Delicate balance among thermal stability, binding affinity, and conformational space explored by single-domain VHH antibodies

AbstractThe high binding affinities and specificities of antibodies have led to their use as drugs and biosensors. Single-domain VHH antibodies exhibit high specificity and affinity but have higher stability and solubility than conventional antibodies as they are single-domain proteins. In this work, based on physicochemical measurements and molecular dynamics (MD) simulations, we have gained insight that will facilitate rational design of single-chain VHH antibodies. We first assessed two homologous VHH antibodies by differential scanning calorimetry (DSC); one had a high (64.8 °C) and the other a low (58.6 °C) melting temperature. We then generated a series of the variants of the low stability antibody and analyzed their thermal stabilities by DSC and characterized their structures through MD simulations. We found that a single mutation that resulted in 8.2 °C improvement in melting temperature resulted in binding affinity an order of magnitude lower than the parent antibody, likely due to a shift of conformational space explored by the single-chain VHH antibody. These results suggest that the delicate balance among conformational stability, binding capability, and conformational space explored by antibodies must be considered in design of fully functional single-chain VHH antibodies.

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UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations

Bioinformatics ◽

10.1093/bioinformatics/btaa897 ◽

2020 ◽

Cited By ~ 1

Author(s):

Paweł Krupa ◽

Agnieszka S Karczyńska ◽

Magdalena A Mozolewska ◽

Adam Liwo ◽

Cezary Czaplewski

Keyword(s):

Protein Complexes ◽

Md Simulations ◽

Protein Docking ◽

Conformational Space ◽

Coarse Grained ◽

Supplementary Information ◽

Replica Exchange ◽

Variable Degree ◽

Single Chain ◽

Simulation Speed

Abstract Motivation The majority of the proteins in living organisms occur as homo- or hetero-multimeric structures. Although there are many tools to predict the structures of single-chain proteins or protein complexes with small ligands, peptide–protein and protein–protein docking is more challenging. In this work, we utilized multiplexed replica-exchange molecular dynamics (MREMD) simulations with the physics-based heavily coarse-grained UNRES model, which provides more than a 1000-fold simulation speed-up compared with all-atom approaches to predict structures of protein complexes. Results We present a new protein–protein and peptide–protein docking functionality of the UNRES package, which includes a variable degree of conformational flexibility. UNRES-Dock protocol was tested on a set of 55 complexes with size from 43 to 587 amino-acid residues, showing that structures of the complexes can be predicted with good quality, if the sampling of the conformational space is sufficient, especially for flexible peptide–protein systems. The developed automatized protocol has been implemented in the standalone UNRES package and in the UNRES server. Availability and implementation UNRES server: http://unres-server.chem.ug.edu.pl; UNRES package and data used in testing of UNRES-Dock: http://unres.pl. Supplementary information Supplementary data are available at Bioinformatics online.

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Improved scFv Anti-HIV-1 p17 Binding Affinity Guided from the Theoretical Calculation of Pairwise Decomposition Energies and Computational Alanine Scanning

BioMed Research International ◽

10.1155/2013/713585 ◽

2013 ◽

Vol 2013 ◽

pp. 1-12 ◽

Cited By ~ 6

Author(s):

Panthip Tue-ngeun ◽

Kanchanok Kodchakorn ◽

Piyarat Nimmanpipug ◽

Narin Lawan ◽

Sawitree Nangola ◽

...

Keyword(s):

Interaction Energy ◽

Binding Affinity ◽

Theoretical Calculations ◽

Single Mutation ◽

Single Chain ◽

Alanine Scanning ◽

Single Chain Fv ◽

Residue Interaction ◽

Computational Alanine Scanning ◽

Hiv 1

Computational approaches have been used to evaluate and define important residues for protein-protein interactions, especially antigen-antibody complexes. In our previous study, pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants has indicated the key specific residues in the complementary determining regions (CDRs) of scFv anti-p17. In this present investigation in order to determine whether a specific side chain group of residue in CDRs plays an important role in bioactivity, computational alanine scanning has been applied. Molecular dynamics simulations were done with several complexes of original scFv anti-p17 and scFv anti-p17mutants with HIV-1 p17 epitope variants with a production run up to 10 ns. With the combination of pairwise decomposition residue interaction and alanine scanning calculations, the point mutation has been initially selected at the position MET100 to improve the residue binding affinity. The calculated docking interaction energy between a single mutation from methionine to either arginine or glycine has shown the improved binding affinity, contributed from the electrostatic interaction with the negative favorably interaction energy, compared to the wild type. Theoretical calculations agreed well with the results from the peptide ELISA results.

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Predicting substitutions to modulate disorder and stability in coiled-coils

BMC Bioinformatics ◽

10.1186/s12859-020-03867-x ◽

2020 ◽

Vol 21 (S19) ◽

Author(s):

Yasaman Karami ◽

Paul Saighi ◽

Rémy Vanderhaegen ◽

Denis Gerlier ◽

Sonia Longhi ◽

...

Keyword(s):

Measles Virus ◽

Rational Design ◽

Tertiary Structure ◽

Md Simulations ◽

Coiled Coils ◽

Conformational Space ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

The Stability ◽

The Impact

Abstract Background Coiled-coils are described as stable structural motifs, where two or more helices wind around each other. However, coiled-coils are associated with local mobility and intrinsic disorder. Intrinsically disordered regions in proteins are characterized by lack of stable secondary and tertiary structure under physiological conditions in vitro. They are increasingly recognized as important for protein function. However, characterizing their behaviour in solution and determining precisely the extent of disorder of a protein region remains challenging, both experimentally and computationally. Results In this work, we propose a computational framework to quantify the extent of disorder within a coiled-coil in solution and to help design substitutions modulating such disorder. Our method relies on the analysis of conformational ensembles generated by relatively short all-atom Molecular Dynamics (MD) simulations. We apply it to the phosphoprotein multimerisation domains (PMD) of Measles virus (MeV) and Nipah virus (NiV), both forming tetrameric left-handed coiled-coils. We show that our method can help quantify the extent of disorder of the C-terminus region of MeV and NiV PMDs from MD simulations of a few tens of nanoseconds, and without requiring an extensive exploration of the conformational space. Moreover, this study provided a conceptual framework for the rational design of substitutions aimed at modulating the stability of the coiled-coils. By assessing the impact of four substitutions known to destabilize coiled-coils, we derive a set of rules to control MeV PMD structural stability and cohesiveness. We therefore design two contrasting substitutions, one increasing the stability of the tetramer and the other increasing its flexibility. Conclusions Our method can be considered as a platform to reason about how to design substitutions aimed at regulating flexibility and stability.

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Hierarchy of π-Stacking Determines the Conformational Preference of Bis-Squaraines

10.26434/chemrxiv.13041830.v1 ◽

2020 ◽

Author(s):

Abhishek Singh ◽

Reman K. Singh ◽

G Naresh Patwari

Keyword(s):

Hydrogen Bonding ◽

Rational Design ◽

Biological Molecules ◽

Conformational Space ◽

X Ray Crystallography ◽

Simple Strategy ◽

Induced Folding ◽

Π Stacking ◽

Varying Length ◽

Dynamics Simulations

The rational design of conformationally controlled foldable modules can lead to a deeper insight into the conformational space of complex biological molecules where non-covalent interactions such as hydrogen bonding and π-stacking are known to play a pivotal role. Squaramides are known to have excellent hydrogen bonding capabilities and hence, are ideal molecules for designing foldable modules that can mimic the secondary structures of bio-molecules. The π-stacking induced folding of bis-squaraines tethered using aliphatic primary and secondary-diamine linkers of varying length is explored with a simple strategy of invoking small perturbations involving the length linkers and degree of substitution. Solution phase NMR investigations in combination with molecular dynamics simulations suggest that bis-squaraines predominantly exist as extended conformations. Structures elucidated by X-ray crystallography confirmed a variety of folded and extended secondary conformations including hairpin turns and 𝛽-sheets which are determined by the hierarchy of π-stacking relative to N–H···O hydrogen bonds.

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Hierarchy of π-Stacking Determines the Conformational Preference of Bis-Squaraines

10.26434/chemrxiv.13041830 ◽

2020 ◽

Author(s):

Abhishek Singh ◽

Reman K. Singh ◽

G Naresh Patwari

Keyword(s):

Hydrogen Bonding ◽

Rational Design ◽

Biological Molecules ◽

Conformational Space ◽

X Ray Crystallography ◽

Simple Strategy ◽

Induced Folding ◽

Π Stacking ◽

Varying Length ◽

Dynamics Simulations

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Faculty Opinions recommendation of Energetically important C-H···F-C pseudohydrogen bonding in water: evidence and application to rational design of oligonucleotides with high binding affinity.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.7475956.7770054 ◽

2011 ◽

Author(s):

Martin Egli

Keyword(s):

Binding Affinity ◽

Rational Design ◽

High Binding ◽

High Binding Affinity

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On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

Polymers ◽

10.3390/polym13010099 ◽

2020 ◽

Vol 13 (1) ◽

pp. 99

Author(s):

Cristian Privat ◽

Sergio Madurga ◽

Francesc Mas ◽

Jaime Rubio-Martínez

Keyword(s):

Molecular Dynamics ◽

Amino Acids ◽

Md Simulations ◽

Point Of View ◽

Conformational Space ◽

Conformational Sampling ◽

Protonation State ◽

Constant Ph ◽

Biochemical Systems ◽

Constant Ph Molecular Dynamics

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.

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Conformational Ensembles by NMR and MD Simulations in Model Heptapeptides with Select Tri-Peptide Motifs

International Journal of Molecular Sciences ◽

10.3390/ijms22031364 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1364

Author(s):

V. V. Krishnan ◽

Timothy Bentley ◽

Alina Xiong ◽

Kalyani Maitra

Keyword(s):

Principal Component ◽

Md Simulations ◽

Conformational Space ◽

Random Coil ◽

Radius Of Gyration ◽

Small Peptides ◽

Conformational Ensembles ◽

Solution State ◽

Peptide Motifs ◽

Explicit Solvent

Both nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations are routinely used in understanding the conformational space sampled by peptides in the solution state. To investigate the role of single-residue change in the ensemble of conformations sampled by a set of heptapeptides, AEVXEVG with X = L, F, A, or G, comprehensive NMR, and MD simulations were performed. The rationale for selecting the particular model peptides is based on the high variability in the occurrence of tri-peptide E*L between the transmembrane β-barrel (TMB) than in globular proteins. The ensemble of conformations sampled by E*L was compared between the three sets of ensembles derived from NMR spectroscopy, MD simulations with explicit solvent, and the random coil conformations. In addition to the estimation of global determinants such as the radius of gyration of a large sample of structures, the ensembles were analyzed using principal component analysis (PCA). In general, the results suggest that the -EVL- peptide indeed adopts a conformational preference that is distinctly different not only from a random distribution but also from other peptides studied here. The relatively straightforward approach presented herein could help understand the conformational preferences of small peptides in the solution state.

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Computational and Rational Design of Single-Chain Antibody against Tick-Borne Encephalitis Virus for Modifying Its Specificity

Viruses ◽

10.3390/v13081494 ◽

2021 ◽

Vol 13 (8) ◽

pp. 1494

Author(s):

Ivan K. Baykov ◽

Pavel Y. Desyukevich ◽

Ekaterina E. Mikhaylova ◽

Olga M. Kurchenko ◽

Nina V. Tikunova

Keyword(s):

Rational Design ◽

Fold Increase ◽

Encephalitis Virus ◽

Chimeric Antibody ◽

Single Chain ◽

Single Chain Antibody ◽

Glycoprotein E ◽

Tick Borne Encephalitis ◽

Tick Borne Encephalitis Virus ◽

Far Eastern

Tick-borne encephalitis virus (TBEV) causes 5−7 thousand cases of human meningitis and encephalitis annually. The neutralizing and protective antibody ch14D5 is a potential therapeutic agent. This antibody exhibits a high affinity for binding with the D3 domain of the glycoprotein E of the Far Eastern subtype of the virus, but a lower affinity for the D3 domains of the Siberian and European subtypes. In this study, a 2.2-fold increase in the affinity of single-chain antibody sc14D5 to D3 proteins of the Siberian and European subtypes of the virus was achieved using rational design and computational modeling. This improvement can be further enhanced in the case of the bivalent binding of the full-length chimeric antibody containing the identified mutation.

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High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

Chemical Science ◽

10.1039/d1sc00145k ◽

2021 ◽

Author(s):

Théo Jaffrelot Inizan ◽

Frédéric Célerse ◽

Olivier Adjoua ◽

Dina El Ahdab ◽

Luc-Henri Jolly ◽

...

Keyword(s):

Molecular Dynamics ◽

High Resolution ◽

Adaptive Sampling ◽

Force Fields ◽

Sampling Strategy ◽

Md Simulations ◽

Conformational Space ◽

Many Body ◽

Polarizable Force Fields ◽

Main Protease

We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFFs).

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