Written by: Genya Gorshtein, MSc Published: September 12, 2023 Contents Introduction Mechanisms That Influence Protein Aggregation and Stability Sequence and Structural Characteristics That Impact Antibody Aggregation and Stability Engineered Antibody Formats Influence Protein Aggregation Strategies to Reduce Antibody Aggregation Propensity Improving Antibody Developability with Next Generation Protein Sequencing and Proteomics [...]
Written by: Genya Gorshtein, MSc Published: June 13, 2023 Contents Introduction How do Primary and Secondary Antibodies Work? How are Primary and Secondary Antibodies Generated? Selecting Primary and Secondary Antibodies for Immunoassays Developing Reliable Reagents for Immunoassays with Rapid Novor Introduction Immunoassays have a [...]
Written by: Vanessa Yoon Calvelo, PhD Published: June 6, 2023 Contents The Drug Development Pathway: Overview and Challenges Early Discovery and Development of Therapeutic Antibodies Target Identification and Validation Antibody Discovery and Expression Lead Characterization and Selection Lead Engineering and Optimization Candidate Selection The Drug Development Pathway: Overview [...]
Tackling Reproducibility in Life Sciences with Next Generation Protein Sequencing and Recombinant Expression
Written by: Genya Gorshtein, MSc Published: May 9, 2023 Contents Introduction Hybridoma Instability Leads to mAb Irreproducibility Batch-to-Batch Variation in Polyclonal Antibodies Antibody Sequencing and Recombinant Expression Ensures Reproducible Antibody Reagents Generating Reproducible Reagents with Rapid Novor Introduction Antibodies (Abs) are indispensable tools in [...]
Written by: Vanessa Yoon Calvelo, PhD Published: April 24, 2023 Contents Introduction Functions of Therapeutic Antibodies Functional Assays for Therapeutic Antibodies Functional Characterization in the Therapeutic Antibody Discovery Process Introduction Monoclonal antibodies (mAbs) and related biological products often present as ideal therapeutics largely due to: Their [...]
Written by: Genya Gorshtein, MSc Published: April 21, 2023 Contents Introduction Target Specification for First Generation Antibodies Patent Strategies for Second-Generation Antibodies Next Generation Protein Sequencing and Proteomics Strengthens IP Protections Introduction Intellectual property (IP) protection is a critical step during the commercialization of antibodies [...]
Written by: Vanessa Yoon Calvelo, PhD Published: April 14, 2023 Contents Introduction Immunochemical Properties of Therapeutic Antibodies Rapid Immunochemical Characterization of Antibodies Introduction Therapeutic antibodies, predominantly monoclonal antibodies (mAbs), are a rapidly expanding class of drugs with over 100 mAb-based biologics now approved for the treatment [...]
Written by: Genya Gorshtein, MSc Published: February 17, 2023 Contents Introduction Target Discovery and Validation Antibody Discovery Characterization and Lead Selection Engineering and Optimization Candidate Selection Therapeutic Antibody Discovery with Rapid Novor Introduction Monoclonal antibodies (mAbs) offer a vast range of configurations for therapeutic applications, [...]
Antibody Affinity and Avidity – The Strength of a Single Interaction Versus a Multivalent Interaction
Written by: Genya Gorshtein, MSc Published: January 6, 2023 Contents Introduction What is Affinity? What is Avidity? Measuring Affinity and Avidity: ELISA or SPR? Measuring Affinity And Avidity For Biological Applications Affinity and Avidity Analysis via SPR with Rapid Novor Introduction Kinetics of antibody-antigen interactions [...]
The great debate on the use of in vivo versus in vitro sources and strategies for antibody discovery and generation continues to thrive among antibody research groups. On one side of the debate is the argument for non-animal-derived antibodies due to the technical advancements of current in vitro technologies, and the moral obligation to reduce animal usage. On the other side of the debate is the counterargument for animal-derived antibodies due to their better performance in affinity, specificity, and reduced immunogenicity risk.
Written by: Genya Gorshtein, MSc Published: November 1, 2022 Contents Introduction Approaches for Engineering Antibody Therapeutics Driving Antibody Engineering with Next Generation Protein Sequencing and Proteomics Introduction Antibody engineering encompasses various development, production strategies, and modification techniques to improve the biological properties of monoclonal antibodies (mAbs) [...]
Written by: Genya Gorshtein, MSc Published: November 25, 2022 Contents Introduction General PROTAC Structure and Function Antibody-Conjugated PROTACs Developing AbPROTACs with De Novo Antibody Sequencing and Proteomics Introduction Small-molecule drug development is aimed at inhibiting disease-promoting protein function through occupancy-driven protein inhibition. A major caveat of [...]
Biological processes are driven by molecules that interact through specific molecular contacts, often to form a stable complex. These interactions are typically defined by the principles of thermodynamics as well as biomolecular structure and recognition. At the simplest level is the interaction between a target molecule with a specific binding site and a probing molecule that binds to that site, resulting in the bound complex.
Written by: Genya Gorshtein, MSc Published: September 14, 2022 Contents Introduction ADCs as Novel Anti-Cancer Chemotherapeutics Key Components of ADCs Future Generation of ADCs De Novo Protein Sequencing Applications in ADC Development Introduction An antibody-drug conjugate (ADC) is a monoclonal antibody (mAb) with a covalently attached [...]
Written by Genya Gorshtein, MSc Updated: January 27, 2023 (Published: August 31, 2022) Contents How is Antibody Diversity Generated? Which Steps Contribute to the Generation of Antibody Diversity? Antibody Loci and V(D)J Recombination Somatic Hypermutation Class Switch Recombination De Novo Proteomic Sequencing of Antibodies How is Antibody [...]
Written by: Genya Gorshtein, MSc Published: August 18, 2022 Contents Introduction How are Polyclonal Antibodies Produced? Applications of Polyclonal Antibodies Challenges of Polyclonal Antibodies De Novo Polyclonal Antibody Sequencing Introduction Polyclonal antibodies (pAbs) are a heterogeneous mix of antibodies derived from B cells in the [...]
Written by: Vanessa Yoon Calvelo, PhD Updated: January 19, 2023 (Published: August 11, 2022) Contents What is Surface Plasmon Resonance Spectroscopy? What is SPR Used For? How Does SPR Work? SPR Experimental Workflow SPR Sensorgram SPR Advantages SPR Applications SPR Antibody-Antigen Interaction Analysis at Rapid Novor What is [...]
Written by Genya Gorshtein, MSc August 10, 2022 Contents General Structure of Antibodies Fab and Fc Fragments Hinge Region CDR and FR Regions Antibody Structure Analysis Services General Structure of Antibodies Antibodies or immunoglobulins (Ig) maintain a common quaternary structure consisting of two identical heavy chains (HCs) and two [...]
Written by: Vanessa Yoon Calvelo, PhD Published: August 3, 2022 Contents What are Biosimilar Drugs? Why are Biosimilars Being Developed? Biosimilars are not the Equivalent of Generics Biosimilar Development Biosimilar Monoclonal Antibodies De Novo Protein Sequencing Solutions in Biosimilar Development What are Biosimilar Drugs? Biosimilar drugs, [...]
Characterization of proteins and protein complexes is a major keystone of structural biology. As our understanding of cellular processes continues to evolve from simple pathways to complicated networks, our need for advanced analytical methods is quite apparent. Mass spectrometry (MS)-based structural approaches can be used to study protein conformational changes and dynamics, protein motion/flexibility, ligand-protein binding, and protein-protein interfaces.
Written by: Vanessa Yoon Calvelo, PhD Published: July 11, 2022 Contents What is Gene Therapy? What are Adeno-Associated Viruses? Engineering of AAVs for Gene Therapy Engineering AAVs for Improved Transduction Engineering AAVs for Improved Immunogenicity De Novo Protein Sequencing Applications in AAV Characterization and Development What is Gene [...]
Written by: Vanessa Yoon Calvelo, PhD Published: June 13, 2022 Contents What is CAR-T Cell Therapy? CAR Structure and Function CAR-T Cell Development Engineering Strategies for CAR-T Cells De Novo Protein Sequencing Applications in CAR-T Cell Development What is CAR-T Cell Therapy? The infusion of T cells [...]
Written by: Vanessa Yoon Calvelo, PhD Updated: January 19, 2023 (Published: June 2, 2022) Contents What are post-translational modifications (PTMs)? Impact of PTMs Types of PTMs PTMs increase microheterogeneity of antibodies Characterization of PTMs by next generation protein sequencing The Importance of Post-Translational Modifications (PTMs) Post-translational [...]
Written by: Yuning Wang, PhD Updated: January 26, 2023 (Published: June 3, 2022) Contents Introduction The Four Levels of Protein Structure How are Protein Structures Studied? Introduction Structural information provides a great deal of understanding of how a protein works, which can allow us to [...]
The most straightforward solution would be to determine sequences of the dominating antibody forms in a polyclonal mixture to enable recombinant antibody generation and ensure reproducibility. This was recently made possible by the development of polyclonal antibody sequencing technology, which will be reviewed in this article.
The origin of hydrogen-deuterium exchange (HDX) dates back to the 1950s, when protein scientist Linderstrøm-Lang created a method involving protein deuteration to distinguish amide hydrogens participating in secondary structures. Today, scientists frequently rely on HDX data to investigate protein structure, conformational dynamics, and protein-ligand interaction.
The acronym “CDR” stands for complementarity determining region, a variable sequence of amino acids that folds into loops capable of binding to an antigenic amino acid sequence, also known as an epitope
Written by: Yuning Wang, PhD Updated: January 18, 2023 (Published: January 21, 2022) Contents Discovery of Camelid Antibodies What are Camelid Antibodies? Structure of Camelid Antibodies and Nanobodies Advantages of Camelid Antibodies and Nanobodies Camelid Antibodies and Nanobodies for Therapeutic and Research Applications How are Camelid Antibodies [...]
Recombinant antibodies are artificially synthesized antibodies. Recombinant antibodies are generated from expression systems (e.g., E.coli, yeast, mammalian cell lines) via transfection with two separate plasmids encoding the amino acid sequences for the light and heavy chains, respectively. In order to recombinantly produce mAbs, the amino acid sequence of the light and heavy chains must be known. There are many ways to obtain the sequence of an antibody.
Written by Yuning Wang, PhD and María Gerpe, PhD November 12, 2021 Contents IgBLAST Definition Why was IgBLAST Created? The Functions of IgBLAST How to Use IgBLAST Limitations of IgBLAST Additional Resources IgBLAST Definition Developed by the National Center for Biotechnology Information (NCBI), IgBlast is [...]
Peptide mapping is a widely used analytical technique to verify the primary structure (amino acid sequence) and characterize the chemical modifications of a protein. It analyzes peptides generated from the digestion of an isolated protein, or a protein mixture
Amino acids are small organic molecules that make up peptides and proteins. All living organisms share the same set of amino acids. Amino acids come together in different orders (sequences) to form proteins. As such, each type of protein has a different three-dimensional structure and biological activity.
The transition from polyclonal antibody drugs to a more targeted monoclonal approach was made possible through a series of scientific and technological advancements; the most notable of which is the hybridoma technique developed by Köhler and Milstein, which allowed the generation of pure antibodies at scale.
Protein sequencing is a method that typically utilizes mass spectrometry (MS) to determine the amino acid code of a protein1. Prior to the development of mass spectrometry, Edman degradation, a method involving the stepwise degradation of peptides to derive the order of amino acids, was the mainstream approach. Nowadays, mass spectrometry is favored due to its ease of use and high throughput capabilities, though Edman degradation is still employed for specific applications in which the technique is well suited.
Monoclonal antibodies (mAbs) are homogenous antibodies that bind to a single epitope on an antigen. Kohler and Milstein generated the first mAbs when they developed hybridoma technology in the 1970s. Because of the specificity, homogeneity and unlimited availability, mAbs are valuable reagents used in a variety of important applications including treatment and diagnosis of diseases
Amino acids (aa)—the building blocks of proteins—are simple molecules characterized by a variable R group flanked either side by an amino group and a carboxyl group. With around 20 different commonly found amino acids, each one can bond with another to produce chains that can be classified as peptides (typically below 50 aa) and proteins (sequences above 50 aa)—molecules ubiquitous to every known organism.
Amino acid sequencing is commonly performed using Edman degradation or mass spectrometry (MS). While mass spectrometry is favoured for its high throughput capabilities and ease of use, both techniques possess their own features and limitations. This article summarizes some of the key pain points inherent in the two methodologies when determining the amino acid sequence.
Antibodies are used in a variety of ways in academia and industry, from tools to therapeutics. Because antibodies are produced using live processes, which are naturally error-prone, validation is required from time to time. Furthermore, to develop biological therapeutics, the protein sequence must be confirmed as part of the regulatory process.
DNA sequencing is the process of determining the precise order of four nucleotides bases—adenine (A), guanine (G), cytosine (C), and thymine (T)—that make up the DNA molecule. From Sanger sequencing to next-generation sequencing (NGS), DNA sequencing’s accessibility and ease of use make it one of the most widely used technologies in life sciences.
As proteins are assembled, they fold into different structural orders: from primary to quaternary. The exact sequence of the primary structure (the amino acid sequence) will dictate how a protein will fold and function. The importance of the primary structure has been noted in several studies, where changes in the original amino acid sequence have resulted in affinity problems, binding disruption, reduced half-life, and higher aggregation odds.
Proteins are composed of peptide chains, which in turn are made up of a string or linear sequence of amino acids. Every amino acid has a basic structure containing an amino (-NH2) group and a carboxylic (-COOH) group (Figure 1B). To form a peptide, amino acids link to each other via a peptide bond, which involves the reaction between the carboxylic group of one amino acid and the amine group of another amino acid.
Protein mass spectrometry refers to the use of mass spectrometry in studying and characterizing proteins, including their quantification, profiling, interaction mapping, and identification of their post-translational modifications. Protein mass spectrometry may also be referred to as mass spectrometry-based proteomics. Mass spectrometry-based proteomics comprises three approaches: top-down, middle-down, and bottom-up proteomics.
Antibody sequences are critical for antibody engineering and protein characterization in therapeutic development. For antibody reagent users, knowing the sequences allows them to perform sequence analysis/alignment to identify binding and cross-reactivity so they can conduct rational experiment design.
Because they share the same mass, isoleucine and leucine are known as isobaric amino acids. Conventional mass spectrometry-based proteomics cannot be easily used to distinguish between isoleucine and leucine.
Amino acid sequencing is the process of identifying the arrangement of amino acids in proteins and peptides. Numerous distinct amino acids have been discovered in nature but all proteins in the human body are comprised of just twenty different types.
Bispecific therapeutics are monoclonal antibodies that carry a specific antigen-binding capability on each arm. Bispecifics are thus capable of having two specificities that can either double the binding affinity of the antibody toward the same antigen (increased avidity), or can now bind to two targets. Bispecifics are most often described as two types: trispecifics and bispecific T-cell engaged antibodies (BiTE).
Written by: María Gerpe, PhD Updated: January 27, 2023 (Published: June 25, 2021) Contents Introduction Types of Antibody Structures Functions of Antibodies Introduction Antibodies or immunoglobulins (Ig) are Y-shaped glycoproteins produced by the adaptive immune system in response to antigens - substances or molecules the immune [...]
Written by María Gerpe, PhD June 18, 2021 Introduction Research publications represent an additional source of validation proof for commercially available antibodies. As such, academic and industry scientists often also rely on publication references to decide which commercial antibody to purchase. Several independent efforts exist to compile such information. For instance, [...]
Nowadays, DNA sequencing is so popular that it is easy to forget that the first sequenced biological material was protein – insulin, by Sanger. Sanger, and another researcher, Edman, separately pioneered protein sequencing.
One of the most important pieces of information researchers need to know during early stage antibody drug research and development is the sequence information of the antibody protein. With the advancement of mass spectrometry instrumentation and technologies, it is helpful, and sometimes critical, to conduct sequence analysis using mass spectrometry experiments.
Recombinant Monoclonal Antibodies (rAbs) are highly reproducible, customizable and pure alternatives to the traditional antibodies produced by hybridomas. Get the antibody protein sequence, either by DNA sequencing or the de novo protein sequencing technology, you can rest assured that you can have the exact antibody made recombinantly anytime in the future.