Binding Rate Constants Research Articles

Light and corona: guided-wave readout for coronavirus spike protein-host-receptor binding.

We show that waveguide sensors can enable a quantitative characterization of coronavirus spike glycoprotein-host-receptor binding-the process whereby coronaviruses enter human cells, causing disease. We demonstrate that such sensors can help quantify and eventually understand kinetic and thermodynamic properties of viruses that control their affinity to targeted cells, which is known to significantly vary in the course of virus evolution, e.g., from SARS-CoV to SARS-CoV-2, making the development of virus-specific drugs and vaccine difficult. With the binding rate constants and thermodynamic parameters as suggested by the latest SARS-CoV-2 research, optical sensors of SARS-CoV-2 spike protein-receptor binding may be within sight.

Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors

Understanding the mechanism of action of compounds capable of inhibiting amyloid-fibril formation is critical to the development of potential therapeutics against protein-misfolding diseases. A fundamental challenge for progress is the range of possible target species and the disparate timescales involved, since the aggregating proteins are simultaneously the reactants, products, intermediates, and catalysts of the reaction. It is a complex problem, therefore, to choose the states of the aggregating proteins that should be bound by the compounds to achieve the most potent inhibition. We present here a comprehensive kinetic theory of amyloid-aggregation inhibition that reveals the fundamental thermodynamic and kinetic signatures characterizing effective inhibitors by identifying quantitative relationships between the aggregation and binding rate constants. These results provide general physical laws to guide the design and optimization of inhibitors of amyloid-fibril formation, revealing in particular the important role of on-rates in the binding of the inhibitors.

In situ monitoring of the selective adsorption mechanism of small environmental pollutant molecules on aptasensor interface by attenuated total reflection surface enhanced infrared absorption spectroscopy (ATR–SEIRAS)

In situ monitoring of the interactions and properties of pollutant molecules at the aptasensor interface is being a very hot and interesting topic in environmental analysis since its charming molecule level understanding of the mechanism of environmental biosensors. Attenuated total reflection surface enhanced infrared absorption spectroscopy (ATR–SEIRAS) provides a unique and convenient technique for the in situ analysis, but is not easy for small molecules. Herein, an ATR–SEIRAS platform has been successfully developed to in situ monitor the selective adsorption mechanism of small pollutant molecule atrazine (ATZ) on the aptasensor interface by characteristic N‒H peak of ATZ for the first time. Based on the constructed ATR–SEIRAS platform, a thermodynamics model is established for the selective adsorption of ATZ on the aptasensor interface, described with Langmuir adsorption with a dissociation constant of 1.1 nM. The adsorption kinetics parameters are further obtained with a binding rate constant of 8.08×105 M−1 s−1. A promising and feasible platform has therefore successfully provided for the study of the selective sensing mechanism of small pollutant molecules on biosensors interfaces, further broadening the application of ATR–SEIRAS technology in the field of small pollutant molecules.

Cadherin clusters stabilized by a combination of specific and nonspecific cis-interactions.

We demonstrate a combined experimental and computational approach for the quantitative characterization of lateral interactions between membrane-associated proteins. In particular, weak, lateral (cis) interactions between E-cadherin extracellular domains tethered to supported lipid bilayers, were studied using a combination of dynamic single-molecule Förster Resonance Energy Transfer (FRET) and kinetic Monte Carlo (kMC) simulations. Cadherins are intercellular adhesion proteins that assemble into clusters at cell-cell contacts through cis- and trans- (adhesive) interactions. A detailed and quantitative understanding of cis-clustering has been hindered by a lack of experimental approaches capable of detecting and quantifying lateral interactions between proteins on membranes. Here single-molecule intermolecular FRET measurements of wild-type E-cadherin and cis-interaction mutants combined with simulations demonstrate that both nonspecific and specific cis-interactions contribute to lateral clustering on lipid bilayers. Moreover, the intermolecular binding and dissociation rate constants are quantitatively and independently determined, demonstrating an approach that is generalizable for other interacting proteins.

Complete Dynamic Reconstruction of C60, C70, and (C59N)2 Encapsulation into an Adaptable Supramolecular Nanocapsule.

The dynamic adaptability of tetragonal prismatic nanocapsule 18+ in the selective separation of fullerenes and endohedral metallofullerenes (EMFs) remains unexplored. Therefore, the essential molecular details of the fullerene recognition and binding process into the coordination capsule and the origins of fullerene selectivity remain elusive. In this work, the key steps of fullerene recognition and binding processes have been deciphered by designing a protocol which combines 1H-1H exchange spectroscopy (2D-EXSY) NMR experiments, long time-scale Molecular Dynamics (MD) and accelerated Molecular Dynamics (aMD) simulations, which are combined to completely reconstruct the spontaneous binding and unbinding pathways from nanosecond to second time-range. On one hand, binding (k'on) and unbinding (koff) rate constants were extracted from 1H-1H exchange spectroscopy (EXSY) NMR experiments for both C60 and C70. On the other hand, MD and aMD allowed monitoring the molecular basis of the encapsulation and guest competition processes at a very early stage under nonequilibrium conditions. The receptor capsule displays dynamical adaptability features similar to those observed in the process of biomolecular recognition in proteins. In addition, the encapsulation of bis-aza[60]fullerene (C59N)2 within a supramolecular coordination capsule has been studied for the first time, showcasing the pros and cons of the dumbbell-shaped guest in the dynamics of the encapsulation process and in the stability of the final bound adduct. The powerful combination of NMR, MD, and aMD methodologies allows to obtain a precise picture of the subtle events directing the encapsulation and is thus a predictive tool for understanding host-guest encapsulation and interactions in numerous supramolecular systems.

Hysteresis and bistability in the succinate-CoQ reductase activity and reactive oxygen species production in the mitochondrial respiratory complex II

The mitochondrial respiratory Complex II (CII) is one of key enzymes of cell energy metabolism, linking the tricarboxylic acid (TCA) cycle and the electron transport chain (ETC). CII reversibly oxidizes succinate to fumarate in the TCA cycle and transfers the electrons, produced by this reaction to the membrane quinone pool, providing ubiquinol QH2 to ETC. CII is also known as a generator of reactive oxygen species (ROS).It was shown experimentally that succinate can serve as not only a substrate in the forward succinate-quinone oxidoreductase (SQR) direction, but also an enzyme activator. Molecular and kinetic mechanisms of this property of CII are still unclear.In order to account for activation of CII by succinate in the forward SQR direction, we developed and analyzed a computational mechanistic model of electron transfer and ROS formation in CII. It was found that re-binding of succinate to the unoccupied dicarboxylate binding site when FAD is reduced with subsequent oxidation of FADH2 creates a positive feedback loop in the succinate oxidation. The model predicts that this positive feedback can result in hysteresis and bistable switches in SQR activity and ROS production in CII. This requires that the rate constant of re-binding of succinate has to be higher than the rate constant of the initial succinate binding to the active center when FAD is oxidized.Hysteresis and bistability in the SQR activity and ROS production in CII can play an important physiological role. In the presence of hysteresis with two stable branches with high and low SQR activity, high SQR activity is maintained even with a very strong drop in the succinate concentration, which may be necessary in the process of cell functioning in stressful situations. For the same reason, a high stationary rate of ROS production in CII can be maintained at low succinate concentrations.

Reverse transcriptase kinetics for one-step RT-PCR

Understanding reverse transcriptase (RT) activity is critical for designing fast one-step RT-PCRs. We report a stopped-flow assay that monitors SYBR Green I fluorescence to investigate RT activity in PCR conditions. We studied the influence of PCR conditions on RT activity and assessed the accuracy of cDNA synthesis predictions for one-step RT-PCR.Nucleotide incorporation increased from 26 to 89 s−1 between 1.5 and 6 mM MgCl2 but was largely unaffected by changes in KCl. Conversely, increasing KCl from 15 to 75 mM increased apparent rate constants for RT-oligonucleotide binding (0.010–0.026 nM−1 s−1) and unbinding (0.2–1.5 s−1). All rate constants increased between 22 and 42 °C.When evaluated by PCR quantification cycle, cDNA predictions differed from experiments using RNase H+ RT (average 1.7 cycles) and RNase H- (average 4.5 cycles). Decreasing H+ RT concentrations 10 to 104-fold from manufacturer recommendations improved cDNA predictions (average 0.8 cycles) and increased RT-PCR assay efficiency.RT activity assays and models can be used to aid assay design and improve the speed of RT-PCRs. RT type and concentration must be selected to promote rapid cDNA synthesis but minimize nonspecific amplification. We demonstrate 2-min one-step RT-PCR of a Zika virus target using reduced RT concentrations and extreme PCR.

Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach.

To improve lead optimization efforts in finding the right ligand, pharmaceutical industries need to know the ligand's binding kinetics, such as binding and unbinding rate constants, which often correlate with the ligand's efficacy in vivo. To predict binding kinetics efficiently, enhanced sampling methods, such as milestoning and the weighted ensemble (WE) method, have been used in molecular dynamics (MD) simulations of these systems. However, a comparison of these enhanced sampling methods in ranking ligands has not been done. Hence, a WE approach called the concurrent adaptive sampling (CAS) algorithm that uses MD simulations was used to rank seven ligands for β-cyclodextrin, a system in which a multiscale milestoning approach called simulation enabled estimation of kinetic rates (SEEKR) was also used, which uses both MD and Brownian dynamics simulations. Overall, the CAS algorithm can successfully rank ligands using the unbinding rate constant koff values and binding free energy ΔG values, as SEEKR did, with reduced computational cost that is about the same as SEEKR. We compare the CAS algorithm simulations with different parameters and discuss the impact of parameters in ranking ligands and obtaining rate constant and binding free energy estimates. We also discuss similarities and differences and advantages and disadvantages of SEEKR and the CAS algorithm for future use.

Species differences in cellular processing of siRNA‐Lipid complex

Lipid‐based nanocarriers provide a means to deliver nucleic acid therapeutics such as short interfering RNA (siRNA); a major challenge is the low success rate in preclinical‐to‐clinical translation. siRNA gene knockdown depends on its ability to reach the intracellular target RISC (RNA Induced Silencing Complex, degrades the targeted mRNA), and is hence determined by the kinetics of multiple cellular processes (see below). The present project used experimental and computational studies to investigate the species differences in the processing of siRNA‐lipid complex (Lipoplex).Experiments were performed using human breast MCF7 tumor cells transfected with Rab5, a marker for early endosomes (EE). Cells were treated with Lipoplex (with fluorescence‐labeled siRNA and lipids), in the presence of fetal bovine serum, mouse plasma, or rat plasma. Pilot studies showed that mouse and human plasma had similar effects on Lipoplex destabilization, cellular uptake and gene knockdown. Time lapse live cell confocal microscopy was used to monitor Lipoplex cellular binding, endocytosis, and siRNA release, every 10 min for 2 h. The results were analyzed using quantitative image analysis for the amounts of siRNA and lipids in individual regions of interest. Over 95% of intracellular siRNA+lipid signals in the first 10 min were co‐localized with Rab5, confirming Lipoplex was endocytosed into EE. Some intracellular siRNA+lipid signals were no longer associated with Rab5 after 30 min, indicating Lipoplex progression through the endocytic pathway. Of the Rab5‐co‐localizaing siRNA+lipid signals, the siRNA‐to‐lipid ratio (Ratio) decreased with time (up to 3‐fold between 10 to 90 min), whereas Ratio in the signals not co‐localizing with Rab5 was up to 4‐fold lower. These findings indicate continuous release of free siRNA from Lipoplex while in EE. A quantitative pharmacology or QP model was developed to describe the first order kinetics of Lipoplex transfer between extracellular fluid/cell membrane/intracellular endocytic organelles and siRNA release into the cytosol. The model assumptions were (a) extracellular Lipoplex destabilization due to interactions with plasma/serum proteins, (b) rapid degradation of free siRNA released from Lipoplex, (c) two pools of membrane‐associated Lipoplex (internalized and not internalized), and (d) Lipoplex degradation/elimination in late endosomes or lysosomes. Fitting the QP model to experimental results yielded the rate constants.We found significant species differences, i.e., 2‐ to >15‐fold variations in rate constants for Lipoplex binding to cell membrane, internalization, release of siRNA into cytosol, and elimination. These results suggest a need of accounting for species differences in cellular processing of Lipoplex during animal‐to‐human translation. This study further demonstrates the utility of QP in difficult‐to‐measure subcellular kinetic processes.Support or Funding InformationSupported in part by research grants (RO1CA158300, RO1CA163015, RO1EB015253) from NCI and NIBIB, and by Mosier Chair of Pharmaceutical Sciences.

Abstract A98: Molecular dynamics study of pH-dependent interactions between immune checkpoint receptor PD-1 and PD-L1

Abstract Understanding of how small variations in checkpoint protein chemistry (e.g., mutations) and tumor immune microenvironment (e.g., pH) influence receptor-ligand binding and define both the mechanisms and magnitude of immune response is of great importance, but the molecular details are still missing. Here, we employ enhanced free-energy sampling molecular dynamics simulations to unveil pH-dependent binding/unbinding mechanisms and kinetics of PD-1/PD-L1 interactions. By identifying the binding pocket in the PD-1/PD-L1 complex, we show a key role of the His68 protonation state in PD-1 in the complex stabilization at low pH. Specifically, we estimate the unbinding free-energy barrier to be around 15 kJ/mol higher at pH 5.5 than at pH 7.4. The estimated ratio of binding (kon) and unbinding (koff) rate constants is found to agree well with recent experimental data on KD values at different pH. Also, simulations show an important role of solvation state of the binding pocket in mediating polar interactions at the PD-1/PD-L1 binding interface. These initial molecular insights are important for further engineering of binding/unbinding kinetics to formulate more efficient immune checkpoint blockade strategies. Citation Format: Vitaly Alexandrov, Konstantin Klyukin. Molecular dynamics study of pH-dependent interactions between immune checkpoint receptor PD-1 and PD-L1 [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2018 Nov 27-30; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(4 Suppl):Abstract nr A98.

Mechanistic Roles of Electrostatic Interactions in the Molecular Recognition of Intrinsically Disordered Proteins

Electrostatic interactions could play important roles in the molecular recognition process of intrinsically disordered proteins (IDPs) as many IDPs and the recognition elements contain charged residues. Previous studies have demonstrated that electrostatic forces could accelerate the encounter process via electrostatic steering effect and increase the efficiency of binding upon encounter for several IDPs. To further investigate the universal role of electrostatic interactions in IDPs molecular recognition, we collected the experimentally determined binding kinetics of IDPs. For many studied IDPs, the association rate constants are reduced for about ten folds when the salt concentration increases from low (~50 mM) to high (~500 mM), indicating the presence of favorable electrostatic interactions. We further performed molecular dynamics simulations using structure‐based coarse‐grained models. Simulations predicted that long‐range electrostatic interactions accelerate the binding rate in a range consistent with experimental results. Simulations also revealed that electrostatic forces generally enhance the binding kinetics by increasing the encounter rate and by enhancing the evolving efficiency. Correlating the charge density with binding kinetics revealed that the overall charge density is relate with enhancement of the capture rate constant and the charge distribution affects both the evolution rate constant and escape rate constant. Analysis of the transition path times showed that electrostatic interactions stabilize the intermediate state along the binding process. Besides affecting the binding kinetics, electrostatic interactions also redistributed the flux among multiple parallel binding transition paths. As a summary, our results suggest that favorable electrostatic interactions are present in many IDPs recognition processes. Under physiological salt concentrations, electrostatic interactions are expected to enhance the binding rate constant by several folds.Support or Funding InformationThis work was supported by Hubei University of Technology

Assessing the binding properties of the anti-PD-1 antibody landscape using label-free biosensors.

Here we describe an industry-wide collaboration aimed at assessing the binding properties of a comprehensive panel of monoclonal antibodies (mAbs) against programmed cell death protein 1 (PD-1), an important checkpoint protein in cancer immunotherapy and validated therapeutic target, with well over thirty unique mAbs either in clinical development or market-approved in the United States, the European Union or China. The binding kinetics of the PD-1/mAb interactions were measured by surface plasmon resonance (SPR) using a Carterra LSA instrument and the results were compared to data collected on a Biacore 8K. The effect of chip type on the SPR-derived binding rate constants and affinities were explored and the results compared with solution affinities from Meso Scale Discovery (MSD) and Kinetic Exclusion Assay (KinExA) experiments. When using flat chip types, the LSA and 8K platforms yielded near-identical kinetic rate and affinity constants that matched solution phase values more closely than those produced on 3D-hydrogels. Of the anti-PD-1 mAbs tested, which included a portion of those known to be in clinical development or approved, the affinities spanned from single digit picomolar to nearly 425 nM, challenging the dynamic range of our methods. The LSA instrument was also used to perform epitope binning and ligand competition studies which revealed over ten unique competitive binding profiles within this group of mAbs.

Single-Molecule Studies of HIV-1 Gag Assembly

Gag is the key structural protein that mediates assembly of nascent HIV-1 virions around viral genomic RNA. Previous studies have established that Gag can spontaneously assemble around a variety of nucleic acid substrates into immature virus-like particles in vitro. Additionally, substrates which include the Psi signal, a small structural element found in the 5’ UTR of the HIV-1 genome, are selectively packaged over other substrates. In fact, the Psi signal is required for selective packaging of the genomic RNA over the large background of other RNAs in the cellular milieu. However, the mechanism of this assembly process and interactions with the Psi signal that lead to specificity are poorly understood. Here we have developed a single-molecule total internal reflection fluorescence microscopy assay to monitor the earliest steps of particle assembly under controlled conditions. Individual fluorescently-labeled Gag monomers are resolved as they spontaneously bind to and dissociate from immobilized RNA substrates derived from the genomic 5’ UTR. Statistical analysis of multiple single-molecule time trajectories allowed for the determination of the relative populations of various assembly intermediates along with rate constants for individual binding and dissociation steps. Experiments were performed under a variety of conditions including varied protein concentrations, mutations to Gag and the RNA substrates, and with proposed small-molecule cofactors present. Taken together, the results from these experiments elucidate details of molecular interactions involved in the initiation of particle assembly that may be opaque to other methodologies.

Ranking of Ligand Binding Kinetics using a Weighted Ensemble Approach and Comparison with Milestoning

In order to improve lead optimization efforts in finding the right ligand, pharmaceutical industries need to know the ligand's binding kinetics, such as binding and unbinding rate constants, which are known to be good indicators of the ligand's efficacy in vivo. To predict binding kinetics quickly, enhanced sampling methods, such as milestoning and the weighted ensemble (WE) method, have been used in molecular dynamics (MD) simulations of these systems. However, a direct comparison of the enhanced sampling methods in ranking ligands has not been done. Hence, a WE approach called the concurrent adaptive sampling (CAS) algorithm was used to rank seven ligands for beta-cyclodextrin, a system in which a milestoning approach called simulation enabled estimation of kinetic rates (SEEKR) was also used. Overall, the CAS algorithm can successfully rank ligands using the unbinding rate constants koff's and binding free energies, as SEEKR did, with reduced computational cost that is about the same as SEEKR. We discuss "best practices" for using WE approaches like the CAS algorithm and pros and cons of each enhanced sampling method for future use.

Determination of Binding Kinetics of Intrinsically Disordered Proteins by Surface Plasmon Resonance.

Surface plasmon resonance (SPR) is an important and convenient method for measuring kinetic rate constants of given molecular interactions, equilibrium binding constants at steady state, or determinations of binding stoichiometry. In its traditional setup, SPR requires that one binding partner is tightly immobilized on the surface of a sensor chip either by direct chemical coupling to the surface-coated carboxymethylated dextran matrix or by non-covalent capture to a high-affinity binding partner that is covalently linked to the surface. The latter design of the sensor surface is highly advantageous compared to the direct chemical coupling as this setup ensures a homogeneous and specific orientation of the immobilized binding partner. This chapter provides guidelines for the design of capturing systems that generally provide high-end kinetic data suitable for determination of binding rate constants. This principle will be illustrated by the binding of synthetic peptides derived from an intrinsically disordered region of the endothelial glycosylphosphatidylinositol-anchored high-density lipoprotein binding protein 1 (GPIHBP1) to captured monoclonal antibodies.

Biodistribution of orally administered 99mTc-heparin to assess eosinophilic esophagitis associated inflammation

Here we explore the biodistribution of 99mTc-heparin, an orally administered radiopharmaceutical candidate expected to identify localized inflammation in eosinophilic esophagitis (EoE). Heparin binds to eosinophil granule proteins in inflamed regions of gastrointestinal (GI) organs, and 99mTc signals their location. This article evaluates the biodistribution of this conjugate first within the esophagus by modeling the reactive transport of 99mTc-heparin based on the kinetics of 99mTc-heparin binding to non-human primate esophagi and second in the remainder of the body by measuring organ specific uptake using single-photon emission computed tomography/computed tomography imaging. Results show that binding and dissociation rate constants remain similar, and that optimal imaging occurs after drinking of the agent is complete. We also find that 99mTc-heparin remains within the GI tract simply transporting through the gut and out. These findings provide a new avenue to clinically explore the utility of 99mTc-heparin to detect eosinophil associated inflammation in the GI tract.

Interface Interaction Behavior of Self-Terminated Oligomer Electrode Additives for a Ni-Rich Layer Cathode in Lithium-Ion Batteries: Voltage and Temperature Effects.

Self-terminated oligomer additives synthesized from bismaleimide and barbituric acid derivatives improve the safety and performance of lithium-ion batteries (LIBs). This study investigates the interface interaction of these additives and the cathode material. Two additives were synthesized by Michael addition (additive A) and aza-Michael addition (additive B). The electrochemical performances of bare and modified LiNi0.6Mn0.2Co0.2O2 (NMC622) materials are studied. The cycling stability and rate capability of NMC622 considerably improve on surface modification with additive B. According to the differential scanning calorimetry results, the exothermic heat of fully deliathiated NMC622 is dramatically decreased through surface modification with both additives. The electrode surface kinetics and interface interaction phenomena of the additives are determined through surface plasma resonance measurements in operando gas chromatography-mass spectroscopy (GCMS) and in situ soft X-ray absorption spectroscopy (XAS). The binding rate constant of additive B onto NMC622 particles is 1.2-2.3 × 104 M-1 s-1 in the temperature range of 299-311 K, which is ascribed to the strong binding affinity toward the electrode surface. This affinity enhances Li+ diffusion, which allows the electrode modified by additive B to provide high electrochemical performance with superior thermal stability. In operando GCMS reveals that gas evolution due to the electrolyte degradation at the NMC622 surface contributes to safety hazards in the bare NMC622 material. In situ soft XAS indicates the occurrence of structural transformation in the bare NMC622 material after it is fully charged and at elevated temperatures. The NMC622 material is stabilized by incorporating additives. The unique performance of additive B can be attributed to its linear structure that allows superior electrode surface adhesion compared with that of additive A. Therefore, this study presents an optimized working principle of self-terminated oligomers, which can be developed and applied to improve the safety and performance of LIBs.

Cover Feature: Ligand Binding Rate Constants in Heme Proteins Using Markov State Models and Molecular Dynamics Simulations (ChemPhysChem 19/2019)

Cover Feature: Ligand Binding Rate Constants in Heme Proteins Using Markov State Models and Molecular Dynamics Simulations (ChemPhysChem 19/2019)

Ligand Binding Rate Constants in Heme Proteins Using Markov State Models and Molecular Dynamics Simulations.

Computer simulation studies of the molecular basis for ligand migration in proteins allow the description of key events such as the transition between docking sites, displacement of existing ligands and solvent molecules, and open/closure of specific "gates", among others. In heme proteins, ligand migration from the solvent to the active site preludes the binding to the heme iron and triggers different functions. In this work, molecular dynamics simulations, a Markov State Model of migration and empirical kinetic equations are combined to study the migration of O2 and NO in two truncated hemoglobins of Mycobacterium tuberculosis (Mt-TrHbN and Mt-TrHbO). For Mt-TrHbN, we show that the difference in the association constant in the oxy and deoxy states relies mainly in the displacement of water molecules anchored in the distal cavity in the deoxy form. The results here provide a valuable approach to study ligand migration in globins.

Does the single-walled carbon nanotube affect the rate constant of binding of biotin to streptavidin? Molecular dynamics simulation perspective

The interaction of biotin and streptavidin in the presence and absence of a carbon nanotube was studied by molecular dynamics simulation. With respect to the Arrhenius dependence of the rate constants with temperature, those of streptavidin–biotin complex formation ([Formula: see text]) and streptavidin–biotin complex dissociation ([Formula: see text]) were calculated from molecular dynamics simulation trajectories. Nanotube has reduced the amount of and k1and k1. However, the biotin position in streptavidin does not change much. The results obtained from MMPBSA calculations show that the contribution of the van der Waals forces to both systems (in the absence and presence of the nanotube) was greater than that of electrostatic forces. The presence of the nanotube also led to the reduction of van der Waals and electrostatic forces in the interaction of biotin with streptavidin. However, this reduction was greater for electrostatic forces. In the absence of a nanotube, there are four hydrogen bonds between streptavidin and biotin, which are related to the residues Ser27, Tyr43, Ser45 and Ser88. In the presence of the nanotube, the hydrogen bonding of biotin with Ser45 is removed.