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A novel empirical free energy function that explains and predicts protein–protein binding affinities

Joseph Audie, Suzanne Scarlata
2007 Biophysical Chemistry  
We used the function to blindly and successfully predict binding affinities for a diverse test set of 31 wild-type protein-protein and protein-peptide complexes (R 2 = 0.79, rmsd = 1.2 kcal mol − 1 ).  ...  Free energy functions can be used to explain and predict the affinity of a ligand for a protein and to score and discriminate between native and non-native binding modes.  ...  Hence, Eq. (12) can be used to accurately predict binding affinities for a range of protein complexes and this, in turn, improves our confidence in the theoretical, statistical and physical legitimacy  ... 
doi:10.1016/j.bpc.2007.05.021 pmid:17600612 fatcat:4rg2c7y6njcntdjzp6e244qxhu

Recent progress in the study of G protein-coupled receptors with molecular dynamics computer simulations

Alan Grossfield
2011 Biochimica et Biophysica Acta - Biomembranes  
In particular, molecular dynamics simulations have become a driving factor in many areas of GPCR biophysics, improving our understanding of lipid-protein interaction, activation mechanisms, and internal  ...  G protein-coupled receptors (GPCRs) are a large, biomedically important family of proteins, and the recent explosion of new high-resolution structural information about them has provided an enormous opportunity  ...  Tod Romo for help making figures and Tod Romo, Nick Leioatts, Josh Horn, and Mark Dumont for critical comments on the manuscript.  ... 
doi:10.1016/j.bbamem.2011.03.010 pmid:21443858 fatcat:33gq5w7b4ncfhkjh3kqdbh6aoi

Utilising Structural Knowledge in Drug Design Strategies: Applications Using Relibase

Judith Günther, Andreas Bergner, Manfred Hendlich, Gerhard Klebe
2003 Journal of Molecular Biology  
We discuss representative examples to address issues such as protein flexibility, water molecules in binding pockets, and ligand specificity as some of the most critical aspects of drug design.  ...  But our knowledge is enhanced also when studying the specific determinants that characterise single targets or target families only, and the factors governing and discriminating their recognition properties  ...  We thank all partners in this project for a fruitful and successful collaboration.  ... 
doi:10.1016/s0022-2836(02)01409-2 pmid:12559927 fatcat:prmd7vod6ffu3kiyys4bzhbw6e

Computationally-predicted CB1 cannabinoid receptor mutants show distinct patterns of salt-bridges that correlate with their level of constitutive activity reflected in G protein coupling levels, thermal stability, and ligand binding

Kwang H. Ahn, Caitlin E. Scott, Ravinder Abrol, William A. Goddard, Debra A. Kendall
2013 Proteins: Structure, Function, and Bioinformatics  
Thus, we demonstrate an excellent correlation with the predicted pattern of key salt-bridges and experimental levels of activity and conformational flexibility.  ...  In contrast, breaking the D2.63 + K3.28 salt-bridge produced the opposite profile suggesting this interaction is critical for the receptor activation.  ...  We then experimentally constructed these mutants to break these salt-bridges and found that they exhibit substantial shifts in G protein coupling, thermal stability, and ligand binding affinity relative  ... 
doi:10.1002/prot.24264 pmid:23408552 pmcid:PMC4872635 fatcat:nceqck53mzbcvlycloar56thx4

Extrapolating the effect of deleterious nsSNPs in the binding adaptability of flavopiridol with CDK7 protein: a molecular dynamics approach

C George Priya Doss, N Nagasundaram, Chiranjib Chakraborty, Luonan Chen, Hailong Zhu
2013 Human Genomics  
d the native protein and proposed mutant models in atomic level using MD approach, and (3) investigated the protein-ligand interactions to analyze the binding ability by docking analysis.  ...  Conclusion: This theoretical approach is entirely based on computational methods, which has the ability to identify the disease-related SNPs in complex disorders by contrasting their costs and capabilities  ...  Salt bridge forming distances of wild type and mutant structures of CDK7 protein. The ordinate is distance (nm) and the abscissa is time (ps).  ... 
doi:10.1186/1479-7364-7-10 pmid:23561625 pmcid:PMC3726351 fatcat:uhvi67xu6vg2nhbj7si3cleyzu

Nanomaterial interactions with biomembranes: Bridging the gap between soft matter models and biological context

Marco Werner, Thorsten Auth, Paul A. Beales, Jean Baptiste Fleury, Fredrik Höök, Holger Kress, Reid C. Van Lehn, Marcus Müller, Eugene P. Petrov, Lev Sarkisov, Jens-Uwe Sommer, Vladimir A. Baulin
2018 Biointerphases  
et al (2018) Nanomaterial interactions with biomembranes: Bridging the gap between soft matter models and biological context Biointerphases, 13(2) http://dx.  ...  Theoretical and experimental model systems may systematically include next levels of complexity: active components such as enzymes, solvent complexity and cosolvency, the nano-object's interplay with proteins  ...  Before disentangling all contributions in biological environments, however, it will be interesting to investigate wrapping and endocytosis as a function of tension in model experiments with reduced complexity  ... 
doi:10.1116/1.5022145 pmid:29614862 fatcat:4rncj3fdizaapmzctbmuchi7e4

Statistics and Physical Origins of pK and Ionization State Changes upon Protein-Ligand Binding

Boris Aguilar, Ramu Anandakrishnan, Jory Z. Ruscio, Alexey V. Onufriev
2010 Biophysical Journal  
This work investigates statistical prevalence and overall physical origins of changes in charge states of receptor proteins upon ligand binding.  ...  ionizable residues in protein-small molecule complexes, 9% in protein-protein, and 12% in protein-nucleic acid complexes experience a substantial pK change upon ligand binding.  ...  The authors thank Jane Richardson for helpful comments, and Emil Alexov for a stimulating discussion. This work was supported in part by National Institutes of Health grant No. R01-GM076121.  ... 
doi:10.1016/j.bpj.2009.11.016 pmid:20197041 pmcid:PMC2830434 fatcat:f6lreahwubbmtlx5eqyqeort6m

Quantitative Description of Polyethylene Glycol in an Alpha-Hemolysin Pore

Arvind Balijepalli, Joesph E. Reiner, Joseph W.F. Robertson, John J. Kasianowicz, Richard W. Pastor
2013 Biophysical Journal  
We present a systematic study of pores bridging the gap between these regimes and evaluating their detection parameters as they relate to pore geometry.  ...  Successful detection experiments involving nanoparticles have largely relied on high-aspect-ratio pores prepared in glass or polymers and, most recently, low-aspect-ratio solid-state pores.  ...  Based on statistics and current amplitude distributions, we are able to identify three such deeply blocked states, each corresponding to the simultaneous presence in the pore of two ligands: either 2xPEG  ... 
doi:10.1016/j.bpj.2012.11.2885 fatcat:wvbqbeykkfcpxpxl62mxpace3u

Phosphorylation of the Retinoic Acid Receptor Alpha Induces a Mechanical Allosteric Regulation and Changes in Internal Dynamics

Yassmine Chebaro, Ismail Amal, Natacha Rochel, Cécile Rochette-Egly, Roland H. Stote, Annick Dejaegere, Marta Filizola
2013 PLoS Computational Biology  
The results show that phosphorylation leads to a reorganization of a local salt bridge network, which induces changes in helix extension and orientation that affects the cyclin H binding site.  ...  Nuclear receptor proteins constitute a superfamily of proteins that function as ligand dependent transcription factors.  ...  Dino Moras and Prof. Bruno Kieffer of the Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) and Dr.  ... 
doi:10.1371/journal.pcbi.1003012 pmid:23637584 pmcid:PMC3630199 fatcat:2fzfjdzukzgovfgddxmgo7okfe

Capturing a crucial 'disorder-to-order transition' at the heart of the coronavirus molecular pathology – triggered by highly persistent, interchangeable salt-bridges [article]

Sourav Roy, Prithwi Ghosh, Abhirup Bandyapadhyay, Sankar Basu
2021 bioRxiv   pre-print
The study further shows the formation of dynamically interchangeable and persistent networks of salt-bridges at the Spike-Furin interface in SARS-CoV-2 involving the three arginines (R682, R683, R685)  ...  Multiplicity and structural degeneracy of plausible salt-bridge network archetypes seems the other key characteristic features of the Spike-Furin binding in SARS-CoV-2 allowing the system to breathe -  ...  Acknowledgment and Funding We convey our sincerest gratitude to Prof. Raghavan Varadarajan, Molecular Biophysics Unit, IISc, Bangalore, India and Prof.  ... 
doi:10.1101/2021.12.29.474439 fatcat:eeu7zh64nre5lk34xf6qnyyqqy

Profiling the Interaction Mechanism of Quinoline/Quinazoline Derivatives as MCHR1 Antagonists: An in Silico Method

Mingwei Wu, Yan Li, Xinmei Fu, Jinghui Wang, Shuwei Zhang, Ling Yang
2014 International Journal of Molecular Sciences  
MD simulations in both water and lipid bilayer systems were performed.  ...  In addition, docking studies and molecular dynamics (MD) simulations were carried out for further elucidation of the binding modes of MCHR1 antagonists.  ...  To the best of our knowledge, this is the first time the role of Tyr272 and Ile100 in hydrogen bonds is noticed in the ligand-MCHR1 complex. (4) In general, a salt bridge with Asp123, several H-bonds with  ... 
doi:10.3390/ijms150915475 pmid:25257526 pmcid:PMC4200842 fatcat:6inmv7gkerg6boyqbskl6yqln4

Cation–π interactions in protein–ligand binding: theory and data-mining reveal different roles for lysine and arginine

Kiran Kumar, Shin M. Woo, Thomas Siu, Wilian A. Cortopassi, Fernanda Duarte, Robert S. Paton
2018 Chemical Science  
and a systematic meta-analysis of X-ray structures.  ...  The interactions of neutral aromatic ligands with cationic arginine, histidine and lysine amino acid residues have been studied with ab initio calculations, symmetry adapted perturbation theory (SAPT),  ...  We acknowledge the EPSRC Centre for Doctoral Training in Theory and Modelling in Chemical Sciences (EP/L015722/1) and use of the Dirac cluster at Oxford.  ... 
doi:10.1039/c7sc04905f pmid:29719674 pmcid:PMC5903419 fatcat:5w6qblh2xngf5hwjf2rplbbbsu

Unexpected features in the Protein Data Bank entries 3qd1 and 4i8e: the structural description of the binding of the serine-rich repeat adhesin GspB to host cell carbohydrate receptor is not a solved issue

Yves A. Muller
2013 Acta Crystallographica. Section F : Structural Biology and Crystallization Communications  
These interactions can easily be interpreted as salt bridges, namely one salt bridge being formed between the sulfonate group of HEPES and Arg484 (distance HEPES O2S to Arg484 NH1 = 3.05 Å , Table 1  ...  (c) Following a single round of refinement, the HEPES molecule becomes well defined by its electron density and contacts protein residues via two salt bridges via Arg484 and Glu401 0 from a symmetry-related  ... 
doi:10.1107/s1744309113014383 pmid:24100551 pmcid:PMC3792659 fatcat:jp3dm2tzxbchjnmd7gfvnn4rcq

Binding Mechanism of the N-Terminal SH3 Domain of CrkII and Proline-Rich Motifs in cAbl

Veer S. Bhatt, Danyun Zeng, Inna Krieger, James C. Sacchettini, Jae-Hyun Cho
2016 Biophysical Journal  
upon the complex formation, and water molecules structured in the binding interface of the nSH3:PRM complex.  ...  The interaction between CrkII and cAbl kinase is involved in the regulation of cell spreading, microbial pathogenesis, and cancer metastasis.  ...  Salt-bridges between the acidic residues in nSH3 domain and K -3 of PRM 758 are shown as dashed lines.  ... 
doi:10.1016/j.bpj.2016.05.008 pmid:27332121 pmcid:PMC4919510 fatcat:6huaoxs53reihef4z6f3vonpzy

Theoretical Modeling of Chemical Equilibrium in Weak Polyelectrolyte Layers on Curved Nanosystems

Estefania Gonzalez Solveyra, Rikkert J. Nap, Kai Huang, Igal Szleifer
2020 Polymers  
cues like pH and salt concentration.  ...  They are also ubiquitous in many biological systems. Here, we present an overview of some of the main theoretical methods that we consider key in the field of weak PE at interfaces.  ...  This phenomenon has been studied by different theoretical methods including scaling theory [51, 174] , self-consistent field approaches [50, 73, 175] , MC simulation [70] , and systematically investigated  ... 
doi:10.3390/polym12102282 pmid:33027995 pmcid:PMC7601300 fatcat:j67ni7atc5bqtawutbzej6xmse
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