Entropic contribution to enhanced thermal stability in the thermostable P450 CYP119

The enhanced thermostability of thermophilic proteins with respect to their mesophilic counterparts is often attributed to the enthalpy effect, arising from strong interactions between protein residues. Intuitively, these strong interresidue interactions will rigidify the biomolecules. However, the present work utilizing neutron scattering and solution NMR spectroscopy measurements demonstrates a contrary example that the thermophilic cytochrome P450, CYP119, is much more flexible than its mesophilic counterpart, CYP101A1, something which is not apparent just from structural comparison of the two proteins. A mechanism to explain this apparent contradiction is that higher flexibility in the folded state of CYP119 increases its conformational entropy and thereby reduces the entropy gain during denaturation, which will increase the free energy needed for unfolding and thus stabilize the protein. This scenario is supported by thermodynamic data on the temperature dependence of unfolding free energy, which shows a significant entropic contribution to the thermostability of CYP119 and lends an added dimension to enhanced stability, previously attributed only to presence of aromatic stacking interactions and salt bridge networks. Our experimental data also support the notion that highly thermophilic P450s such as CYP119 may use a mechanism that partitions flexibility differently from mesophilic P450s between ligand binding and thermal stability.

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D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect

Molecules ◽

10.3390/molecules26092622 ◽

2021 ◽

Vol 26 (9) ◽

pp. 2622

Author(s):

Romina Oliva ◽

Abdul Rajjak Shaikh ◽

Andrea Petta ◽

Anna Vangone ◽

Luigi Cavallo

Keyword(s):

Three Dimensional ◽

Salt Bridge ◽

Structural Effect ◽

Host Cells ◽

Heptad Repeat ◽

Genomic Sequences ◽

Strong Interactions ◽

Virus Infectivity ◽

S Protein ◽

Global Threat

The crown of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is constituted by its spike (S) glycoprotein. S protein mediates the SARS-CoV-2 entry into the host cells. The “fusion core” of the heptad repeat 1 (HR1) on S plays a crucial role in the virus infectivity, as it is part of a key membrane fusion architecture. While SARS-CoV-2 was becoming a global threat, scientists have been accumulating data on the virus at an impressive pace, both in terms of genomic sequences and of three-dimensional structures. On 15 February 2021, from the SARS-CoV-2 genomic sequences in the GISAID resource, we collected 415,673 complete S protein sequences and identified all the mutations occurring in the HR1 fusion core. This is a 21-residue segment, which, in the post-fusion conformation of the protein, gives many strong interactions with the heptad repeat 2, bringing viral and cellular membranes in proximity for fusion. We investigated the frequency and structural effect of novel mutations accumulated over time in such a crucial region for the virus infectivity. Three mutations were quite frequent, occurring in over 0.1% of the total sequences. These were S929T, D936Y, and S949F, all in the N-terminal half of the HR1 fusion core segment and particularly spread in Europe and USA. The most frequent of them, D936Y, was present in 17% of sequences from Finland and 12% of sequences from Sweden. In the post-fusion conformation of the unmutated S protein, D936 is involved in an inter-monomer salt bridge with R1185. We investigated the effect of the D936Y mutation on the pre-fusion and post-fusion state of the protein by using molecular dynamics, showing how it especially affects the latter one.

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Salt-bridge networks within globular and disordered proteins: characterizing trends for designable interactions

Journal of Molecular Modeling ◽

10.1007/s00894-017-3376-y ◽

2017 ◽

Vol 23 (7) ◽

Cited By ~ 17

Author(s):

Sankar Basu ◽

Debasish Mukharjee

Keyword(s):

Salt Bridge ◽

Disordered Proteins ◽

Bridge Networks

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A Possible Mechanism of Graphene Oxide to Enhance Thermostability of D-Psicose 3-Epimerase Revealed by Molecular Dynamics Simulations

International Journal of Molecular Sciences ◽

10.3390/ijms221910813 ◽

2021 ◽

Vol 22 (19) ◽

pp. 10813

Author(s):

Congcong Li ◽

Zhongkui Lu ◽

Min Wang ◽

Siao Chen ◽

Lu Han ◽

...

Keyword(s):

Molecular Dynamics ◽

Thermal Stability ◽

Graphene Oxide ◽

Md Simulations ◽

Strong Interactions ◽

Limiting Factor ◽

Active Site Residues ◽

Detailed Mechanism ◽

Dynamics Simulations ◽

Thermal Stability Of

Thermal stability is a limiting factor for effective application of D-psicose 3-epimerase (DPEase) enzyme. Recently, it was reported that the thermal stability of DPEase was improved by immobilizing enzymes on graphene oxide (GO) nanoparticles. However, the detailed mechanism is not known. In this study, we investigated interaction details between GO and DPEase by performing molecular dynamics (MD) simulations. The results indicated that the domain (K248 to D268) of DPEase was an important anchor for immobilizing DPEase on GO surface. Moreover, the strong interactions between DPEase and GO can prevent loop α1′-α1 and β4-α4 of DPEase from the drastic fluctuation. Since these two loops contained active site residues, the geometry of the active pocket of the enzyme remained stable at high temperature after the DPEase was immobilized by GO, which facilitated efficient catalytic activity of the enzyme. Our research provided a detailed mechanism for the interaction between GO and DPEase at the nano–biology interface.

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Molecular dynamics complemented by site-directed mutagenesis reveals significant difference between the interdomain salt bridge networks stabilizing oligopeptidases B from bacteria and protozoa in their active conformations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2019.1692694 ◽

2019 ◽

Vol 38 (16) ◽

pp. 4868-4882 ◽

Cited By ~ 1

Author(s):

Dmitry E. Petrenko ◽

Anna G. Mikhailova ◽

Vladimir I. Timofeev ◽

Yulia К. Agapova ◽

David M. Karlinsky ◽

...

Keyword(s):

Molecular Dynamics ◽

Salt Bridge ◽

Site Directed Mutagenesis ◽

Directed Mutagenesis ◽

Significant Difference ◽

Bridge Networks

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Finite-temperature effects in enzymatic reactions — Insights from QM/MM free-energy simulations

Canadian Journal of Chemistry ◽

10.1139/v09-092 ◽

2009 ◽

Vol 87 (10) ◽

pp. 1322-1337 ◽

Cited By ~ 48

Author(s):

Hans Martin Senn ◽

Johannes Kästner ◽

Jürgen Breidung ◽

Walter Thiel

Keyword(s):

Free Energy ◽

Finite Temperature ◽

Temperature Effects ◽

Density Functional ◽

Umbrella Sampling ◽

Chorismate Mutase ◽

Enzymatic Reactions ◽

Energy Data ◽

Energy Simulations ◽

Entropic Contribution

We report potential-energy and free-energy data for three enzymatic reactions: carbon–halogen bond formation in fluorinase, hydrogen abstraction from camphor in cytochrome P450cam, and chorismate-to-prephenate Claisen rearrangement in chorismate mutase. The results were obtained by combined quantum mechanics/molecular mechanics (QM/MM) optimizations and two types of QM/MM free-energy simulations (free-energy perturbation and umbrella sampling) using semi-empirical or density-functional QM methods. Based on these results and our previously published free-energy data on electrophilic substitution in para-hydroxybenzoate hydroxylase, we discuss the importance of finite-temperature effects in the chemical step of enzyme reactions. We find that the entropic contribution to the activation barrier is generally rather small, usually of the order of 5 kJ mol–1 or less, consistent with the notion that enzymes bind and pre-organize the reactants in the active site. A somewhat larger entropic contribution is encountered in the case of chorismate mutase where the pericyclic transition state is intrinsically more rigid than the chorismate reactant (also in the enzyme). The present results suggest that barriers from QM/MM geometry optimization may often be close to free-energy barriers for the chemical step in enzymatic reactions.

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Structure and Properties of Composite Films of Cellulose and Chitosan from Ionic Liquid

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.499.80 ◽

2012 ◽

Vol 499 ◽

pp. 80-84

Author(s):

Huai Fang Wang ◽

Wei Han Huang ◽

Zhi Kai Wang

Keyword(s):

Mechanical Properties ◽

Thermal Stability ◽

Ionic Liquid ◽

Antimicrobial Property ◽

Composite Films ◽

Antibacterial Properties ◽

Strong Interactions ◽

Structure And Properties ◽

Blend Films ◽

Methyl Imidazole

A series of blend films of cellulose and chitosan were prepared from 1-ethyl-3-methyl imidazole acetate ([Emim] Ac) by coagulating with ethanol. Structure, mechanical properties, thermal stability and antibacterial properties were investigated. The results showed that there were strong interactions and good compatibility between cellulose and chitosan in blend films. The blend films possess good mechanical properties and thermal stability, and the existence of chitosan endows blend films with antimicrobial property.

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Solution NMR Spectroscopy as a Useful Tool to Investigate Colloidal Nanocrystal Dispersions from the Capping Ligand's Point of View

MRS Proceedings ◽

10.1557/proc-984-0984-mm14-07 ◽

2006 ◽

Vol 984 ◽

Author(s):

Jose C Martins ◽

Iwan Moreels ◽

Zeger Hens

Keyword(s):

Quantum Dots ◽

Free Energy ◽

Field Gradient ◽

Dynamic Equilibrium ◽

Semiconductor Nanocrystals ◽

Point Of View ◽

Solution Nmr ◽

Free Energy Of Adsorption ◽

Ligand Interaction ◽

Pulsed Field

AbstractColloidal semiconductor nanocrystals or quantum dots are an important building block in bottom-up nanotechnology. They consist of an inorganic, crystalline core surrounded by a monolayer of organic ligands. As these ligands can be modified or exchanged for others, they provide a convenient way to give the quantum dots functionality. Here, we show that solution NMR techniques, including diffusion pulsed field gradient spectroscopy, is a very useful tool to investigate the ligands of colloidal nanocrystals. This is demonstrated using InP quantum dots with trioctylphospine oxide ligands as an example. Combining 1H-13C HSQC spectroscopy with pulsed field gradient diffusion NMR, an unequivocal identification of the resonances of the bound ligands is possible. This leads to the determination of the diffusion coefficient of the nanocrystals in solution and allows to verify capping exchange procedures. By calibrating the surface area of the NMR resonances using a solute of known concentration, the density of ligands at the nanocrystal surface can be quantified. We could demonstrate that a dynamic equilibrium exists between bound and free ligands. Analysis of the corresponding adsorption isotherm - determined using 1H NMR - leads to an estimation of the free energy of adsorption and the free energy of ligand-ligand interaction at the nanocrystals surface. Similar investigations are in progress on capped PbSe and ZnO2 nanoparticles. Preliminary results strongly support the generic nature of the approach described for the case of TOPO capped InP nanocrystals.

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Electrospun Silk-Boron Nitride Nanofibers with Tunable Structure and Properties

Polymers ◽

10.3390/polym12051093 ◽

2020 ◽

Vol 12 (5) ◽

pp. 1093

Author(s):

Ye Xue ◽

Xiao Hu

Keyword(s):

Thermal Stability ◽

Boron Nitride ◽

Hexagonal Boron Nitride ◽

Environmental Research ◽

Strong Interactions ◽

Helical Structures ◽

Scanning Calorimetry ◽

Modulated Differential Scanning Calorimetry ◽

Good Thermal Stability ◽

Thermal Stability Of

In this study, hexagonal boron nitride (h-BN) nanosheets and Bombyx mori silk fibroin (SF) proteins were combined and electrospun into BNSF nanofibers with different ratios. It was found that the surface morphology and crosslinking density of the nanofibers can be tuned through the mixing ratios. Fourier transform infrared spectroscopy study showed that pure SF electrospun fibers were dominated by random coils and they gradually became α-helical structures with increasing h-BN nanosheet content, which indicates that the structure of the nanofiber material is tunable. Thermal stability of electrospun BNSF nanofibers were largely improved by the good thermal stability of BN, and the strong interactions between BN and SF molecules were revealed by temperature modulated differential scanning calorimetry (TMDSC). With the addition of BN, the boundary water content also decreased, which may be due to the high hydrophobicity of BN. These results indicate that silk-based BN composite nanofibers can be potentially used in biomedical fields or green environmental research.

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Molecular Dynamics Simulation of Barnase: Contribution of Noncovalent Intramolecular Interaction to Thermostability

Mathematical Problems in Engineering ◽

10.1155/2013/504183 ◽

2013 ◽

Vol 2013 ◽

pp. 1-12 ◽

Cited By ~ 1

Author(s):

Zhiguo Chen ◽

Yi Fu ◽

Wenbo Xu ◽

Ming Li

Keyword(s):

Molecular Dynamics ◽

Thermal Stability ◽

Molecular Dynamics Simulation ◽

Root Mean Square ◽

Clinical Medicine ◽

Intramolecular Interaction ◽

Salt Bridge ◽

Dynamics Simulation ◽

Mean Square ◽

Thermal Stability Of

Bacillus amyloliquefaciensribonuclease Barnase (RNase Ba) is a 12 kD (kilodalton) small extracellular ribonuclease. It has broad application prospects in agriculture, clinical medicine, pharmaceutical, and so forth. In this work, the thermal stability of Barnase has been studied using molecular dynamics simulation at different temperatures. The present study focuses on the contribution of noncovalent intramolecular interaction to protein stability and how they affect the thermal stability of the enzyme. Profiles of root mean square deviation and root mean square fluctuation identify thermostable and thermosensitive regions of Barnase. Analyses of trajectories in terms of secondary structure content, intramolecular hydrogen bonds and salt bridge interactions indicate distinct differences in different temperature simulations. In the simulations, Four three-member salt bridge networks (Asp8-Arg110-Asp12, Arg83-Asp75-Arg87, Lys66-Asp93-Arg69, and Asp54-Lys27-Glu73) have been identified as critical salt bridges for thermostability which are maintained stably at higher temperature enhancing stability of three hydrophobic cores. The study may help enlighten our knowledge of protein structural properties, noncovalent interactions which can stabilize secondary peptide structures or promote folding, and also help understand their actions better. Such an understanding is required for designing efficient enzymes with characteristics for particular applications at desired working temperatures.

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