Creative Biolabs is a world’s leading service provider for bio-molecular interaction analysis. Our expert team offers the most professional solutions and the advanced technologies which will ensure the progress of our customers’ research. Our expertise including but not limited to identifying, analyzing, and validating the bio-molecular interactions and also the discovery of novel drug target.

The interactions between bio-molecules play key roles in many essential biological processes. While some proteins function independently, a large number of proteins are only active in complex forms, which are defined by their interactions with other biomolecules, such as proteins, DNAs, RNAs, lipids, and metals. The bio-molecular interaction not only describes the physical contact among protein partners but also expands to the functional correlations in metabolic pathways, signaling pathways and even genetic co-regulations. Bio-molecular interactions are essential in almost all the aspects of cellular processes, such as signal transduction, regulation of metabolic pathways, environment sensing, cellular motion. Therefore, understanding the contact between bio-molecules take place in fundamental cellular processes and how bio-molecule complexes function in a cellular network becomes increasingly important.

Protein-Protein Interaction Assay

Protein-protein interactions (PPIs) as putative therapeutic targets for new treatments is challenging but gaining ground in the drug discovery industry for its significant progress in many diseases including cancer, cardiovascular disease and so on. Creative Biolabs has extensive experiences and advanced approaches on protein-protein interaction study. We could help you map the interacting network for your target proteins, validate the binding partners, and also design, discover and decipher the novel drugs.

Fig.1 Protein-protein interaction.

In Creative Biolabs, the approaches for PPI detection are mainly classified into three types, in vivo, in vitro, and in silico methods. In vivo techniques include yeast two-hybrid system (Y2H), mammalian two-hybrid system (M2H), bacterial two-hybrid system (B2H), reverse two-hybrid system (rY2H), etc. For in vitro way, Co-immunoprecipitation (Co-IP), pull-down assay, protein-fragment complementation assay (PCA), phage display, X-ray crystallography for PPI detection, NMR spectroscopy, and surface plasmon resonance (SPR) can be offered. And in silico groups consist of text mining and computational analyses, are displayed on a computer or by computer simulation, involving gene fusion, sequence-based approaches, chromosome proximity, and so on.

Protein-Nucleic Acid Interaction Assay

Protein-nucleic acid interactions (PNIs) are fundamental for maintaining genome and reproducing life in central biological process ranging from DNA replication and repair to RNA packaging and maturation, recombination and transcription of DNA to translation and transport of RNA. These specific interactions are susceptible to monitor through several well-established analytical modes from Creative Biolabs involving biochemical, biophysical, genetic, and immunological techniques based on the diverse purpose of our clients.

In Creative Biolabs, in vitro services used for PNI contain electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation (ChIP), DNA/RNA pull-down, as well as other sensitive techniques such as aptamer by SELEX, X-ray crystallography, surface plasmon resonance (SPR), and NMR spectroscopy. For in vivo assays, there are yeast one-hybrid (Y1H), yeast three-hybrid (Y3H) and fluorescent resonance energy transfer (FRET). And the identification of PNI in silico is aided by sequence-based, structure-based, or other database and bioinformatics simulation through computational intelligence.

Fig.2 Protein-DNA interaction.

Small Molecule-Target Interaction Assay

Although therapeutic biomacromolecules have made great progress in recent years, small-molecule drugs still dominate the treatment of human diseases. Small molecule drugs bind to targets in the body, such as receptors, DNA, and enzymes, thereby affecting related pathways and cellular processes. Thus, the discovery of potential targets of compound drugs serves as an important foundation for explaining their pharmacology, toxicity reducing and efficacy enhancing, and even developing novel drug candidates. On the other hand, compared with conventional phenotypic-based drug development, target-based drug development has greatly accelerated the process of new drug discovery.

Fig. 3 Comparison of phenotypic- and target-based drug discovery.¹

Several high-throughput approaches have been developed for rapid target screening and identification for small molecule drugs over these years. Relying on the high-resolution mass spectrometry platform, Creative Biolabs provides both in vivo and in vitro small molecule-target interaction assay services with high quality and wide coverage. Based on our existing successful experience, our tailored services for target identification mainly include activity-based protein profiling (ABPP), drug affinity responsive target stability, limited proteolysis-mass spectrometry (LiP-MS), and cell-based thermal shift assay. Our experienced and professional scientists will customize the most suitable methods and services for each project.

Creative Biolabs has long-devoted in providing bio-molecular interaction analysis solutions. From experiment design to data analysis, we offer one-stop and step-to-step custom services to facilitate your project success.

Published Data

• Interaction Proteomics Using Intracellular NMR Spectroscopy

Fig. 4 Interaction surface maps of ubiquitin-ligand complexes. (Leonard Breindel, 2018)

This paper summarizes methods of intracellular nuclear magnetic resonance (NMR) spectroscopy to study the proteomics of interactions in prokaryotes and eukaryotes. Scientists describe the use of intracellular NMR spectroscopy to analyze high-resolution protein structures and discuss methods for determining and analyzing both high-affinity and low-affinity protein-target interactions, including intrinsically disordered proteins. These methods provide detailed insights into important functional interactions. Intracellular NMR spectroscopy enables researchers to study molecular structures and interactions under physiological conditions, revealing the structural basis of biological activity.

• Biomolecular Interaction Study of Mitochondrial Proteins Related to Alzheimer's Disease

Fig. 5 Simulation of the concurrent interactions between Aβ, cypD, and 17β-HSD10. (Erika Hemmerová, 2020)

One of the key features of Alzheimer's disease (AD) is the accumulation of amyloid beta (Aβ) peptide in the mitochondrial matrix and the progressive mitochondrial dysfunction caused by Aβ peptide. In mitochondria, Aβ interacts with many biomolecules, including cyclophilin D (cypD) and 17β-hydroxysteroid dehydrogenase type 10 (17β-HSD10), and affects its physiological function. In this paper, scientists used surface plasmon resonance (SPR) method to study the interaction of Aβ with cypD and 17β-HSD10 in vitro, and determined the kinetic parameters of these interactions, so as to directly compare the relative affinity between Aβ and its mitochondrial binding chaperone. In addition, the researchers used determined individual interaction characteristics to simulate the concurrent interaction of Aβ with cypD and 17β-HSD10 in different models related to AD progress.

FAQ

1. What is biomolecular interaction analysis?

   Biomolecular interaction analysis refers to the techniques and methods to study and detect the interaction between proteins, nucleic acids, lipids, and small molecules. These interactions play a key role in a variety of biological processes inside and outside the cell, including signal transduction, metabolic regulation, gene expression and cellular communication. Common techniques include surface plasmon resonance (SPR), coprecipitation test (Co-IP), yeast two-hybrid (Y2H), fluorescence resonance energy transfer (FRET) and bimolecular fluorescence complementarity (BiFC).

2. What is the role of surface plasmon resonance (SPR) in biomolecular interaction analysis?

   SPR detects real-time, label-free molecular interactions. It measures the binding and dissociation of biomolecules on the surface of the sensor by detecting the plasmon resonance when light is reflected on the metal surface. This technique can provide kinetic parameters of the interaction, such as binding rate constant (kon), dissociation rate constant (koff) and affinity constant (KD). Because of its high sensitivity and real-time detection, SPR is widely used in drug screening, antibody characterization, protein-protein interaction and biosensor development.

3. What is the role of mass spectrometry in the study of biomolecular interactions?

   Protein identification: Mass spectrometry can identify the protein composition in samples from immunoprecipitation, pull-down assays, or affinity purification.
   Protein quantification: Mass spectrometry provides quantitative information to help researchers understand the abundance changes of interacting proteins under different conditions, thus revealing dynamic interaction networks.
   Modification analysis: Mass spectrometry can detect post-translational modifications (such as phosphorylation, acetylation, and methylation) of proteins, which play an important role in the regulation of protein-protein interactions.
   Complex assembly: The assembly sequence and structural characteristics of the protein complex can be analyzed by mass spectrometry, and the functional mechanism of the complex can be revealed.

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