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Crystal contacts as nature's docking solutions

Evgeny Krissinel
2010 Journal of Computational Chemistry  
As found, the failure rate of docking may be quantitatively interpreted if both calculation errors and misrepresentation effects are taken into account.  ...  The assumption that crystal contacts reflect natural macromolecular interactions makes a basis for many studies in structural biology.  ...  crystal contact.  ... 
doi:10.1002/jcc.21303 pmid:19421996 fatcat:yyancya3ozax3db6cv2mecx5xy

Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches

Aljaž Gaber, Miha Pavšič
2021 International Journal of Molecular Sciences  
Moreover, aspects of symmetry are critical in the modeling of protein homo-oligomers either by docking or by homology-based approaches.  ...  we give an overview of approaches aimed at modeling homo-oligomers using computational methods that specifically address their internal symmetry and allow the incorporation of other experimental data as  ...  Protein Homo-Oligomerization as an Efficient Design Principle Homo-oligomerization is believed to be nature's solution to form large proteins by avoiding efficiency problems with the synthesis of long  ... 
doi:10.3390/ijms22169081 pmid:34445785 pmcid:PMC8396596 fatcat:yd4qi4zhlbbapfl5v242ml2axy

SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models

Aroop Sircar, Jeffrey J. Gray, Tanja Kortemme
2010 PLoS Computational Biology  
Structural analysis shows that diverse paratope conformations are sampled, but docked paratope backbones are not necessarily closer to the crystal structure conformations than the starting homology models  ...  docking predictions.  ...  Slide into glancing contact as defined by at least one antibodyantigen atomic contact within 1 Å of van der Waals contact distances. 3.  ... 
doi:10.1371/journal.pcbi.1000644 pmid:20098500 pmcid:PMC2800046 fatcat:sv32ykks25afhcus325agi266u

Interaction of the Disordered Yersinia Effector Protein YopE with Its Cognate Chaperone SycE

Xin Hu, Michael S. Lee, Anders Wallqvist
2009 Biochemistry  
Starting from de novo models, we generated ensembles of unfolded conformations of the Yersinia effector YopE using REMD simulations and docked them to the chaperone SycE using a multistep protein docking  ...  in solution (7) .  ...  Second, the conformations actually sampled by an unfolding protein at low temperatures must be greatly reduced compared to the space of all possible conformations (i.e., nature's solution to Levinthal's  ... 
doi:10.1021/bi9017347 pmid:19877667 fatcat:r5ufrs6ic5bzpoltrzu7ez4r6i

Probing protein flexibility reveals a mechanism for selective promiscuity

Nicolas A Pabon, Carlos J Camacho
2017 eLife  
Specificity is then established by additional contacts that stabilize the PD-1 cavity into distinct bound-like modes.  ...  Co-crystal structures, MDs and docking studies of PD-L1/2 suggest that the homologous interface residues Tyr123/112 (see Figure 2b,c ) may serve as anchors.  ...  Flexible human regulatory proteins such as MDM2 and PD-1 usually only crystallize when ligandbound.  ... 
doi:10.7554/elife.22889 pmid:28432789 pmcid:PMC5446241 fatcat:75dyhs7ydve2vgxrjg2u5pohgy

Structural Basis of Substrate Conversion in a New Aromatic Peroxygenase

Klaus Piontek, Eric Strittmatter, René Ullrich, Glenn Gröbe, Marek J. Pecyna, Martin Kluge, Katrin Scheibner, Martin Hofrichter, Dietmar A. Plattner
2013 Journal of Biological Chemistry  
Results: Based on two crystal structures the substrate conversion of APOs is elucidated.  ...  Here, the first two crystal structures of a heavily glycosylated fungal aromatic peroxygenase (AaeAPO) are described. They reveal different pH-dependent ligand binding modes.  ...  Docking solutions for the two larger and bulkier PAHs show serious clashes with the protein that would require substantial rearrangements of side chains as well as of the backbone.  ... 
doi:10.1074/jbc.m113.514521 pmid:24126915 pmcid:PMC3843090 fatcat:3ai2clw22rfxbeg5ipe5s63n2y

Insights into Complex Oxidation during BE-7585A Biosynthesis: Structural Determination and Analysis of the Polyketide Monooxygenase BexE

David R. Jackson, Xia Yu, Guojung Wang, Avinash B. Patel, Jordi Calveras, Jesus F. Barajas, Eita Sasaki, Mikko Metsä-Ketelä, Hung-wen Liu, Jürgen Rohr, Shiou-Chuan Tsai
2016 ACS Chemical Biology  
Here, we present the crystal structure and functional analysis of BexE, the oxygenase proposed to catalyze this key oxidative rearrangement step that generates the angucyclinone framework.  ...  The structural analysis, docking simulations, and biochemical assays provide insights into the role of BexE in BE-7585A biosynthesis and lay the groundwork for engineering such framework-modifying enzymes  ...  The BexF model was docked with the BexE structure in an orientation that positions their active site entrances in close contact ( Figure S3 ).  ... 
doi:10.1021/acschembio.5b00913 pmid:26813028 pmcid:PMC4902875 fatcat:pkeowpnupfeqfcjfl75kzjpjuu

Neutrons reveal how nature uses structural themes and variation in biological regulation

Jill Trewhella
2006 Physica. B, Condensed matter  
In achieving this regulation, nature uses a number of 'second messengers' that are released inside cells in response to first messengers, such as hormones that bind to the cell surface.  ...  Divalent calcium and cyclic nucleotides, like cAMP, are among nature's second messengers that bind to receptor proteins inside cells order to regulate the activities of various targets, including many  ...  well as a recent crystal structure [22] .  ... 
doi:10.1016/j.physb.2006.05.118 fatcat:3c3c7jfaizcn5fplwpkabytdyu

Metal-Directed Protein Self-Assembly

Eric N. Salgado, Robert J. Radford, F. Akif Tezcan
2010 Accounts of Chemical Research  
Proteins are also Nature's metal ligands of choice.  ...  We will start this Account by first describing the challenges of using entire proteins as molecular building blocks.  ...  For inspiration, we turned to crystal packing interactions (CPIs), which provide a source of feasible protein-protein docking geometries.  ... 
doi:10.1021/ar900273t pmid:20192262 pmcid:PMC2873059 fatcat:mxi2xjy2f5cqldoui3lgqh7wgu

Crystal structure of the cell wall anchor domain of MotB, a stator component of the bacterial flagellar motor: Implications for peptidoglycan recognition

A. Roujeinikova
2008 Proceedings of the National Academy of Sciences of the United States of America  
MotB-C is a dimer, both in solution and in the crystal.  ...  The two glycan chains of the PG ligand can be modeled as semirigid helices and docked into the grooves harboring the NAM molecules on the opposite faces of the dimer.  ...  MotB-C Dimerization in Solution and the Crystal.  ... 
doi:10.1073/pnas.0803039105 pmid:18647830 pmcid:PMC2492448 fatcat:vgbbn6l2lvdktder2wndrxlt3u

The Plasticity of the β-Trefoil Fold Constitutes an Evolutionary Platform for Protease Inhibition

Mohamed Azarkan, Sergio Martinez-Rodriguez, Lieven Buts, Danielle Baeyens-Volant, Abel Garcia-Pino
2011 Journal of Biological Chemistry  
Solution structure of PPI and the PPI-trypsin complexes.  ...  Enzymase International is gratefully acknowledged for having generously supplied C. papaya latex as a spray-dried powder.  ...  Here we report the crystal structure of PPI in two crystal forms, together with the solution structure of its complexes with one and two trypsin units, as determined by small angle x-ray scattering (SAXS  ... 
doi:10.1074/jbc.m111.291310 pmid:22027836 pmcid:PMC3243510 fatcat:ssss5abvprbqre4s3ptg25eg24

Structure of ADP-aluminium fluoride-stabilized protochlorophyllide oxidoreductase complex

J. Moser, C. Lange, J. Krausze, J. Rebelein, W.-D. Schubert, M. W. Ribbe, D. W. Heinz, D. Jahn
2013 Proceedings of the National Academy of Sciences of the United States of America  
Apparently, the docking of L 2 on NB induces a linear arrangement of the two redox-active clusters with the substrate, Pchlide (Fig. 1D) .  ...  Upon complex formation, substantial ATP-dependent conformational rearrangements of L 2 trigger the protein-protein interactions with (NB) 2 as well as the electron transduction via redox-active [4Fe-4S  ...  We especially thank Simone Virus and Marion Schwietering for help with protein crystallization. This work was supported by the Deutsche Forschungsgemeinschaft (Grant JA470/9-2).  ... 
doi:10.1073/pnas.1218303110 pmid:23341615 pmcid:PMC3568340 fatcat:suky3usth5dc3cdlurir2yygzy

Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway

Steve Bonilla, Charles Limouse, Namita Bisaria, Magdalena Gebala, Hideo Mabuchi, Daniel Herschlag
2017 Journal of the American Chemical Society  
bond interactions form after the docking transition state.  ...  common kinetic and ionic effect for all variants, suggesting that the global conformational search and compaction electrostatics are energetically independent from the formation of the tertiary motif contacts  ...  (B) Overlay of four crystal structures of the GAAA/11ntR motif. Backbone of tetraloop and tetraloopreceptor are colored as in (A).  ... 
doi:10.1021/jacs.7b08870 pmid:29185740 pmcid:PMC5748328 fatcat:rscp6hzpyncp5amyligq6m5jme

Crystal structure of bacterial multidrug efflux transporter AcrB

Satoshi Murakami, Ryosuke Nakashima, Eiki Yamashita, Akihito Yamaguchi
2002 Nature  
We have determined the crystal structure of AcrB at 3.5 Å resolution. Three AcrB protomers are organized as a homotrimer in the shape of a jellyfish.  ...  The top of the headpiece opens like a funnel, where TolC might directly dock into AcrB.  ...  The diameter of the top of the TolC docking domain is about the same as that of the bottom of TolC.  ... 
doi:10.1038/nature01050 pmid:12374972 fatcat:aiqnoscjffbb5davweb5m3u7wa

Crystal Structure of Bacterial Multi-Drug Efflux Transporter AcrB

2003 Nihon Kessho Gakkaishi  
We have determined the crystal structure of AcrB at 3.5 Å resolution. Three AcrB protomers are organized as a homotrimer in the shape of a jellyfish.  ...  The top of the headpiece opens like a funnel, where TolC might directly dock into AcrB.  ...  The diameter of the top of the TolC docking domain is about the same as that of the bottom of TolC.  ... 
doi:10.5940/jcrsj.45.256 fatcat:pdvpgme26vcedjnfvi7j4qeffy
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