Biophysics is an interdisciplinary science that applies the theories and methods of physics to understand biological systems. It encompasses a wide range of topics, from the molecular mechanisms within cells to the physical properties of organisms and ecosystems. The goal of biophysics is to uncover the physical principles underlying the structure and function of biological molecules, cells, and cellular systems, providing a deeper understanding of life itself. The Institute of Biophysics, Czech Academy of Sciences (IBP) stands as a beacon of excellence in the field of biophysical research in the Czech Republic. This article delves into its history, structure, research areas, and major scientific achievements, highlighting the role of IBP in the global scientific community.

• Keywords
• Biophysical methods, Biophysics, DNA damage repair, Ionizing radiation, Radiotherapy,
• Publication type
• Journal Article MeSH
• Review MeSH

This year we celebrate seventy years since the establishment of the Institute of Biophysics of the Czechoslovak Academy of Sciences (IBP) (founded on January 1, 1955). If we look into the biography of Professor Emil Paleček (born on October 3, 1930), one of the most world-recognized personalities associated with the Institute and one of the most cited Czech scientists, known as the founder of nucleic acids electrochemistry, we are drawn to the same year, i.e. 1955, as the year in which Emil Paleček finished his studies in biochemistry and joined the IBP, where he worked with admirable vitality, enthusiasm and dedication until his death (October 30, 2018). In the context of celebration of founding of the Institute, we would like to commemorate in this article a personality who significantly influenced the history of the Institute alongside the important discoveries and research directions that defined his extremely successful career. We prefer this form, which is a sort of a mini-review of the most important results of the laboratory obtained under EP's leadership over 63 years, presented in mutual context and natural relations. For his life's work, Professor Paleček received many prestigious awards, with the Czech Head Award in 2014 and the Neuron Foundation Award in 2017 being the most distinguished.

• Keywords
• Electrochemistry, Glycans, Modification, Nucleic acids, Proteins, Structure,
• Publication type
• Journal Article MeSH
• Review MeSH

The redox behavior and chemisorption of cysteamine (CA) at a charged mercury surface are described, with an emphasis on its acid-base properties supported by molecular dynamics and quantum mechanical calculations. It was found that CA forms chemisorbed layers on the surface of the mercury electrode. The formation of Hg-CA complexes is connected to mercury disproportionation, as reflected in peaks SII and SI at potentials higher than the electrode potential of zero charge (p.z.c.). Both the process of chemisorption of CA and its consequent redox transformation are proton-dependent. Also, depending on the protonation of CA, the formation of typical populations of chemisorbed conformers can be observed. In addition, cystamine (CA disulfide dimer) can be reduced on the mercury surface. Between the potentials of this reduction and peak SI, the p.z.c. of the electrode used can be found. Furthermore, CA can serve as an LMW catalyst for hydrogen evolution. The mechanistic insights presented here can be used for follow-up research on CA chemisorption and targeted modification of other metallic surfaces.

• Publication type
• Journal Article MeSH

The glycoprofiling of two proteins, the free form of the prostate-specific antigen (fPSA) and zinc-α-2-glycoprotein (ZA2G), was assessed to determine their suitability as prostate cancer (PCa) biomarkers. The glycoprofiling of proteins was performed by analysing changes in the glycan composition on fPSA and ZA2G using lectins (proteins that recognise glycans, i.e. complex carbohydrates). The specific glycoprofiling of the proteins was performed using magnetic beads (MBs) modified with horseradish peroxidase (HRP) and antibodies that selectively enriched fPSA or ZA2G from human serum samples. Subsequently, the antibody-captured glycoproteins were incubated on lectin-coated ELISA plates. In addition, a novel glycoprotein standard (GPS) was used to normalise the assay. The glycoprofiling of fPSA and ZA2G was performed in human serum samples obtained from men undergoing a prostate biopsy after an elevated serum PSA, and prostate cancer patients with or without prior therapy. The results are presented in the form of an ROC (Receiver Operating Curve). A DCA (Decision Curve Analysis) to evaluate the clinical performance and net benefit of fPSA glycan-based biomarkers was also performed. While the glycoprofiling of ZA2G showed little promise as a potential PCa biomarker, the glycoprofiling of fPSA would appear to have significant clinical potential. Hence, the GIA (Glycobiopsy ImmunoAssay) test integrates the glycoprofiling of fPSA (i.e. two glycan forms of fPSA). The GIA test could be used for early diagnoses of PCa (AUC = 0.83; n = 559 samples) with a potential for use in therapy-monitoring (AUC = 0.90; n = 176 samples). Moreover, the analysis of a subset of serum samples (n = 215) revealed that the GIA test (AUC = 0.81) outperformed the PHI (Prostate Health Index) test (AUC = 0.69) in discriminating between men with prostate cancer and those with benign serum PSA elevation.

• MeSH
• Early Detection of Cancer MeSH
• Glycoproteins MeSH
• Humans MeSH
• Biomarkers, Tumor MeSH
• Prostatic Neoplasms * pathology   MeSH
• Polysaccharides MeSH
• Prostate pathology   MeSH
• Prostate-Specific Antigen * MeSH
• ROC Curve MeSH
• Check Tag
• Humans MeSH
• Male MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Glycoproteins MeSH
• Biomarkers, Tumor MeSH
• Polysaccharides MeSH
• Prostate-Specific Antigen * MeSH

Prostate cancer (PCa) is the second most common cancer. In this paper, the isolation and properties of exosomes as potential novel liquid biopsy markers for early PCa liquid biopsy diagnosis are investigated using two prostate human cell lines, i.e., benign (control) cell line RWPE1 and carcinoma cell line 22Rv1. Exosomes produced by both cell lines are characterised by various methods including nanoparticle-tracking analysis, dynamic light scattering, scanning electron microscopy and atomic force microscopy. In addition, surface plasmon resonance (SPR) is used to study three different receptors on the exosomal surface (CD63, CD81 and prostate-specific membrane antigen-PMSA), implementing monoclonal antibodies and identifying the type of glycans present on the surface of exosomes using lectins (glycan-recognising proteins). Electrochemical analysis is used to understand the interfacial properties of exosomes. The results indicate that cancerous exosomes are smaller, are produced at higher concentrations, and exhibit more nega tive zeta potential than the control exosomes. The SPR experiments confirm that negatively charged α-2,3- and α-2,6-sialic acid-containing glycans are found in greater abundance on carcinoma exosomes, whereas bisecting and branched glycans are more abundant in the control exosomes. The SPR results also show that a sandwich antibody/exosomes/lectins configuration could be constructed for effective glycoprofiling of exosomes as a novel liquid biopsy marker.

• Keywords
• exosomes, microscopy techniques, nanoparticle tracking analysis, prostate cancer, self-assembled monolayer, surface plasmon resonance,
• MeSH
• Exosomes * chemistry   MeSH
• Carcinoma * metabolism   pathology   MeSH
• Lectins analysis   metabolism   MeSH
• Humans MeSH
• Polysaccharides analysis   metabolism   MeSH
• Liquid Biopsy MeSH
• Check Tag
• Humans MeSH
• Male MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Lectins MeSH
• Polysaccharides MeSH

Electrochemical methods can be used not only for the sensitive analysis of proteins but also for deeper research into their structure, transport functions (transfer of electrons and protons), and sensing their interactions with soft and solid surfaces. Last but not least, electrochemical tools are useful for investigating the effect of an electric field on protein structure, the direct application of electrochemical methods for controlling protein function, or the micromanipulation of supramolecular protein structures. There are many experimental arrangements (modalities), from the classic configuration that works with an electrochemical cell to miniaturized electrochemical sensors and microchip platforms. The support of computational chemistry methods which appropriately complement the interpretation framework of experimental results is also important. This text describes recent directions in electrochemical methods for the determination of proteins and briefly summarizes available methodologies for the selective labeling of proteins using redox-active probes. Attention is also paid to the theoretical aspects of electron transport and the effect of an external electric field on the structure of selected proteins. Instead of providing a comprehensive overview, we aim to highlight areas of interest that have not been summarized recently, but, at the same time, represent current trends in the field.

• Keywords
• Electrode, Microdevice, Peptide, Protein, Sensor,
• MeSH
• Electrochemical Techniques * methods   MeSH
• Electrochemistry MeSH
• Oxidation-Reduction MeSH
• Proteins * MeSH
• Electron Transport MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Names of Substances
• Proteins * MeSH

Aberrant glycosylation of glycoproteins has been linked with various pathologies. Therefore, understanding the relationship between aberrant glycosylation patterns and the onset and progression of the disease is an important research goal that may provide insights into cancer diagnosis and new therapy development. In this study, we use a surface plasmon resonance imaging biosensor and a lectin array to investigate aberrant glycosylation patterns associated with oncohematological disease-myelodysplastic syndromes (MDS). In particular, we detected the interaction between the lectins and glycoproteins present in the blood plasma of patients (three MDS subgroups with different risks of progression to acute myeloid leukemia (AML) and AML patients) and healthy controls. The interaction with lectins from Aleuria aurantia (AAL) and Erythrina cristagalli was more pronounced for plasma samples of the MDS and AML patients, and there was a significant difference between the sensor response to the interaction of AAL with blood plasma from low and medium-risk MDS patients and healthy controls. Our data also suggest that progression from MDS to AML is accompanied by sialylation of glycoproteins and increased levels of truncated O-glycans and that the number of lectins that allow discriminating different stages of disease increases as the disease progresses.

• MeSH
• Leukemia, Myeloid, Acute * MeSH
• Biosensing Techniques * MeSH
• Glycoproteins metabolism   MeSH
• Glycosylation MeSH
• Plasma metabolism   MeSH
• Lectins MeSH
• Humans MeSH
• Myelodysplastic Syndromes * therapy   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Glycoproteins MeSH
• Lectins MeSH

In recent decades, it has become clear that most of human proteins are glycosylated and that protein glycosylation plays an important role in health and diseases. At present, simple, fast and inexpensive methods are sought for clinical applications and particularly for improved diagnostics of various diseases, including cancer. We propose a label- and reagent-free electrochemical method based on chronopotentiometric stripping (CPS) analysis and a hanging mercury drop electrode for the detection of interaction of sialylated protein biomarker a prostate specific antigen (PSA) with two important lectins: Sambucus nigra agglutinin (SNA) and Maackia amurensis agglutinin (MAA). Incubation of PSA-modified electrode with specific SNA lectin resulted in an increase of CPS peak H of the complex as compared to this peak of individual PSA. By adjusting polarization current and temperature, PSA-MAA interaction can be either eliminated or distinguished from the more abundant PSA-SNA complex. CPS data were in a good agreement with the data obtained by complementary methods, namely surface plasmon resonance and fluorescent lectin microarray. It can be anticipated that CPS will find application in glycomics and proteomics.

• Keywords
• A prostate specific antigen, Chronopotentiometric analysis, Lectin-glycoprotein interaction, Mercury electrode, Sialylated glycan isomers,
• MeSH
• Agglutinins metabolism   MeSH
• Sambucus nigra chemistry   MeSH
• Electric Conductivity * MeSH
• Electrochemistry MeSH
• N-Acetylneuraminic Acid metabolism   MeSH
• Maackia chemistry   MeSH
• Prostate-Specific Antigen chemistry   metabolism   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Agglutinins MeSH
• N-Acetylneuraminic Acid MeSH
• Prostate-Specific Antigen MeSH

An impedimetric lectin biosensor for the detection of changes in the glycan structure of antibodies isolated from human serum is here correlated with the progression of rheumatoid arthritis (RA). The biosensor was built up from a mixed self-assembled monolayer (SAM) on gold consisting of two different thiolated zwitterionic derivatives, carboxybetaine and sulfobetaine, to resist nonspecific interactions. The carboxyl-terminated one was applied also for the covalent immobilization of lectin Ricinus communis agglutinin I (RCA-I). The process of building a bioreceptive layer was optimized and characterized using a diverse range of techniques. Impedimetric assays were integrated on a chip consisting of eight gold working electrodes, which is an important step toward the achievement of a moderate level of multiplexing for the analysis of human serum samples. At the end, the results obtained by the impedimetric analysis of immunoglobulins G (IgGs) isolated from serum samples were compared with those of two other standard bioanalytical methods employing lectins, that is, lectin microarrays (MAs) and enzyme-linked lectin binding assays (ELLBAs). The impedimetric results agreed very well with the DAS28 index (RA disease activity score 28), suggesting that impedimetric assays could be used for the development of a new diagnostic procedure sensitive to glycosylation changes in human IgGs and thus RA progression.

• MeSH
• Biosensing Techniques * instrumentation   methods   MeSH
• Protein Array Analysis * instrumentation   methods   MeSH
• Electrodes MeSH
• Glycosylation MeSH
• Immunoassay instrumentation   methods   MeSH
• Immunoglobulin G analysis   blood   MeSH
• Humans MeSH
• Polysaccharides analysis   blood   MeSH
• Arthritis, Rheumatoid blood   MeSH
• Plant Lectins chemistry   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Immunoglobulin G MeSH
• Polysaccharides MeSH
• Ricinus communis agglutinin-1 MeSH Browser
• Plant Lectins MeSH

An ultrasensitive impedimetric glycan-based biosensor for reliable and selective detection of inactivated, but intact influenza viruses H3N2 was developed. Such glycan-based approach has a distinct advantage over antibody-based detection of influenza viruses since glycans are natural viral receptors with a possibility to selectively distinguish between potentially pathogenic influenza subtypes by the glycan-based biosensors. Build-up of the biosensor was carefully optimized with atomic force microscopy applied for visualization of the biosensor surface after binding of viruses with the topology of an individual viral particle H3N2 analyzed. The glycan biosensor could detect a glycan binding lectin with a limit of detection (LOD) of 5 aM. The biosensor was finally applied for analysis of influenza viruses H3N2 with LOD of 13 viral particles in 1 μl, what is the lowest LOD for analysis of influenza viral particles by the glycan-based device achieved so far. The biosensor could detect H3N2 viruses selectively with a sensitivity ratio of 30 over influenza viruses H7N7. The impedimetric biosensor presented here is the most sensitive glycan-based device for detection of influenza viruses and among the most sensitive antibody or aptamer based biosensor devices.

• Keywords
• Biosensors, Electrochemical impedance spectroscopy, Glycans, Influenza virus, Lectins, SAMs,
• MeSH
• Biosensing Techniques methods   MeSH
• Influenza, Human diagnosis   virology   MeSH
• Dielectric Spectroscopy methods   MeSH
• Humans MeSH
• Limit of Detection MeSH
• Polysaccharides chemistry   MeSH
• Influenza A Virus, H3N2 Subtype isolation & purification   MeSH
• Influenza A Virus, H7N7 Subtype isolation & purification   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Evaluation Study MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Polysaccharides MeSH