Written by Genya Gorshtein, MSc 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) as therapeutic [...]
Written by Genya Gorshtein, MSc 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 this therapeutic [...]
Written by Vanessa Yoon Calvelo, PhD September 15, 2022 Contents Analyzing Biomolecular Interactions SPR Applications for Biomolecular Interactions SPR – A golden standard for biomolecular interaction analysis Analyzing Biomolecular Interactions Biological processes are driven by molecules that interact through specific molecular contacts, often to form a stable [...]
Written by Genya Gorshtein, MSc 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 cytotoxic payload [...]
Written by Genya Gorshtein, MSc August 31, 2022 Contents Introduction Antibody Loci and V(D)J Recombination Somatic Hypermutation Class Switch Recombination De Novo Proteomic Sequencing of Antibodies Introduction Without the presence of an antigen, the human immune system can generate more than 1012 different antibodies and as many [...]
Written by Genya Gorshtein, MSc 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 adaptive immune system. [...]
Written by Vanessa Yoon Calvelo, PhD August 11, 2022 Contents What is Surface Plasmon Resonance Spectroscopy? How Does SPR Work? SPR Experimental Workflow SPR Sensorgram SPR Advantages Antibody-Antigen Binding Analysis with SPR SPR Antibody-Antigen Interaction Analysis at Rapid Novor What is Surface Plasmon Resonance Spectroscopy? Surface plasmon [...]
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 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, also known [...]
Written by Vanessa Yoon Calvelo, PhD July 21, 2022 Contents Mass spectrometry-based approaches for structural analysis of proteins HDX-MS Applications for ‘Difficult’ Proteins HDX-MS – A powerful analytical technique for protein characterization Mass spectrometry-based approaches for structural analysis of proteins Characterization of proteins and protein complexes is [...]
Written by Vanessa Yoon Calvelo, PhD 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 Therapy? [...]
Written by Vanessa Yoon Calvelo, PhD 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 directed [...]
Written by Vanessa Yoon Calvelo, PhD 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 What are Post-Translational Modifications? Post-translational modifications (PTMs) are processing events typically driven by [...]
Written by Yuning Wang, PhD June 3, 2022 Contents Background Four levels of protein structure How are protein structures studied? Background Structural information provides a great deal of understanding of how a protein works, which can allow us to elucidate molecular mechanisms underlying human diseases. Rapidly developing [...]
Written by Yuning Wang, PhD May 31, 2022 Contents Background What is Polyclonal Antibody Sequencing? Applications of Polyclonal Antibody Sequencing Advantages of Polyclonal Antibody Sequencing World’s First: De Novo Polyclonal Antibody Sequencing at Rapid Novor Background The native immune system produces polyclonal antibodies (pAb) by different B-cell [...]
Written by Yuning Wang, PhD May 13, 2022 Contents What is HDX-MS? HDX-MS Workflow Applications of HDX-MS HDX-MS Advantages HDX-MS Epitope Mapping of Antibodies HDX-MS Epitope Mapping at Rapid Novor What is HDX-MS? The origin of hydrogen-deuterium exchange (HDX) dates back to the 1950s, when protein scientist [...]
Written by Yuning Wang, PhD March 15, 2022 Contents What are CDRs? Antibody CDRs De Novo Protein Sequencing as a Tool for Identifying CDRs Sequences Applying De Novo Protein Sequencing to Identify CDRs Sequences Annotation Schemes for Identifying CDRs by Sequence Rapid Novor can Help with Identifying CDRs by Sequence [...]
Written by Yuning Wang, PhD January 21, 2022 Contents Discovery of Camelid Antibodies What are Camelid Antibodies? Structure of Camelid Antibodies and Nanobodies Applications of Nanobodies How are Nanobodies Developed? References Discovery of Camelid Antibodies Three decades ago, the discovery1 of a peculiar [...]
Written by María Gerpe, PhD January 2, 2022 Contents What are Recombinant Antibodies? What is the Difference Between Recombinant and Traditional Antibodies? Why are Recombinant Antibodies Important? Types of Recombinant Antibodies How are Recombinant Sequences Obtained? Additional Resources References What are Recombinant Antibodies? [...]
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.
Written by Yuning Wang, PhD August 1, 2021 What is DNA Sequencing? 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 [...]
Written by María Gerpe, PhD July 23, 2021 Why the Amino Acid Sequence Matters 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 therefore function. The importance of [...]
Proteins are composed of peptide chains, which in turn are made up of a string or linear sequence of amino acids (Figure 1A). 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 (Figure 1B). As such, the primary structure of a protein is typically recorded starting at the amino-terminal (N) end and continuing to the carboxyl-terminal (C) end. The primary protein structure may be directly sequenced from a sample of the protein itself or inferred from the DNA sequence.
Protein mass spectrometry refers to the use of mass spectrometry in the study and characterization of proteins, including their quantification, profiling, interaction mapping, and identification of their post-translational modifications (1,2). Protein mass spectrometry may also be referred to as mass spectrometry-based proteomics. Mass spectrometry-based proteomics consist of 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 June 25, 2021 Introduction Antibodies or immunoglobulins (Ig) are Y-shaped glycoproteins produced by the adaptive immune system in response to antigens - substances or molecules the immune system deems as foreign. Antibodies bind to an antigen and either directly neutralize it, or activate other parts of [...]
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.