNA-protein complexes, which are crucial in gene expression, replication, and DNA repair. Mass photometry not only allows the detection of DNA binding but also provides information on how the oligomeric state of the protein changes upon DNA binding.Complex formation: Ribosomes are macromolecular assemblies of protein and RNA, and are central sites for protein synthesis. Bacterial ribosomes (an example from E. coli) are >2 MDa in size. Magnesium ions play a subtle yet important role in the assembly of intact (70S) complexes. In the absence of magnesium, E. coli ribosomes rapidly disassemble into their 30S and 50S subunits. Mass photometry allows us to monitor these processes.