A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer

ABSTRACT

We present a simple coarse-grained model of the effective interaction for charged amino acid residues, such as Glu and Lys, in a water solvent. The free-energy profile as a function of the distance between two charged amino acid side-chain analogues in an explicit water solvent is calculated with all-atom molecular dynamics simulation and thermodynamic integration method. The calculated free-energy profile is applied to the coarse-grained potential of the effective interaction between two amino acid residues. The Langevin dynamics simulations with our coarse-grained potential are performed for association of a small protein complex, GCN4-pLI tetramer. The tetramer conformation reproduced by our coarse-grained model is similar to the X-ray crystallographic structure. We show that the effective interaction between charged amino acid residues stabilises association and orientation of protein complex. We also investigate the association pathways of GCN4-pLI tetramer.     

Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect

ABSTRACT

We present a simple coarse-grained model with the molecular crowding effect in solvent to investigate the structure and dynamics of protein complexes including association and/or dissociation processes and investigate some physical properties such as the structure and the reaction rate from the viewpoint of the hydrophobic intermolecular interactions of protein complex. In the present coarse-grained model, a function depending upon the density of hydrophobic amino acid residues in a binding area of the complex is introduced, and the function involves the molecular crowding effect for the intermolecular interactions of hydrophobic amino acid residues between proteins. We propose a hydrophobic intermolecular potential energy between proteins by using the density-dependent function. The present coarse-grained model is applied to the complex of cytochrome f and plastocyanin by using the Langevin dynamics simulation to investigate some physical properties such as the complex structure, the electron transfer reaction rate constant from plastocyanin to cytochrome f and so on. We find that for proceeding the electron transfer reaction, the distance between metals in their active sites is necessary within about 18 Å. We discuss some typical complex structures formed in the present simulation in relation to the molecular crowding effect on hydrophobic interactions.     

Theoretical study of conformational transition of CDK4 by association of cyclin D3

ABSTRACT

We present coarse-grained simulations to investigate folding and association of cyclin-dependent kinase 4 (CDK4) with cyclin D3. In our simulations, the Gō-like model and our coarse-grained model are applied to describe intramolecular and intermolecular interaction of protein molecules, respectively. We investigate conformational stability of each state of CDK4 with/without association to cyclin D3 on a single basin potential with reference to each state of CDK4. The results of simulations for the native CDK4 with cyclin D3 are consistent with an experimental observation. The open CDK4 may associate to cyclin D3 on a different interface from cyclin D3-native CDK4 complex structure. If the open CDK4 associates to cyclin D3, the open CDK4 can slightly fold and become smaller, suggesting an unfolded intermediate. After a double-basin potential with reference to the native and open states of CDK4 is given, the open CDK4 associated with cyclin D3 can smoothly shift to the native CDK4. We propose a structure of a potential candidate of an unfolded intermediate during activation of CDK4.     

Information Loss in Coarse-Graining of Stochastic Particle Dynamics

Recently a new class of approximating coarse-grained stochastic processes and associated Monte Carlo algorithms were derived directly from microscopic stochastic lattice models for the adsorption/desorption and diffusion of interacting particles^(12,13,15). The resulting hierarchy of stochastic processes is ordered by the level of coarsening in the space/time dimensions and describes mesoscopic scales while retaining a significant amount of microscopic detail on intermolecular forces and particle fluctuations. Here we rigorously compute in terms of specific relative entropy the information loss between non-equilibrium exact and approximating coarse-grained adsorption/desorption lattice dynamics. Our result is an error estimate analogous to rigorous error estimates for finite element/finite difference approximations of Partial Differential Equations. We prove this error to be small as long as the level of coarsening is small compared to the range of interaction of the microscopic model. This result gives a first mathematical reasoning for the parameter regimes for which approximating coarse-grained Monte Carlo algorithms are expected to give errors within a given tolerance. MSC (2000) subject classifications: 82C80; 60J22; 94A17     

Study on the relationship between structure and taste activity of the umami peptide of Stropharia rugosoannulata prepared by ultrasound

Through virtual screening, electronic tongue verification, and molecular docking technology, the structure-taste activity relationship of 47 kinds of umami peptides (octapeptide - undecapeptide) from Stropharia rugosoannulata prepared by simultaneous ultrasonic-assisted directional enzymatic hydrolysis was analyzed. The umami peptides of S.rugosoannulata can form hydrogen bond interaction and electrostatic interaction with umami receptors T1R1/T1R3. The amino acid residues at the peptides' N-terminal and C-terminal play a vital role in binding with the receptors to form a stable complex. D, E, and R are the primary amino acids in the peptides that easily bind to T1R1/T1R3. The basic amino acid in the peptides is more easily bound to T1R1, and the acidic amino acid is more easily bound to T1R3. The active amino acid sites of the receptors to which the peptides bind account for 42%−65% of the total active amino acid residues in the receptors. ASP147 and ASP219 are the critical amino acid residues for T1R1 to recognize the umami peptides, and ARG64, GLU45, and GLU48 are the critical amino acid residues for T1R3 to recognize the umami peptides. The increase in the variety and quantity of umami peptides is the main reason for improving the umami taste of the substrate prepared by synchronous ultrasound-assisted directional enzymatic hydrolysis. This study provides a theoretical basis for understanding simultaneous ultrasound-assisted directional enzymatic hydrolysis for preparing umami peptides from S.rugosoannulata, enhancing the flavor of umami, and the relationship between peptide structure and taste activity.     

Spectroscopic study and application of the interaction mechanism of meloxicam with trypsin

Abstract

In order to explore the interaction between meloxicam and trypsin, the interaction mechanism between meloxicam and trypsin was studied by fluorescence spectrum, UV-vis absorption spectrum, circular dichroism spectrum, and molecular docking simulation under the experimental condition of pH = 7.40. The results of spectral experiments showed that meloxicam could effectively quench the internal fluorescence of trypsin in the form of static quenching, formed a stable complex at 1:1, and changed the conformation of trypsin. The results of thermodynamic constant showed that ΔG?H?S?>?0 indicates that the main force type of the binding system was hydrophobic interaction and hydrogen bonding. Molecular docking technique showed that the best binding site between meloxicam and trypsin was near the catalytic active center of trypsin, and the interaction between them changed the microenvironment of amino acid residues in the catalytic active center of trypsin. The mathematical model of drug and protein showed that when the concentration ratio of meloxicam to trypsin was 1:1, the protein binding rate of the binding system was 5.15%. The concentration ratio of meloxicam to trypsin was 30: 1, and the protein binding rate was 45.4%. The results showed that when the drug concentration was high, the binding effect of the system had a great influence on the concentration of free trypsin.     

Interaction of hen egg white lysozyme with cefpiramide sodium: multi-spectroscopic and computational simulations

Abstract

Under simulated physiological conditions (pH?=?7.40), the interaction between cefpiramide sodium and hen egg white lysozyme was studied with multi-spectroscopy and molecular docking. The results showed that cefpiramide sodium quenched the fluorescence of hen egg white lysozyme by static quenching, and the number of binding site n was about 1. The binding distance (r) between cefpiramide sodium and hen egg white lysozyme was obtained based on the Förster nonradioactive resonance energy transfer and r was less than 7?nm, which indicated that there was a non-radiative energy transition in the system. The thermodynamic parameters were obtained from the van't Hoff equation, and the Gibbs free energy ΔG?H?S?>?0, indicating hydrophobic interaction played a major role in forming the cefpiramide sodium-hen egg white lysozyme complex. Synchronous spectra, circular dichroism spectra and UV-Vis spectra showed that cefpiramide sodium changed the conformation of hen egg white lysozyme. The molecular docking results showed that the binding position of cefpiramide sodium was close to the active center composed of Asp52 and Glu35 residues, suggesting that cefpiramide sodium could change the microenvironment of amino acid residues at the catalytic active center of hen egg white lysozyme.     

Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines

Protein machines are clusters of protein assemblies that function in order to control the transfer of matter and energy in cells. For a specific protein machine, its working mechanisms are not only determined by the static crystal structures, but also related to the conformational transition dynamics and the corresponding energy profiles. With the rapid development of crystallographic techniques, the spatial scale of resolved structures is reaching up to thousands of residues, and the concomitant conformational changes become more and more complicated, posing a great challenge for computational biology research. Previously, a coarse-grained (CG) model aiming at conformational free energy evaluation was developed and showed excellent ability to reproduce the energy profiles by accurate electrostatic interaction calculations. In this study, we extended the application of the CG model to a series of large-scale protein machine systems. The spike protein trimer of SARS-CoV-2, ATP citrate lyase (ACLY) tetramer, and P4-ATPases systems were carefully studied and discussed as examples. It is indicated that the CG model is effective to depict the energy profiles of the conformational pathway between two endpoint structures, especially for large-scale systems. Both the energy change and energy barrier between endpoint structures provide reasonable mechanism explanations for the associated biological processes, including the opening of receptor binding domain (RBD) of spike protein, the phospholipid transportation of P4-ATPase, and the loop translocation of ACLY. Taken together, the CG model provides a suitable alternative in mechanistic studies related to conformational change in large-scale protein machines.     

Replicator Dynamics and Mathematical Description of Multi-Agent Interaction in Complex Systems

Abstract

We consider the general properties of the replicator dynamical system from the standpoint of its evolution and stability. Vector field analysis as well as spectral properties of such system has been studied. A Lyaponuv function for the investigation of the evolution of the system has been proposed. The generalization of replicator dynamics to the case of multi-agent systems is introduced. We propose a new mathematical model to describe the multi-agent interaction in complex system.     

Spectroscopic Identification of Interactions of Pb2+ with Bovine Serum Albumin

The effect of Pb²⁺ targeted to bovine serum albumin (BSA) in vitro was investigated by fluorescence, synchronous fluorescence, UV absorption and circular dichroism (CD) spectrophotometry. The characteristic fluorescence of BSA was quenched, which indicated that Pb²⁺ changed the skeleton of BSA and caused the gradual exposure of aromatic amino acid residues (Trp, Tyr, Phe) in the internal hydrophobic region of BSA. When the concentration of Pb²⁺ was higher than 1 × 10⁻⁴ mol/L, the BSA was completely denatured. The excess lead ion interacted with the aromatic amino acid residues of BSA exposed to the solution, which decreased the fluorescence of BSA further. According to the experiment results, we found that a lead-BSA complex was formed following static quenching and the binding site was calculated approximately equal to 1. This work reflected the interaction mechanism of BSA and Pb²⁺ from the perspective of spectroscopy.     

Computational studies on non-succinimide-mediated stereoinversion mechanism of aspartic acid residues assisted by phosphate

ABSTRACT

Although nearly all of the amino acids that constitute proteins are l-amino acids, d-amino acid residues in human proteins have been recently reported. d-amino acid residues cause a change in the three-dimensional structure of proteins, and d-aspartic acid (Asp) residues are considered to be one of the causes of age-related diseases. The stereoinversion of Asp residues in peptides and proteins is thought to proceed via a succinimide intermediate; however, it has been reported that stereoinversion can occur even under conditions where a succinimide intermediate cannot be formed. In order to elucidate the non-succinimide-mediated stereoinversion pathway, we investigated the stereoinversion of l-Asp to d-Asp catalysed by phosphate and estimated the activation barrier using B3LYP/6?31+G(d,p) density functional theory (DFT) calculations. For the DFT calculations, a model compound in which the Asp residue is capped with acetyl and methyl-amino groups on the N- and C-termini, respectively, was used. The calculated activation barrier was not excessively high for the stereoinversion to occur in vivo. Therefore, this stereoinversion mechanism may compete with the succinimide-mediated mechanism.     

Influence on drug efficacy of the binding behavior of pioglitazone hydrochloride with tryptophan residues,and tyrosine residues in bovine transferrin

Abstract

The interaction of pioglitazone hydrochloride bound to tryptophan residues and tyrosine residues in bovine transferrin was investigated using synchronous fluorescence spectroscopy at various temperatures (298, 310, and 318?K). From binding constants and thermodynamic parameters, it was shown that 1:1 stable compound was formed by the electrostatic force interaction of pioglitazone hydrochloride bound to tryptophan residues and tyrosine residues in bovine transferrin. The extent of binding between pioglitazone hydrochloride and tryptophan residues in bovine transferrin was more than that between pioglitazone hydrochloride and tyrosine residues in bovine transferrin. At 310?K, the fluorescence quenching ratio number of tyrosine residues and tryptophan residues in bovine transferrin were 47.52% and 54.19%, respectively, which indicated that the fluorescence contribution of tryptophan residues was greater. At 310?K, pioglitazone hydrochloride-tyrosine residues(in bovine transferrin) binding rate were 55.60–73.82%, and the combined model was W?=??0.0315R²???0.1520R?+?0.7385. The value of Hill’s coefficients was greater than 1, which suggested that there was a positive cooperativity between pioglitazone hydrochloride and subsequent ligands. The results of molecular docking were consistent with that of experimental calculation.     

Quantum chemical studies on a series of transition metal carbon dioxide complexes: Metal–carbon bonding and electronic structures

The bonding features and electronic structures of a series of transition metal carbon dioxide complexes have been studied by density functional theory (DFT) calculations combined with natural bond orbital (NBO) analysis and energy-decomposition analysis (EDA). NBO analysis shows that the interaction between the metal center and the carbon atom of the carbon dioxide ligand (M–C) is stronger than the other interaction between the metal center and the carbon dioxide ligand. Natural hybrid orbital (NHO) analysis gives the detailed bonding features of the M–C bond for each complex. The NBO charge distribution on the carbon dioxide unit in all studied complexes is negative, which indicates charge transfer from the metal center to the carbon dioxide ligand for all studied complexes. The hyperconjugation effect of the metal center and the two C–O bonds of the carbon dioxide ligand has been estimated using the NBO second-order perturbation stabilization energy. It was found that the NBO second-order stabilization energy of C–O?→?nM* is sensitive to the coordinated sphere and the metal center. Frontier molecular orbital (FMO) analysis shows that complexes 1 and 4 may be good nucleophilic reagents for activation of the carbon dioxide molecule. However, the EDAs show that the M–CO₂ bond interaction energy of complex 4 is about two times as large as that of complex 1. The high M–CO₂ bond interaction energy of complex 4 may limit its practical application.     

Interaction mechanisms of ionic liquids [Cnmim]Br (n=4, 6, 8, 10) with bovine serum albumin

It is important to study the interaction of ionic liquids (ILs) with protein for the applications of ILs in biochemical process, and help the researchers to choose and design the better ILs to serve as a solvent. In this work, the interaction between 1-alkyl-3-methylimidazolium bromide [C_nmim]Br (n=4, 6, 8, 10) and bovine serum albumin (BSA) was systematically investigated for the first time by multi-spectroscopic approach (fluorescence, UV–vis and FT-IR spectroscopy) and density functional theory (DFT). [C_nmim]Br (n=4, 6, 8, 10) can bind to BSA by H-bond interaction between their cationic headgroups and Asp/Glu amino acid residue at the surface of BSA, and hydrophobic interaction between their hydrocarbon chains and the hydrophobic amino acid residues in the interior of BSA. On the basis of thermodynamic parameters and the similar structure of [C_nmim]Br (n=4, 6, 8, 10), it can be inferred that the hydrophobic interaction plays a major role in the interaction of [C₁₀mim]Br with BSA, while the hydrogen bond and van der Waals force play a major role in the interaction of [C_nmim]Br (n=4, 6, 8) with BSA. Synchronous fluorescence and FT-IR spectra indicate that [C₁₀mim]Br could markedly change the secondary structure of BSA, while [C_nmim]Br (n=4, 6, 8) could slightly change the secondary structure of BSA. The results allowed us to understand (i) the effect of the alkyl chain length of the cation on the mechanism of ILs–protein interaction and (ii) the effect of the alkyl chain length of the cation on the protein secondary structure.     

Identification of functionally key residues in maltose transporter with an elastic network model-based thermodynamic method

Periplasmic binding protein-dependent maltose transport system (MBP-MalFGK₂) of Escherichia coli, an important member of the Adenosine triphosphate-binding cassette transporter superfamily, is in charge of the transportation of maltoses across cellular membrane. Studies have shown that this transport processes are activated by the binding of maltose and are accompanied by large-scale cooperative movements between different domains which are mediated by a network of important residues related to signal transduction and allosteric regulation. In this paper, the functionally crucial residues and long-range allosteric pathway of the regulation of the system by substrate were identified by utilising a coarse-grained thermodynamic method proposed by our group. The residues whose perturbations markedly change the binding free energy between maltoses and MBP-MalFGK₂ were considered to be key residues. In result, the key residues in 62 clusters distributed in different subdomains were identified successfully, and the results from our calculation are highly consistent with experimental and theoretical observations. Furthermore, we explored the long-range cooperation within the transporter. These studies will help us better understand the physical mechanism of the effects of the maltose on MBP-MalFGK₂ by long-range allosteric modulation.     

Modeling hydrogen exchange of proteins by a multiscale method

We proposed a practical way for mapping the results of coarse-grained molecular simulations to the observables in hydrogen change experiments. By combining an atomic-interaction based coarse-grained model with an all-atom structure reconstruction algorithm, we reproduced the experimental hydrogen exchange data with reasonable accuracy using molecular dynamics simulations. We also showed that the coarse-grained model can be further improved by imposing experimental restraints from hydrogen exchange data via an iterative optimization strategy. These results suggest that it is feasible to develop an integrative molecular simulation scheme by incorporating the hydrogen exchange data into the coarse-grained molecular dynamics simulations and therefore help to overcome the accuracy bottleneck of coarse-grained models.     

Pairing mechanism in the doped Hubbard antiferromagnet: the 4×4 model as a test case

We introduce a local formalism, in terms of eigenstates of number operators, having well defined point symmetry, to solve the Hubbard model at weak coupling on a N × N square lattice (for even N). The key concept is that of W = 0 states, that are the many-body eigenstates of the kinetic energy with vanishing Hubbard repulsion. At half filling, the wave function demonstrates an antiferromagnetic order, a lattice step translation being equivalent to a spin flip. Further, we state a general theorem which allows to find all the W = 0 pairs (two-body W = 0 singlet states). We show that, in special cases, this assigns the ground state symmetries at least in the weak coupling regime. The N = 4 case is discussed in detail. To study the doped half filled system, we enhance the group theory analysis of the 4×4 Hubbard model introducing an Optimal Group which explains all the degeneracies in the one-body and many-body spectra. We use the Optimal Group to predict the possible ground state symmetries of the 4×4 doped antiferromagnet by means of our general theorem and the results are in agreement with exact diagonalization data. Then we create W = 0 electron pairs over the antiferromagnetic state. We show analitycally that the effective interaction between the electrons of the pairs is attractive and forms bound states. Computing the corresponding binding energy we are able to definitely predict the exact ground state symmetry. Received 24 October 2000     

Hydration effects on enzyme–substrate complex of nylon oligomer hydrolase: inter-fragment interaction energy study by the fragment molecular orbital method

Fragment molecular orbital calculations were successfully applied to a nylon oligomer hydrolase, NylB, to investigate the hydration effects on an enzyme–substrate binding structure. Statistically corrected inter-fragment interaction energy analyses were performed on this system to quantitatively characterise the interactions between the substrate, 6-aminohexanoate linear dimer (ALD), and the amino acid residues, such as Asp181, Ser112, and Ile 345, which are regarded as important for enzyme–substrate complex formation by NylB. We found that the direct interaction between ALD and NylB is weakened by hydration, because water molecules cause charge translation or polarisation of ALD or each amino acid residue. However, including the interaction energy between ALD and water molecules greatly stabilises this complex. These results indicate the importance of the hydration effects in enzyme–substrate complex formation.