scholarly journals Crystal structure of papain-E64-c complex. Binding diversity of E64-c to papain S2 and S3 subsites

1992 ◽  
Vol 287 (3) ◽  
pp. 797-803 ◽  
Author(s):  
M J Kim ◽  
D Yamamoto ◽  
K Matsumoto ◽  
M Inoue ◽  
T Ishida ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Cysteine Proteinase ◽  
Complex Structure ◽  
Binding Mode ◽  
Accessible Surface Area ◽  
Cysteine Proteinase Inhibitor ◽  
Binding Modes ◽  
Replacement Method ◽  
Solvent Molecules

In order to investigate the binding mode of E64-c (a synthetic cysteine proteinase inhibitor) to papain at the atomic level, the crystal structure of the complex was analysed by X-ray diffraction at 1.9 A (1 A is expressed in SI units as 0.1 nm) resolution. The crystal has a space group P2(1)2(1)2(1) with a = 43.37, b = 102.34 and c = 49.95 A. A total of 21,135 observed reflections were collected from the same crystal, and 14811 unique reflections of up to 1.9 A resolution [Fo > 3 sigma(Fo)] were used for the structure solution and refinement. The papain structure was determined by means of the molecular replacement method, and then the inhibitor was observed on a (2 magnitude of Fo-magnitude of Fc) difference Fourier map. The complex structure was finally refined to R = 19.4% including 207 solvent molecules. Although this complex crystal (Form II) was polymorphous as compared with the previously analysed one (Form I), the binding modes of leucine and isoamylamide moieties of E64-c were significantly different from each other. By the calculation of accessible surface area for each complex atom, these two different binding modes were both shown to be tight enough to prevent the access of solvent molecules to the papain active site. With respect to the E64-c-papain binding mode, molecular-dynamics simulations proposed two kinds of stationary states which were derived from the crystal structures of Forms I and II. One of these, which corresponds to the binding mode simulated from Form I, was essentially the same as that observed in the crystal structure, and the other was somewhat different from the crystal structure of Form II, especially with respect to the binding of the isoamylamide moiety with the papain S subsites. The substrate specificity for the papain active site is discussed on the basis of the present results.

Structure and substrate docking of a hydroxy(phenyl)pyruvate reductase from the higher plantColeus blumeiBenth.

2010 ◽  
Vol 66 (5) ◽  
pp. 593-603 ◽  
Author(s):  
Verena Janiak ◽  
Maike Petersen ◽  
Matthias Zentgraf ◽  
Gerhard Klebe ◽  
Andreas Heine
Keyword(s):  
Crystal Structure ◽  
Complex Structure ◽  
Binding Mode ◽  
Binding Modes ◽  
Active Centre ◽  
Aromatic Substrates ◽  
Coleus Blumei ◽  
The Family ◽  
Docking Energy ◽  
Catalytic Cleft

Hydroxy(phenyl)pyruvate reductase [H(P)PR] belongs to the family of D-isomer-specific 2-hydroxyacid dehydrogenases and catalyzes the reduction of hydroxyphenylpyruvates as well as hydroxypyruvate and pyruvate to the corresponding lactates. Other non-aromatic substrates are also accepted. NADPH is the preferred cosubstrate. The crystal structure of the enzyme fromColeus blumei(Lamiaceae) has been determined at 1.47 Å resolution. In addition to the apoenzyme, the structure of a complex with NADP+was determined at a resolution of 2.2 Å. H(P)PR is a dimer with a molecular mass of 34 113 Da per subunit. The structure is similar to those of other members of the enzyme family and consists of two domains separated by a deep catalytic cleft. To gain insights into substrate binding, several compounds were docked into the cosubstrate complex structure using the programAutoDock. The results show two possible binding modes with similar docking energy. However, only binding modeAprovides the necessary environment in the active centre for hydride and proton transfer during reduction, leading to the formation of the (R)-enantiomer of lactate and/or hydroxyphenyllactate.

scholarly journals Complexed Crystal Structure of Saccharomyces cerevisiae Dihydroorotase with Inhibitor 5-Fluoroorotate Reveals a New Binding Mode

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Hong-Hsiang Guan ◽  
Yen-Hua Huang ◽  
En-Shyh Lin ◽  
Chun-Jung Chen ◽  
Cheng-Yang Huang
Keyword(s):  
Crystal Structure ◽  
Saccharomyces Cerevisiae ◽  
Active Site ◽  
Structural Similarity ◽  
Binding Mode ◽  
Site Directed Mutagenesis ◽  
Molecular Evidence ◽  
Binding Modes ◽  
Pyrimidine Nucleotides ◽  
Quenching Method

Dihydroorotase (DHOase) possesses a binuclear metal center in which two Zn ions are bridged by a posttranslationally carbamylated lysine. DHOase catalyzes the reversible cyclization of N-carbamoyl aspartate (CA-asp) to dihydroorotate (DHO) in the third step of the pathway for the biosynthesis of pyrimidine nucleotides and is an attractive target for potential anticancer and antimalarial chemotherapy. Crystal structures of ligand-bound DHOase show that the flexible loop extends toward the active site when CA-asp is bound (loop-in mode) or moves away from the active site, facilitating the product DHO release (loop-out mode). DHOase binds the product-like inhibitor 5-fluoroorotate (5-FOA) in a similar mode to DHO. In the present study, we report the crystal structure of DHOase from Saccharomyces cerevisiae (ScDHOase) complexed with 5-FOA at 2.5 Å resolution (PDB entry 7CA0). ScDHOase shares structural similarity with Escherichia coli DHOase (EcDHOase). However, our complexed structure revealed that ScDHOase bound 5-FOA differently from EcDHOase. 5-FOA ligated the Zn atoms in the active site of ScDHOase. In addition, 5-FOA bound to ScDHOase through the loop-in mode. We also characterized the binding of 5-FOA to ScDHOase by using the site-directed mutagenesis and fluorescence quenching method. Based on these lines of molecular evidence, we discussed whether these different binding modes are species- or crystallography-dependent.

scholarly journals Dissimilar Ligands Bind in a Similar Fashion: A Guide to Ligand Binding-Mode Prediction with Application to CELPP Studies

2021 ◽  
Vol 22 (22) ◽  
pp. 12320
Author(s):  
Xianjin Xu ◽  
Xiaoqin Zou
Keyword(s):  
Molecular Similarity ◽  
Complex Structure ◽  
Binding Mode ◽  
Molecular Structures ◽  
Complex Structures ◽  
Binding Modes ◽  
Ligand Complex ◽  
Systematic Analysis ◽  
Binding Mode Prediction ◽  
Similarity Principle

The molecular similarity principle has achieved great successes in the field of drug design/discovery. Existing studies have focused on similar ligands, while the behaviors of dissimilar ligands remain unknown. In this study, we developed an intercomparison strategy in order to compare the binding modes of ligands with different molecular structures. A systematic analysis of a newly constructed protein–ligand complex structure dataset showed that ligands with similar structures tended to share a similar binding mode, which is consistent with the Molecular Similarity Principle. More importantly, the results revealed that dissimilar ligands can also bind in a similar fashion. This finding may open another avenue for drug discovery. Furthermore, a template-guiding method was introduced for predicting protein–ligand complex structures. With the use of dissimilar ligands as templates, our method significantly outperformed the traditional molecular docking methods. The newly developed template-guiding method was further applied to recent CELPP studies.

scholarly journals Influence of the α-Methoxy Group on the Reaction of Temocillin with Pseudomonas aeruginosa PBP3 and CTX-M-14 β-Lactamase

2019 ◽  
Vol 64 (1) ◽  
Author(s):  
Michael D. Sacco ◽  
Kyle G. Kroeck ◽  
M. Trent Kemp ◽  
Xiujun Zhang ◽  
Logan D. Andrews ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Active Site ◽  
Methoxy Group ◽  
Complex Structure ◽  
Antibacterial Properties ◽  
Multidrug Resistant ◽  
Binding Modes ◽  
Content Type ◽  
The Stability ◽  
M 14

ABSTRACT The prevalence of multidrug-resistant Pseudomonas aeruginosa has led to the reexamination of older “forgotten” drugs, such as temocillin, for their ability to combat resistant microbes. Temocillin is the 6-α-methoxy analogue of ticarcillin, a carboxypenicillin with well-characterized antipseudomonal properties. The α-methoxy modification confers resistance to serine β-lactamases, yet temocillin is ineffective against P. aeruginosa growth. The origins of temocillin’s inferior antibacterial properties against P. aeruginosa have remained relatively unexplored. Here, we analyze the reaction kinetics, protein stability, and binding conformations of temocillin and ticarcillin with penicillin-binding protein 3 (PBP3), an essential PBP in P. aeruginosa. We show that the 6-α-methoxy group perturbs the stability of the PBP3 acyl-enzyme, which manifests in an elevated off-rate constant (koff) in biochemical assays comparing temocillin with ticarcillin. Complex crystal structures with PBP3 reveal similar binding modes of the two drugs but with important differences. Most notably, the 6-α-methoxy group disrupts a high-quality hydrogen bond with a conserved residue important for ligand binding while also being inserted into a crowded active site, possibly destabilizing the active site and enabling water molecule from bulk solvent to access and cleave the acyl-enzyme bond. This hypothesis is supported by the observation that the acyl-enzyme complex of temocillin has reduced thermal stability compared with ticarcillin. Furthermore, we explore temocillin’s mechanism of β-lactamase inhibition with a high-resolution complex structure of CTX-M-14 class A serine β-lactamase. The results suggest that the α-methoxy group prevents hydrolysis by locking the compound into an unexpected conformation that impedes access of the catalytic water to the acyl-enzyme adduct.

scholarly journals Crystal Structure of Red Sea Bream Transglutaminase

2000 ◽  
Vol 276 (15) ◽  
pp. 12055-12059 ◽  
Author(s):  
Kazuyoshi Noguchi ◽  
Kohki Ishikawa ◽  
Kei-ichi Yokoyama ◽  
Tomoko Ohtsuka ◽  
Noriki Nio ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Red Sea ◽  
Active Site ◽  
Factor Xiii ◽  
Coagulation Factor ◽  
Sea Bream ◽  
Tissue Type ◽  
Acyl Donor ◽  
Red Sea Bream ◽  
Replacement Method

The crystal structure of the tissue-type transglutaminase from red sea bream liver (fish-derived transglutaminase, FTG) has been determined at 2.5-Å resolution using the molecular replacement method, based on the crystal structure of human blood coagulation factor XIII, which is a transglutaminase zymogen. The model contains 666 residues of a total of 695 residues, 382 water molecules, and 1 sulfate ion. FTG consists of four domains, and its overall and active site structures are similar to those of human factor XIII. However, significant structural differences are observed in both the acyl donor and acyl acceptor binding sites, which account for the difference in substrate preferences. The active site of the enzyme is inaccessible to the solvent, because the catalytic Cys-272 hydrogen-bonds to Tyr-515, which is thought to be displaced upon acyl donor binding to FTG. It is postulated that the binding of an inappropriate substrate to FTG would lead to inactivation of the enzyme because of the formation of a new disulfide bridge between Cys-272 and the adjacent Cys-333 immediately after the displacement of Tyr-515. Considering the mutational studies previously reported on the tissue-type transglutaminases, we propose that Cys-333 and Tyr-515 are important in strictly controlling the enzymatic activity of FTG.

scholarly journals GMP and IMP Are Competitive Inhibitors of CMY-10, an Extended-Spectrum Class C β-Lactamase

2017 ◽  
Vol 61 (5) ◽  
Author(s):  
Jung-Hyun Na ◽  
Young Jun An ◽  
Sun-Shin Cha
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Binding Mode ◽  
Competitive Inhibitor ◽  
Phosphate Group ◽  
The Other ◽  
Extended Spectrum ◽  
Competitive Inhibitors ◽  
Class C

ABSTRACT Nucleotides were effective in inhibiting the class C β-lactamase CMY-10. IMP was the most potent competitive inhibitor, with a Ki value of 16.2 μM. The crystal structure of CMY-10 complexed with GMP or IMP revealed that nucleotides fit into the R2 subsite of the active site with a unique vertical binding mode where the phosphate group at one terminus is deeply bound in the subsite and the base at the other terminus faces the solvent.

scholarly journals Structures of FHOD1-Nesprin1/2 complexes reveal alternate binding modes for the FH3 domain of formins

2020 ◽  
Author(s):  
Sing Mei Lim ◽  
Victor E. Cruz ◽  
Susumu Antoku ◽  
Gregg G. Gundersen ◽  
Thomas U. Schwartz
Keyword(s):  
Complex Structure ◽  
Binding Mode ◽  
Eukaryotic Cells ◽  
Binding Modes ◽  
Actin Network ◽  
Nuclear Movement ◽  
Spectrin Repeat ◽  
Major Activity ◽  
Binding Partners ◽  
Cytoskeletal Network

ABSTRACTThe nuclear position in eukaryotic cells is controlled by a nucleo-cytoskeletal network, with important roles in cell differentiation, division and movement. Forces are transmitted through conserved linker of nucleoskeleton and cytoskeleton (LINC) complexes that traverse the nuclear envelope and engage on either side of the membrane with diverse binding partners. Nesprin-2 giant (Nes2G), a LINC element in the outer nuclear membrane, connects to the actin network directly as well as through FHOD1, a formin whose major activity is bundling actin. Much of the molecular details of this process remain poorly understood. Here, we report the crystal structure of Nes2G bound to FHOD1. We show that the G-binding domain of FHOD1 is rather a spectrin repeat binding enhancer for the neighboring FH3 domain, possibly establishing a common binding mode among this subclass of formins. The FHOD1-Nes2G complex structure suggests that spectrin repeat binding by FHOD1 is likely not regulated by the DAD helix of FHOD1. Finally, we establish that Nes1G also has one FHOD1 binding spectrin repeat, indicating that these abundant, giant Nesprins have overlapping functions in actin-bundle recruitment for nuclear movement.

Fragment Pose Prediction Using Non-Equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations

2019 ◽  
Author(s):  
Nathan M. Lim ◽  
Meghan Osato ◽  
Gregory L. Warren ◽  
David L. Mobley
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Monte Carlo ◽  
Ligand Binding ◽  
Md Simulations ◽  
Binding Mode ◽  
Protein Crystal ◽  
Pose Prediction ◽  
Binding Modes ◽  
Non Equilibrium

<div>Part of early stage drug discovery involves determining how molecules may bind to the target protein. Through understanding where and how molecules bind, chemists can begin to build ideas on how to design improvements to increase binding affinities. In this retrospective study, we compare how computational approaches like docking, molecular dynamics (MD) simulations, and a non-equilibrium candidate Monte Carlo (NCMC) based method (NCMC+MD) perform in predicting binding modes for a set of 12 fragment-like molecules which bind to soluble epoxide hydrolase. We evaluate each method's effectiveness in identifying the dominant binding mode and finding any additional binding modes (if any). Then, we compare our predicted binding modes to experimentally obtained X-ray crystal structures.</div><div>We dock each of the 12 small molecules into the apo-protein crystal structure and then run simulations up to 1 microsecond each. Small and fragment-like molecules likely have smaller energy barriers separating different binding modes by virtue of relatively fewer and weaker interactions relative to drug-like molecules, and thus likely undergo more rapid binding mode transitions. We expect, thus, to see more rapid transitions betweeen binding modes in our study. </div><div><br></div><div>Following this, we build Markov State Models (MSM) to define our stable ligand binding modes. We investigate if adequate sampling of ligand binding modes and transitions between them can occur at the microsecond timescale using traditional MD or a hybrid NCMC+MD simulation approach. Our findings suggest that even with small fragment-like molecules, we fail to sample all the crystallographic binding modes using microsecond MD simulations, but using NCMC+MD we have better success in sampling the crystal structure while obtaining the correct populations.</div>

scholarly journals The C-terminal extension landscape of naturally presented HLA-I ligands

2018 ◽  
Vol 115 (20) ◽  
pp. 5083-5088 ◽  
Author(s):  
Philippe Guillaume ◽  
Sarah Picaud ◽  
Petra Baumgaertner ◽  
Nicole Montandon ◽  
Julien Schmidt ◽  
...  
Keyword(s):  
Crystal Structure ◽  
T Cells ◽  
High Resolution ◽  
Antigen Presentation ◽  
Structural Properties ◽  
Structural Changes ◽  
Binding Mode ◽  
Binding Modes ◽  
The Common ◽  
Direct Recognition

HLA-I molecules play a central role in antigen presentation. They typically bind 9- to 12-mer peptides, and their canonical binding mode involves anchor residues at the second and last positions of their ligands. To investigate potential noncanonical binding modes, we collected in-depth and accurate HLA peptidomics datasets covering 54 HLA-I alleles and developed algorithms to analyze these data. Our results reveal frequent (442 unique peptides) and statistically significant C-terminal extensions for at least eight alleles, including the common HLA-A03:01, HLA-A31:01, and HLA-A68:01. High resolution crystal structure of HLA-A68:01 with such a ligand uncovers structural changes taking place to accommodate C-terminal extensions and helps unraveling sequence and structural properties predictive of the presence of these extensions. Scanning viral proteomes with the C-terminal extension motifs identifies many putative epitopes and we demonstrate direct recognition by human CD8+ T cells of a 10-mer epitope from cytomegalovirus predicted to follow the C-terminal extension binding mode.

scholarly journals Structure of NADP+-bound 7β-hydroxysteroid dehydrogenase reveals two cofactor-binding modes

2017 ◽  
Vol 73 (5) ◽  
pp. 246-252 ◽  
Author(s):  
Rui Wang ◽  
Jiaquan Wu ◽  
David Kin Jin ◽  
Yali Chen ◽  
Zhijia Lv ◽  
...  
Keyword(s):  
Ursodeoxycholic Acid ◽  
Active Site ◽  
Enterohepatic Circulation ◽  
Hydroxysteroid Dehydrogenase ◽  
Binding Mode ◽  
Binding Modes ◽  
Potential Toxicity ◽  
Secondary Bile Acid ◽  
Cofactor Binding ◽  
Related Enzyme

In mammals, bile acids/salts and their glycine and taurine conjugates are effectively recycled through enterohepatic circulation. 7β-Hydroxysteroid dehydrogenases (7β-HSDHs; EC 1.1.1.201), including that from the intestinal microbeCollinsella aerofaciens, catalyse the NADPH-dependent reversible oxidation of secondary bile-acid products to avoid potential toxicity. Here, the first structure of NADP+bound to dimeric 7β-HSDH is presented. In one active site, NADP+adopts a conventional binding mode similar to that displayed in related enzyme structures. However, in the other active site a unique binding mode is observed in which the orientation of the nicotinamide is different. Since 7β-HSDH has become an attractive target owing to the wide and important pharmaceutical use of its product ursodeoxycholic acid, this work provides a more detailed template to support rational protein engineering to improve the enzymatic activities of this useful biocatalyst, further improving the yield of ursodeoxycholic acid and its other applications.

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