Structural Biology
Identifying and developing molecules with optimal properties against a validated target is fundamental in pharmaceutical research. Knowledge of the target’s three-dimensional structure may accelerate such development. Structural biologists require a range of techniques to interrogate both small and large molecules in three dimensions. Cryo-EM is an aspirational structural technique for many, but cost, infrastructure and skills often prevent its adoption.
Making cryo-EM for structural biology accessible means building flexible models for working with companies of all stages and sizes. NanoImaging Services offers a range of options across the development spectrum, providing quick and easy access to the answers that cryo-EM can reveal, including our specialized feasibility assessment Starter Pack, which provides answers on protein suitability in under a week. Partner with the original and most experienced cryo-EM CRO (contract research organization) to access expertise and cutting edge instruments to fast track your protein structure determination, single particle analysis (SPA), structure based drug design (SBDD) projects.
Single Particle Analysis & Protein Structure Determination: A Powerful Tool For High-Resolution, Proprietary Drug Discovery Projects
Single particle analysis (SPA) extends the information obtainable from Transmission Electron Microscopy (TEM) images of samples and allows for high-resolution structure determination of proteins, protein complexes, antibodies, and viruses. We provide services for all stages of single particle analysis needs, including a feasibility assessment with our Starter Pack.
Functional insights into macromolecules activity can be found in the arrangement of their structural components. Investigating the atomic framework of a biomolecule could unwind its biochemical mechanism, providing answers to many relevant biological questions, thus facilitating drug discovery processes. X-ray crystallography has always been the analytical technique of choice for structure determination. Nevertheless, the crystallization process can be a bottleneck, sometimes requiring extensive modifications of a protein’s native structure to make it suitable for crystal formation and structure determination. Macromolecular analysis with NMR spectroscopy can be done in solution on full length proteins, but unfortunately its use is limited to small, highly homogenous, generally soluble biomolecules (globular proteins vs membrane proteins). On the other hand, cryo-EM does not require crystallization or absolute sample homogeneity, but it has its own limitations (e.g. protein size, complex stability, vitrification steps, preferred orientation, etc.). Yet multiple technological and methodological developments are pushing the boundaries of grid preparation and data collection, making cryo-EM the most suitable biophysical technique in structure biology. At NIS we have extensive experience in providing structural information for a large variety of drug targets, including soluble proteins and protein/DNA complexes, ion channels, GPCRs, PROTACs and molecular glues.
Single Particle Analysis & Protein Structure Determination: A Powerful Tool For High-Resolution, Proprietary Drug Discovery Projects
Single particle analysis (SPA) extends the information obtainable from Transmission Electron Microscopy (TEM) images of samples and allows for high-resolution structure determination of proteins, protein complexes, antibodies, and viruses. We provide services for all stages of single particle analysis needs, including a feasibility assessment with our Starter Pack.
Functional insights into macromolecules activity can be found in the arrangement of their structural components. Investigating the atomic framework of a biomolecule could unwind its biochemical mechanism, providing answers to many relevant biological questions, thus facilitating drug discovery processes. X-ray crystallography has always been the analytical technique of choice for structure determination. Nevertheless, the crystallization process can be a bottleneck, sometimes requiring extensive modifications of a protein’s native structure to make it suitable for crystal formation and structure determination. Macromolecular analysis with NMR spectroscopy can be done in solution on full length proteins, but unfortunately its use is limited to small, highly homogenous, generally soluble biomolecules (globular proteins vs membrane proteins). On the other hand, cryo-EM does not require crystallization or absolute sample homogeneity, but it has its own limitations (e.g. protein size, complex stability, vitrification steps, preferred orientation, etc.). Yet multiple technological and methodological developments are pushing the boundaries of grid preparation and data collection, making cryo-EM the most suitable biophysical technique in structure biology. At NIS we have extensive experience in providing structural information for a large variety of drug targets, including soluble proteins and protein/DNA complexes, ion channels, GPCRs, PROTACs and molecular glues.
Design Drug Molecules to Best Interact with a Target for Structure Based Drug Design
Cryo-EM is perfect for analyzing small molecules binding to large biological entities including DNA, RNA, and proteins. Using our services, structural biologists can easily answer medicinal chemists’ questions regarding the interactions of the small molecules with the chosen target and suggest ways to help design and optimize drug candidates.
Structure based drug design (SBDD) refers to the process of identifying and optimizing a drug candidate using three-dimensional structural information to complement and/or inform chemistry and biology experiments. Knowledge of the specific interactions that a drug candidate makes with the target of choice may help in hypothesizing and designing novel derivative chemical entities with improved potency and pharmacologic characteristics. Using cryo-EM as a protein structure determination technique allows to interrogate macromolecules and macromolecular complexes in close to native conditions, thus providing more biologically relevant information.
Single Particle Analysis & Protein Structure Determination: A Powerful Tool For High-Resolution, Proprietary Drug Discovery Projects
Single particle analysis (SPA) extends the information obtainable from Transmission Electron Microscopy (TEM) images of samples and allows for high-resolution structure determination of proteins, protein complexes, antibodies, and viruses. We provide services for all stages of single particle analysis needs, including a feasibility assessment with our Starter Pack.
Functional insights into macromolecules activity can be found in the arrangement of their structural components. Investigating the atomic framework of a biomolecule could unwind its biochemical mechanism, providing answers to many relevant biological questions, thus facilitating drug discovery processes. X-ray crystallography has always been the analytical technique of choice for structure determination. Nevertheless, the crystallization process can be a bottleneck, sometimes requiring extensive modifications of a protein’s native structure to make it suitable for crystal formation and structure determination. Macromolecular analysis with NMR spectroscopy can be done in solution on full length proteins, but unfortunately its use is limited to small, highly homogenous, generally soluble biomolecules (globular proteins vs membrane proteins). On the other hand, cryo-EM does not require crystallization or absolute sample homogeneity, but it has its own limitations (e.g. protein size, complex stability, vitrification steps, preferred orientation, etc.). Yet multiple technological and methodological developments are pushing the boundaries of grid preparation and data collection, making cryo-EM the most suitable biophysical technique in structure biology. At NIS we have extensive experience in providing structural information for a large variety of drug targets, including soluble proteins and protein/DNA complexes, ion channels, GPCRs, PROTACs and molecular glues.
Design Drug Molecules to Best Interact with a Target for Structure Based Drug Design
Cryo-EM is perfect for analyzing small molecules binding to large biological entities including DNA, RNA, and proteins. Using our services, structural biologists can easily answer medicinal chemists’ questions regarding the interactions of the small molecules with the chosen target and suggest ways to help design and optimize drug candidates.
Structure based drug design (SBDD) refers to the process of identifying and optimizing a drug candidate using three-dimensional structural information to complement and/or inform chemistry and biology experiments. Knowledge of the specific interactions that a drug candidate makes with the target of choice may help in hypothesizing and designing novel derivative chemical entities with improved potency and pharmacologic characteristics. Using cryo-EM as a protein structure determination technique allows to interrogate macromolecules and macromolecular complexes in close to native conditions, thus providing more biologically relevant information.
Biotherapeutics Antibody Engineering & Targeted Protein Degradation
Increasingly, structural biologists partner with NIS to investigate protein-protein complexes, such as how monoclonal antibodies (MAbs) bind to their target. Using cryo-EM, we provide the structural information required to guide the modification of MAbs to generate highly specific and effective antibodies with optimized processing, stability, and tolerance.
In the past decade, the field of targeted protein degradation has grown exponentially becoming a new therapeutic route for the treatment of several diseases. The research has gone beyond laboratory experiments and it resulted with the first molecules in clinical trials. Among the TPD family the most studied subclasses are the Proteolysis Targeting Chimeras (PROTACs) and molecular glues. A PROTAC is a bivalent chemical probe that binds to both an E3 ligase and a protein of interest (POI) to induce the protein ubiquitination and subsequent degradation by the proteasome. Molecular glues, instead, are monovalent small molecules that promote novel protein-protein interactions leading to POI ubiquitination and subsequent proteosomal degradation. Recently, cryo-EM has emerged as a new tool for the development and characterization of a variety of targets enabling their structure based drug design (SBDD).
Making cryo-EM accessible means building flexible models for working with companies of all stages and sizes. NanoImaging Services offers a range of options across the development spectrum with six simple steps.
Types of protein structures we have imaged
Frequently Asked Questions
Explore how our experts can help you.
Why choose cryo-EM over other analytical methods?
Cryo-EM allows for the direct visualization of biological molecules at moderate-to-high resolution without the need for crystallization, making it a powerful tool for structural biology. Additionally, cryo-EM can be used to study proteins in their native state, without the need for modification or crystallization, which can introduce artifacts or alter the structure of the protein.
Why should I use cryo-EM instead of X-ray Crystallography or Nuclear Magnetic Resonance (NMR) spectroscopy?
Cryo-EM has several advantages over these techniques, including the ability to capture heterogeneous or dynamic molecular states in drug targets that are difficult or impossible to crystallize, including large (>300kDa) structures, protein:protein or protein:nucleic acid complexes, and membrane proteins. Additionally, cryo-EM requires smaller sample amounts than X-ray crystallography and NMR, using as little as 0.5-1 mg of protein at 1 mg/mL to obtain a structure. This can be particularly important for reagents generated from mammalian cells or are otherwise difficult to obtain. Overall, cryo-EM can address roadblocks with difficult samples such as preferred orientation, flexibility, aggregation, and more. Learn more about overcoming the challenges of preferred orientation in our blog post here.
Can we obtain additional/new information from cryo-EM after other methods failed?
Yes, cryo-EM can provide valuable information even after other methods have failed. Cryo-EM can visualize large and complex structures that are difficult to crystallize, and it can also capture dynamic states of proteins and macromolecular complexes that are not easily accessible through other methods. Additionally, cryo-EM can reveal conformational changes that occur in response to ligand binding or post-translational modifications, which may not be apparent from other techniques.
Is cryo-EM 3 Å resolution better than crystallography 3 Å?
It is difficult to compare the resolution of cryo-EM and crystallography maps solely based on a resolution limit since cryo-EM is a direct imaging method and the maps are not “phased” as in crystallography. As a direct method, the resulting maps from a cryo-EM data collection appear to be a “better” resolution than the refined nominal resolution may indicate. For instance, cryo-EM can provide structures with sidechains and small molecule ligand poses unambiguously defined at a nominal resolution of 3.5 Å, whereas density generated from a crystallographic experiment at that resolution cannot.
What is the likelihood of success for my sample?
Each sample is different and we recommend an initial consultation with our team to provide an accurate estimation for success. NIS will always be fully transparent in regard to samples that might need more optimization or if a project might not be suitable for cryo-EM.
What kind of samples do you have experience with?
NIS has solved over 150 3D structures with cryo-EM, with 76% of protein structures solved at 3.5 Å or better resolution.
We have extensive experience with a wide range of samples for cryo-EM, including large (>300 kDa) and medium-sized (>100 kDa) proteins, with and without ligands of interest. We have also worked with proteins/nucleic acid complexes, multi-domain proteins, and multi-component complexes. We are experienced in handling challenging samples, including membrane proteins including GPCRs and ion channels. Additionally, we have solved structures of complexes utilizing PROTACs and molecular glues, and have significant experience studying antibody:epitope interactions at moderate and high resolutions. Our team is dedicated to providing high-quality cryo-EM services to our clients and working with them to advance their research in diverse biological systems.
We are not sure if we can fully commit to a cryo-EM project. What are our options?
At NIS, we understand that committing to a cryo-EM project can be a big decision. That's why we offer a Starter Pack service, which includes a negative stain test and an initial feasibility assessment to help you evaluate the suitability of your sample for cryo-EM. The feasibility assessment can provide valuable information on sample quality and the potential for obtaining high-resolution structures. This service can help you make an informed decision about whether to proceed with a full cryo-EM project and can provide a cost-effective way to explore the capabilities of cryo-EM for your research. Read our blog about a proof of concept study here.
Are there size requirements?
Ideally, your sample is at least 100 kDa of ordered mass. While less than 100 kDa is still feasible, the difficulty, timelines, and cost of the project will likely increase.
What quantity of my sample is required?
Cryo-EM has an advantage over other methods in that only a small quantity is required. 1 mg of your protein/complex at 1 - 5 mg/mL concentration is an appropriate starting target. Depending on your sample, we might ask for a higher concentration, however, this can be discussed with our technical team on a call.
Are all reagents and buffer conditions amenable to cryo-EM?
Most reagents and buffer conditions are amenable to cryo-EM. Exceptions include DMSO >0.5% which may interfere with the vitrification process and cause crystal formation. Similarly, excessive glycerol or sucrose can increase sample viscosity and cause issues with particle alignment during data collection.
Do you do different concentration ranges, how does it work?
If your project is feasible for cryo-EM, it may undergo several optimization steps where different concentrations/grid types will be tried. Protein concentration and buffer composition is a strong determinant of both ice thickness and particle distribution and is a primary variable tested during our feasibility assessment. Generally, soluble proteins are tested at 1-5 mg/mL concentration, while integral membrane proteins are better behaved at higher concentrations.
What is the wait time to start a project?
There is usually a 2-week lead time or less to initiate a project. It is best to ship your sample to us as soon as possible after your sample submission meeting, as there are frequent changes to schedules and microscope time can become unexpectedly available.
What are the turnaround times?
Turnaround times for structural biology projects are typically 4-8 weeks from sample to map, depending on the desired project goals. To obtain a more accurate timeline estimate, we recommend you set up an initial meeting with our team.
Do we prepare target proteins?
At NIS, we specialize in providing high-quality cryo-EM services to our clients, and we do not offer protein preparation services. However, we recognize the importance of sample quality in obtaining high-resolution structures through cryo-EM, and we offer ‘gene-to-structure’ protein consultancy services to help our clients optimize their sample preparation and experimental design.
What is the timeline for protein production to structure?
In our experience, protein production takes between 4-6 months at most structural biology CROs. From sample receipt to structure, the timeline is typically 4-8 weeks, depending on the difficulty of the project. To get a more accurate estimation of timelines, we recommend you set up a meeting with our experts.
What documentation does NIS handle?
We support and value our clients IP confidentiality. Our in-house contracts team will work closely and efficiently with your legal team to execute all necessary contracts. A CDA/NDA usually takes about a week or less to complete, and an MSA usually takes about 2-3 weeks. We prefer to put a CDA/NDA in place before our introductory meeting so that the conversation we can discuss project specific details.
