共查询到20条相似文献，搜索用时 10 毫秒
1.
Wenying Qin Russell A. Judge Kenton L. Longenecker Larry R. Solomon John E. Harlan 《Acta Crystallographica. Section F, Structural Biology Communications》2012,68(5):601-605
Successfully forming ligand–protein complexes with specific compounds can be a significant challenge in supporting structure‐based drug design for a given protein target. In this respect, an on‐column ligand‐ and detergent‐exchange method was developed to obtain ligand–protein complexes of an adamantane series of compounds with 11β‐hydroxysteroid dehydrogenase type 1 (11β‐HSD1) after a variety of other complexation methods had failed. This report describes the on‐column exchange method and an unexpected byproduct of the method in which artificial trimers were observed in the structures. 相似文献
2.
Artem G. Evdokimov Matthew Pokross Richard Walter Marlene Mekel Brooke Cox Chuiying Li Randy Bechard Frank Genbauffe Ryan Andrews Conrad Diven Brian Howard Vinit Rastogi Jeffrey Gray Matthew Maier Kevin G. Peters 《Acta Crystallographica. Section D, Structural Biology》2006,62(12):1435-1445
Protein tyrosine phosphatases (PTPs) play roles in many biological processes and are considered to be important targets for drug discovery. As inhibitor development has proven challenging, crystal structure‐based design will be very helpful to advance inhibitor potency and selectivity. Successful application of protein crystallography to drug discovery heavily relies on high‐quality crystal structures of the protein of interest complexed with pharmaceutically interesting ligands. It is very important to be able to produce protein–ligand crystals rapidly and reproducibly for as many ligands as necessary. This study details our efforts to engineer the catalytic domain of human protein tyrosine phosphatase β (HPTPβ‐CD) with properties suitable for rapid‐turnaround crystallography. Structures of apo HPTPβ‐CD and its complexes with several novel small‐molecule inhibitors are presented here for the first time. 相似文献
3.
Bruce T. Fahr Michelle M. Sopko Joni W. Lam Tom O'Brien Nathan D. Waal Phuongly Pham Hans E. Purkey Brian C. Raimundo Michael J. Romanowski 《Acta Crystallographica. Section F, Structural Biology Communications》2005,61(5):451-458
Caspase‐1 is a key endopeptidase responsible for the post‐translational processing of the IL‐1β and IL‐18 cytokines and small‐molecule inhibitors that modulate the activity of this enzyme are predicted to be important therapeutic treatments for many inflammatory diseases. A fragment‐assembly approach, accompanied by structural analysis, was employed to generate caspase‐1 inhibitors. With the aid of Tethering® with extenders (small molecules that bind to the active‐site cysteine and contain a free thiol), two novel fragments that bound to the active site and made a disulfide bond with the extender were identified by mass spectrometry. Direct linking of each fragment to the extender generated submicromolar reversible inhibitors that significantly reduced secretion of IL‐1β but not IL‐6 from human peripheral blood mononuclear cells. Thus, Tethering with extenders facilitated rapid identification and synthesis of caspase‐1 inhibitors with cell‐based activity and subsequent structural analyses provided insights into the enzyme's ability to accommodate different inhibitor‐binding modes in the active site. 相似文献
4.
Robert Cheng Brunella Felicetti Shilpa Palan Ian Toogood‐Johnson Christoph Scheich John Barker Mark Whittaker Thomas Hesterkamp 《Protein science : a publication of the Protein Society》2010,19(1):168-173
The Mapkap kinases 2 and 3 (MK2 and MK3) have been implicated in intracellular signaling pathways leading to the production of the pro‐inflammatory cytokine tumor necrosis factor alpha. MK2 has been pursued by the biopharmaceutical industry for many years for the development of a small molecule anti‐inflammatory treatment and drug‐like inhibitors have been described. The development of some of these compounds, however, has been slowed by the absence of a high‐resolution crystal structure of MK2. Herein we present a high‐resolution (1.9 Å) crystal structure of the highly homologous MK3 in complex with a pharmaceutical lead compound. While all of the canonical features of Ser/Thr kinases in general and MK2 in particular are recapitulated in MK3, the detailed analysis of the binding interaction of the drug‐like ligand within the adenine binding pocket allows relevant conclusions to be drawn for the further design of potent and selective drug candidates. 相似文献
5.
Mariejoy Therese Jumawid Tsuyoshi Takahashi Toshimasa Yamazaki Hiroshi Ashigai Hisakazu Mihara 《Protein science : a publication of the Protein Society》2009,18(2):384-398
The construction of novel functional proteins has been a key area of protein engineering. However, there are few reports of functional proteins constructed from artificial scaffolds. Here, we have constructed a genetic library encoding α3β3 de novo proteins to generate novel scaffolds in smaller size using a binary combination of simplified hydrophobic and hydrophilic amino acid sets. To screen for folded de novo proteins, we used a GFP‐based screening system and successfully obtained the proteins from the colonies emitting the very bright fluorescence as a similar intensity of GFP. Proteins isolated from the very bright colonies (vTAJ) and bright colonies (wTAJ) were analyzed by circular dichroism (CD), 8‐anilino‐1‐naphthalenesulfonate (ANS) binding assay, and analytical size‐exclusion chromatography (SEC). CD studies revealed that vTAJ and wTAJ proteins had both α‐helix and β‐sheet structures with thermal stabilities. Moreover, the selected proteins demonstrated a variety of association states existing as monomer, dimer, and oligomer formation. The SEC and ANS binding assays revealed that vTAJ proteins tend to be a characteristic of the folded protein, but not in a molten‐globule state. A vTAJ protein, vTAJ13, which has a packed globular structure and exists as a monomer, was further analyzed by nuclear magnetic resonance. NOE connectivities between backbone signals of vTAJ13 suggested that the protein contains three α‐helices and three β‐strands as intended by its design. Thus, it would appear that artificially generated α3β3 de novo proteins isolated from very bright colonies using the GFP fusion system exhibit excellent properties similar to folded proteins and would be available as artificial scaffolds to generate functional proteins with catalytic and ligand binding properties. 相似文献
6.
One approach to incorporate protein flexibility in molecular docking is the use of an ensemble consisting of multiple protein structures. Sequentially docking each ligand into a large number of protein structures is computationally too expensive to allow large-scale database screening. It is challenging to achieve a good balance between docking accuracy and computational efficiency. In this work, we have developed a fast, novel docking algorithm utilizing multiple protein structures, referred to as ensemble docking, to account for protein structural variations. The algorithm can simultaneously dock a ligand into an ensemble of protein structures and automatically select an optimal protein structure that best fits the ligand by optimizing both ligand coordinates and the conformational variable m, where m represents the m-th structure in the protein ensemble. The docking algorithm was validated on 10 protein ensembles containing 105 crystal structures and 87 ligands in terms of binding mode and energy score predictions. A success rate of 93% was obtained with the criterion of root-mean-square deviation <2.5 A if the top five orientations for each ligand were considered, comparable to that of sequential docking in which scores for individual docking are merged into one list by re-ranking, and significantly better than that of single rigid-receptor docking (75% on average). Similar trends were also observed in binding score predictions and enrichment tests of virtual database screening. The ensemble docking algorithm is computationally efficient, with a computational time comparable to that for docking a ligand into a single protein structure. In contrast, the computational time for the sequential docking method increases linearly with the number of protein structures in the ensemble. The algorithm was further evaluated using a more realistic ensemble in which the corresponding bound protein structures of inhibitors were excluded. The results show that ensemble docking successfully predicts the binding modes of the inhibitors, and discriminates the inhibitors from a set of noninhibitors with similar chemical properties. Although multiple experimental structures were used in the present work, our algorithm can be easily applied to multiple protein conformations generated by computational methods, and helps improve the efficiency of other existing multiple protein structure(MPS)-based methods to accommodate protein flexibility. 相似文献
7.
C. Abad‐Zapatero R. Oliete S. Rodriguez‐Puente J. Pous L. Martinelli M. E. Johnson A. Guasch 《Acta Crystallographica. Section F, Structural Biology Communications》2011,67(10):1300-1308
The use of relative humidity control of protein crystals to overcome some of the shortcomings of soaking ligands (i.e. inhibitors, substrate analogs, weak ligands) into pre‐grown apoprotein crystals has been explored. Crystals of PurE (EC 4.1.1.21), an enzyme from the purine‐biosynthesis pathway of Bacillus anthracis, were used as a test case. The findings can be summarized as follows: (i) using humidity control, it is possible to improve/optimize the diffraction quality of crystals soaked in solutions of organic solvent (DMSO, ethanol) containing ligands/inhibitors; (ii) optimization of the relative humidity can compensate for the deterioration of the diffraction pattern that is observed upon desalting crystals grown in high salt; (iii) combining desalting protocols with the addition of PEG it is possible to achieve very high concentrations of weak ligands (in the 5–10 mM range) in soaking solutions and (iv) fine control of the relative humidity of crystals soaked in these solutions can compensate for the deterioration of crystal diffraction and restore `high‐resolution' diffraction for structure‐based and fragment‐based drug design. It is suggested that these experimental protocols may be useful in other protein systems and may be applicable in academic or private research to increase the probability of obtaining structures of protein–ligand complexes at high resolution. 相似文献
8.
The G-quadruplexes are four-stranded nucleic acid structures with guanine-rich sequences that play important biological roles in, for example, regulating telomerase association and activity. Recent evidence supports the hypothesis that the telomeric G-quadruplex DNA represents a target of novel anticancer drug medication. In this work, we present results of the molecular electrostatic potential (MEP), together with the HOMO and LUMO frontier orbitals, which are physical quantities of concern in the docking of compounds on the G-quadruplex. The calculations are performed in the frame of density functional theory at the B88LYP/6-31G* level of theory. Additional functionals that introduce dispersion effects were also taken into consideration. The MEP potential and electron density of the frontier molecular orbitals of the G-quadruplex exhibit topological deformations due to the coiled conformation of the compound when they are compared with the MEP and corresponding electron density of a DNA duplex with similar nucleic acid composition. The electrostatic active zone of the G-quadruplex is localized on the top part of the quadruplex structure where the MEP acquires the most negative values. Additional computations on a set of three daunomycins, a common anticancer drug for duplex DNA, indicate an electrostatic fastening between the quadruplex and the set of daunomycins. In this regard, the G-quadruplex electrostatic interactions favor the stacking of ligands. Finally, some implications on molecular drug design are briefly discussed. 相似文献
9.
Adolfo H. Moraes Daniela Ackerbauer Maria Kostadinova Merima Bublin Guilherme Augusto de Oliveira Fátima Ferreira Fabio C. L. Almeida Heimo Breiteneder Ana Paula Valente 《Proteins》2014,82(11):3032-3042
Beta‐parvalbumins from different fish species have been identified as the main elicitors of IgE‐mediated reactions in fish‐allergic individuals. Here, we report for the first time the NMR determination of the structure and dynamics of the major Atlantic cod (Gadus morhua) allergen Gad m 1 and compare them with other known parvalbumins. Although the Gad m 1 structure and accessibility of putative IgE epitopes are similar to parvalbumins in mackerel and carp, the charge distribution at the putative epitopes is different. The determination of the Gad m 1 structure contributes to a better understanding of cross‐reactivity among fish parvalbumins. In addition, the high‐pressure NMR and temperature variation experiments revealed the important contribution of the AB motif and other regions to the protein folding. This structural information could assist the future identification of hot spots for targeted mutations to develop hypoallergenic Ca2+‐free forms for potential use in immunotherapy. Proteins 2014; 82:3032–3042. © 2014 Wiley Periodicals, Inc. 相似文献
10.
Ian W. Davis Kaushik Raha Martha S. Head David Baker 《Protein science : a publication of the Protein Society》2009,18(9):1998-2002
It is difficult to properly validate algorithms that dock a small molecule ligand into its protein receptor using data from the public domain: the predictions are not blind because the correct binding mode is already known, and public test cases may not be representative of compounds of interest such as drug leads. Here, we use private data from a real drug discovery program to carry out a blind evaluation of the RosettaLigand docking methodology and find that its performance is on average comparable with that of the best commercially available current small molecule docking programs. The strength of RosettaLigand is the use of the Rosetta sampling methodology to simultaneously optimize protein sidechain, protein backbone and ligand degrees of freedom; the extensive benchmark test described here identifies shortcomings in other aspects of the protocol and suggests clear routes to improving the method. 相似文献
11.
Benjamin M. Scott William P. Sheffield 《Protein science : a publication of the Protein Society》2020,29(4):856-871
α1‐Antitrypsin (α1‐AT) serves as an archetypal example for the serine proteinase inhibitor (serpin) protein family and has been used as a scaffold for protein engineering for >35 years. Techniques used to engineer α1‐AT include targeted mutagenesis, protein fusions, phage display, glycoengineering, and consensus protein design. The goals of engineering have also been diverse, ranging from understanding serpin structure–function relationships, to the design of more potent or more specific proteinase inhibitors with potential therapeutic relevance. Here we summarize the history of these protein engineering efforts, describing the techniques applied to engineer α1‐AT, specific mutants of interest, and providing an appended catalog of the >200 α1‐AT mutants published to date. 相似文献
12.
The protein folding problem represents one of the most challenging problems in computational biology. Distance constraints and topology predictions can be highly useful for the folding problem in reducing the conformational space that must be searched by deterministic algorithms to find a protein structure of minimum conformational energy. We present a novel optimization framework for predicting topological contacts and generating interhelical distance restraints between hydrophobic residues in alpha-helical globular proteins. It should be emphasized that since the model does not make assumptions about the form of the helices, it is applicable to all alpha-helical proteins, including helices with kinks and irregular helices. This model aims at enhancing the ASTRO-FOLD protein folding approach of Klepeis and Floudas (Journal of Computational Chemistry 2003;24:191-208), which finds the structure of global minimum conformational energy via a constrained nonlinear optimization problem. The proposed topology prediction model was evaluated on 26 alpha-helical proteins ranging from 2 to 8 helices and 35 to 159 residues, and the best identified average interhelical distances corresponding to the predicted contacts fell below 11 A in all 26 of these systems. Given the positive results of applying the model to several protein systems, the importance of interhelical hydrophobic-to-hydrophobic contacts in determining the folding of alpha-helical globular proteins is highlighted. 相似文献
13.
Solvation plays an important role in ligand‐protein association and has a strong impact on comparisons of binding energies for dissimilar molecules. When databases of such molecules are screened for complementarity to receptors of known structure, as often occurs in structure‐based inhibitor discovery, failure to consider ligand solvation often leads to putative ligands that are too highly charged or too large. To correct for the different charge states and sizes of the ligands, we calculated electrostatic and non‐polar solvation free energies for molecules in a widely used molecular database, the Available Chemicals Directory (ACD). A modified Born equation treatment was used to calculate the electrostatic component of ligand solvation. The non‐polar component of ligand solvation was calculated based on the surface area of the ligand and parameters derived from the hydration energies of apolar ligands. These solvation energies were subtracted from the ligand‐receptor interaction energies. We tested the usefulness of these corrections by screening the ACD for molecules that complemented three proteins of known structure, using a molecular docking program. Correcting for ligand solvation improved the rankings of known ligands and discriminated against molecules with inappropriate charge states and sizes. Proteins 1999;34:4–16. © 1999 Wiley‐Liss, Inc. 相似文献
14.
A structure‐based comparison of the ligand‐binding domains of 35 nuclear receptors from five different subfamilies is presented. Their ligand and coactivator binding sites are characterized using knowledge‐based contact preference fields for hydrophobic and hydrophilic interactions implemented in the MOE modeling environment. Additionally, for polar knowledge‐based field points the preference for negative or positive electrostatic interactions is estimated using the Poisson‐Boltzmann equation. These molecular‐interaction fields are used to cluster the nuclear receptor family based on similarities of their binding sites. By analyzing the similarities and differences of hydrophobic and polar fields in binding pockets of related receptors it is possible to identify conserved interactions in ligand and coactivator binding pockets, which support e.g. design of specific ligands during lead optimization or virtual screening as docking filter. Examples of remarkable similarities between ligand binding sites of members from phylogenetically different nuclear receptor families (RXR, RAR, HNF4, NR5) and differences between closely related subtypes (LXR, RAR, TR) are discussed in more detail. Significant similarities and differences of coactivator binding sites are shown for NR3Cs, LXRs and PPARs. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 884–894, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com 相似文献
15.
Protein structure prediction techniques proceed in two steps, namely the generation of many structural models for the protein of interest, followed by an evaluation of all these models to identify those that are native‐like. In theory, the second step is easy, as native structures correspond to minima of their free energy surfaces. It is well known however that the situation is more complicated as the current force fields used for molecular simulations fail to recognize native states from misfolded structures. In an attempt to solve this problem, we follow an alternate approach and derive a new potential from geometric knowledge extracted from native and misfolded conformers of protein structures. This new potential, Metric Protein Potential (MPP), has two main features that are key to its success. Firstly, it is composite in that it includes local and nonlocal geometric information on proteins. At the short range level, it captures and quantifies the mapping between the sequences and structures of short (7‐mer) fragments of protein backbones through the introduction of a new local energy term. The local energy term is then augmented with a nonlocal residue‐based pairwise potential, and a solvent potential. Secondly, it is optimized to yield a maximized correlation between the energy of a structural model and its root mean square (RMS) to the native structure of the corresponding protein. We have shown that MPP yields high correlation values between RMS and energy and that it is able to retrieve the native structure of a protein from a set of high‐resolution decoys. Proteins 2013. © 2012 Wiley Periodicals, Inc. 相似文献
16.
Vetting MW Bareich DC Yu M Blanchard JS 《Protein science : a publication of the Protein Society》2008,17(10):1781-1790
The three ribosomal proteins L7, S5, and S18 are included in the rare subset of prokaryotic proteins that are known to be N(alpha)-acetylated. The GCN5-related N-acetyltransferase (GNAT) protein RimI, responsible for the N(alpha)-acetylation of the ribosomal protein S18, was cloned from Salmonella typhimurium LT2 (RimI(ST)), overexpressed, and purified to homogeneity. Steady-state kinetic parameters for RimI(ST) were determined for AcCoA and a peptide substrate consisting of the first six amino acids of the target protein S18. The crystal structure of RimI(ST) was determined in complex with CoA, AcCoA, and a CoA-S-acetyl-ARYFRR bisubstrate inhibitor. The structures are consistent with a direct nucleophilic addition-elimination mechanism with Glu103 and Tyr115 acting as the catalytic base and acid, respectively. The RimI(ST)-bisubstrate complex suggests that several residues change conformation upon interacting with the N terminus of S18, including Glu103, the proposed active site base, facilitating proton exchange and catalysis. 相似文献
17.
Among the six complementarity-determining regions (CDRs) in the variable domains of an antibody, the third CDR of the heavy chain (CDR-H3), which lies in the center of the antigen-binding site, plays a particularly important role in antigen recognition. CDR-H3 shows significant variability in its length, sequence, and structure. Although difficult, model building of this segment is the most critical step in antibody modeling. Since our first proposal of the \"H3-rules,\" which classify CDR-H3 structure based on amino acid sequence, the number of experimentally determined antibody structures has increased. Here, we revise these H3-rules and propose an improved classification scheme for CDR-H3 structure modeling. In addition, we determine the common features of CDR-H3 in antibody drugs as well as discuss the concept of \"antibody druggability,\" which can be applied as an indicator of antibody evaluation during drug discovery. 相似文献
18.
《Acta Crystallographica. Section D, Structural Biology》2018,74(10):1015-1026
Here, new crystal structures are presented of the isolated membrane‐proximal D1 and distal D2 domains of protein tyrosine phosphatase epsilon (PTPϵ), a protein tyrosine phosphatase that has been shown to play a positive role in the survival of human breast cancer cells. A triple mutant of the PTPϵ D2 domain (A455N/V457Y/E597D) was also constructed to reconstitute the residues of the PTPϵ D1 catalytic domain that are important for phosphatase activity, resulting in only a slight increase in the phosphatase activity compared with the native D2 protein. The structures reported here are of sufficient resolution for structure‐based drug design, and a microarray‐based assay for high‐throughput screening to identify small‐molecule inhibitors of the PTPϵ D1 domain is also described. 相似文献
19.
Ligand induced fit phenomenon occurring at the ligand binding domain of the liver X receptor beta (LXRbeta) was investigated by means of molecular dynamics. Reliability of a 4-ns trajectory was tested from two distinct LXRbeta crystal complexes 1PQ6B/GW and 1PQ9B/T09 characterized by an open and a closed state of the pocket, respectively. Crossed complexes 1PQ6B/T09 and 1PQ9B/GW were then submitted to the same molecular dynamic conditions, which were able to recover LXRbeta conformations similar to the original crystallography data. Analysis of \"open to closed\" and \"closed to open\" conformational transitions pointed out the dynamic role of critical residues lining the ligand binding pocket involved in the local remodeling upon ligand binding (e.g., Phe271, Phe329, Phe340, Arg319, Glu281). Altogether, the present study indicates that the molecular dynamic protocol is a consistent approach for managing LXRbeta-related induced fit process. This protocol could therefore be used for refining ligand docking solutions of a structure-based design strategy. 相似文献
20.
Myra Kinalwa Ewan W Blanch Andrew J Doig 《Protein science : a publication of the Protein Society》2011,20(10):1668-1674
Knowledge of the fold class of a protein is valuable because fold class gives an indication of protein function and evolution. Fold class can be accurately determined from a crystal structure or NMR structure, though these methods are expensive, time-consuming, and inapplicable to all proteins. In contrast, vibrational spectra [infra-red, Raman, or Raman optical activity (ROA)] are rapidly obtained for proteins under wide range of biological molecules under diverse experimental and physiological conditions. Here, we show that the fold class of a protein can be determined from Raman or ROA spectra by converting a spectrum into data of 10 cm−1 bin widths and applying the random forest machine learning algorithm. Spectral data from 605 and 1785 cm−1 were analyzed, as well as the amide I, II, and III regions in isolation and in combination. ROA amide II and III data gave the best performance, with 33 of 44 proteins assigned to one of the correct four top-level structural classification of proteins (SCOP) fold class (all α, all β, α and β, and disordered). The method also shows which spectral regions are most valuable in assigning fold class. 相似文献