Febrile temperatures increase in vitro antibody affinity for malarial and dengue antigens

ThermoPCD: a database of molecular dynamics trajectories of antibody-antigen complexes at physiologic and fever-range temperatures

Progression of various cancers and autoimmune diseases is associated with changes in systemic or local tissue temperatures, which may impact current therapies. The role of fever and acute inflammation-range temperatures on the stability and activity of antibodies relevant for cancers and autoimmunity is unknown. To produce molecular dynamics (MD) trajectories of immune complexes at relevant temperatures, we used the Research Collaboratory for Structural Bioinformatics (RCSB) database to identify 50 antibody:antigen complexes of interest, in addition to single antibodies and antigens, and deployed Groningen Machine for Chemical Simulations (GROMACS) to prepare and run the structures at different temperatures for 100-500 ns, in single or multiple random seeds. MD trajectories are freely available. Processed data include Protein Data Bank outputs for all files obtained every 50 ns, and free binding energy calculations for some of the immune complexes. Protocols for using the data are also available. Individual datasets contain unique DOIs. We created a web interface, ThermoPCD, as a platform to explore the data. The outputs of ThermoPCD allow the users to relate thermally-dependent changes in epitopes:paratopes interfaces to their free binding energies, or against own experimentally derived binding affinities. ThermoPCD is a free to use database of immune complexes' trajectories at different temperatures that does not require registration and allows for all the data to be available for download. Database URL: https://sites.google.com/view/thermopcd/home.

Febrile temperatures modulate the formation of immune complexes relevant for autoimmune diseases

BACKGROUND

Autoimmune disorders encompass a diverse subset of diseases whose common symptoms include, among others, fever. Fever of unknown origins, once an infectious or tumor agent have been ruled out as possible causes, may originate with an autoimmune disease.

OBJECTIVE

To determine the role of febrile temperatures on the stability of antigens pertinent to autoimmunity, and on the immune complexes they form with commercial therapeutic monoclonal antibodies.

METHODS

Using molecular dynamics simulations, the binding between four antigens belonging to a set of autoimmune diseases and their individual monoclonal antibodies was investigated under different febrile temperatures.

RESULTS

It was determined that at febrile temperatures, monoclonal antibodies used in the therapy of autoimmune diseases bind with higher binding free energy to pertinent antigens, once the autoimmune condition has been established and treatment is warranted.

CONCLUSION

Performing molecular dynamics simulations at fever temperatures may be important for delineating the role antibodies may play in other diseases, including in cancers and infections.

Fever temperatures modulate intraprotein dynamics and enhance the binding affinity between monoclonal antibodies and the Spike protein from SARS-CoV-2

Fever is a typical symptom of most infectious diseases. While prolonged fever may be clinically undesirable, mild reversible fever (<39℃, 312 K) can potentiate the immune responses against pathogens. Here, using molecular dynamics and free energy calculations, we investigated the effect of febrile temperatures (38℃ to 40℃, 311 K to 313 K) on the immune complexes formed by the SARS-CoV-2 spike protein with two neutralizing monoclonal antibodies. In analyzing the conformational dynamics of the interactions between the antibodies and the spike protein under different thermal conditions, we found that, at mild fever temperatures (311–312 K), the binding affinities of the two antibodies improve when compared to the physiological body temperature (37℃, 310 K). Furthermore, only at 312 K, antibodies exert distinct mechanical effects on the receptor binding domains of the spike protein that may hinder SARS-CoV-2 infectivity. Enhanced antibody binding affinity may thus be obtained using appropriate temperature conditions.

Fever as an evolutionary agent to select immune complexes interfaces

We herein analyzed all available protein–protein interfaces of the immune complexes from the Protein Data Bank whose antigens belong to pathogens or cancers that are modulated by fever in mammalian hosts. We also included, for comparison, protein interfaces from immune complexes that are not significantly modulated by the fever response. We highlight the distribution of amino acids at these viral, bacterial, protozoan and cancer epitopes, and at their corresponding paratopes that belong strictly to monoclonal antibodies. We identify the “hotspots”, i.e. residues that are highly connected at such interfaces, and assess the structural, kinetic and thermodynamic parameters responsible for complex formation. We argue for an evolutionary pressure for the types of residues at these protein interfaces that may explain the role of fever as a selective force for optimizing antibody binding to antigens.

Fever temperatures impair hemolysis caused by strains of Escherichia coli and Staphylococcus aureus

Hemolysis modulates susceptibility to bacterial infections and predicts poor sepsis outcome. Hemolytic bacteria use hemolysins to induce erythrocyte lysis and obtain the heme that is essential for bacterial growth. Hemolysins are however potent immunogens and infections with hemolytic bacteria may cause a reversible fever response from the host that will aid in pathogen clearance. We hypothesized that fever temperatures impact the growth and infectivity of two hemolytic bacteria that are known to evoke fever in patients. To that end, we used high-sensitivity microcalorimetry to measure the evolution of heat production in fever-inducing strains of Escherichia coli and Staphylococcus aureus, under different temperature conditions. We determined specific bacterial aggregation profiles at temperatures equal to or exceeding 38.5 °C. Two melting temperatures peaks ranged from 38 °C to 43 °C for either species, a feature that we assigned to the formation of hemolysin aggregates of different oligomerization order. In order to measure the role of fever temperatures on hemolysis, we incubated the pathogens on blood agar plates at relevant temperatures, measuring the presence of hemolysis at 37 °C and its absence at 40.5 °C, respectively. We conclude that fever temperatures affect the kinetics of hemolysin pore formation and subsequently the hemolysis of red blood cells in vitro. We reveal the potential of microcalorimetry to monitor heat response from fever inducing bacterial species. Furthermore, these results help establish an additional positive role of febrile temperatures in modulating the immune response to infections, through the abolishment of hemolysis.

The role of temperature in the binding of the disordered epitope region of human thrombopoietin to antibody: A molecular dynamics simulations study

The N-terminal domain (163 residues) of Human thrombopoietin (hTPO) is highly conserved and responsible for the receptor-binding. The crystal structure of free hTPO is not yet available, but the crystal structure of its receptor-binding domain (hTPO₁₆₃) is available in complex with the TN1-Fab antibody. According to a thermodynamic study of hTPO₁₆₃ binding to TN1-Fab Ab, the ΔH value for binding becomes more negative with an increase in temperature from 283 K to 303 K. The objective of our study is to understand how the free hTPO₁₆₃ behaves dynamically and to study the effect of temperature on the association of hTPO₁₆₃ to TN1-Fab antibody through molecular dynamics simulations. We studied the Ag-Ab interactions at two different temperatures 298 K and 303 K. The discontinuous epitope region (residues 98-115) of free hTPO₁₆₃ displays a conformational switch and it gets stabilized upon binding to the Ab at 303 K. Based on our results, it may be surmised that the epitope region 98-115 is behaving like a disordered epitope. The disordered epitopes are known to be more efficient in binding with the antibody. We also find that, there is an increase in number of hydrogen-bonding interactions and hydrophobic contacts with an increase in the temperature from 298 K to 303 K. Thus, this observation explains a possible reason behind the more negative value of ΔH at the higher temperature 303 K as compared to 298 K.

Plasmonic Layer as a Localized Temperature Control Element for Surface Plasmonic Resonance-Based Sensors

Surface plasmon resonance (SPR) sensing is a well-established high-sensitivity, label-free and real-time detection technique for biomolecular interaction study. Its primary working principle consists of the measurement of the optical refractive index of the medium that is in close vicinity of the sensor surface. Bio-functionalization techniques allow biomolecular events to be located in such a way. Since optical refractive indices of any medium varies with the temperature, the place where the measurement takes place shall be within a temperature-controlled environment in order to ensure any temperature fluctuation is interpreted as a biomolecular event. Since the SPR measurement probes the sensed medium within the penetration depth of the plasmonic wave, which is less or in the order of 1 µm, we propose to use the metallic film constituting the detection surface as a localized heater aiming at controlling finely and quickly the temperature of the sensed medium. The Joule heating principle is then used and the modeling of the heater is reported as well as its validation by thermal IR imaging. Using water as a demonstration medium, SPR measurement results at different temperatures are successfully compared to the theoretical optical refractive index of water versus temperature.