scholarly journals Cross-Species Analysis of Glycosaminoglycan Binding Proteins Reveals Some Animal Models Are “More Equal” than Others

Molecules ◽  
2019 ◽  
Vol 24 (5) ◽  
pp. 924 ◽  
Author(s):  
Eric Boittier ◽  
Neha Gandhi ◽  
Vito Ferro ◽  
Deirdre Coombe
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Informed Choice ◽  
Toxicity Assessment ◽  
Sequence Alignments ◽  
Human Situation ◽  
Species Analysis ◽  
Surface Electrostatic Potentials ◽  
And Function ◽  
Preclinical Work

Glycosaminoglycan (GAG) mimetics are synthetic or semi-synthetic analogues of heparin or heparan sulfate, which are designed to interact with GAG binding sites on proteins. The preclinical stages of drug development rely on efficacy and toxicity assessment in animals and aim to apply these findings to clinical studies. However, such data may not always reflect the human situation possibly because the GAG binding site on the protein ligand in animals and humans could differ. Possible inter-species differences in the GAG-binding sites on antithrombin III, heparanase, and chemokines of the CCL and CXCL families were examined by sequence alignments, molecular modelling and assessment of surface electrostatic potentials to determine if one species of laboratory animal is likely to result in more clinically relevant data than another. For each protein, current understanding of GAG binding is reviewed from a protein structure and function perspective. This combinatorial analysis shows chemokine dimers and oligomers can present different GAG binding surfaces for the same target protein, whereas a cleft-like GAG binding site will differently influence the types of GAG structures that bind and the species preferable for preclinical work. Such analyses will allow an informed choice of animal(s) for preclinical studies of GAG mimetic drugs.

scholarly journals BiRDS - Binding Residue Detection from Protein Sequences using Deep ResNets

2021 ◽  
Author(s):  
Vineeth Chelur ◽  
U. Deva Priyakumar
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Tertiary Structure ◽  
Solvent Accessibility ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Relative Solvent Accessibility ◽  
Single Chain ◽  
Sequence Alignments ◽  
Multiple Sequence

Protein-drug interactions play important roles in many biological processes and therapeutics. Prediction of the active binding site of a protein helps discover and optimise these interactions leading to the design of better ligand molecules. The tertiary structure of a protein determines the binding sites available to the drug molecule. A quick and accurate prediction of the binding site from sequence alone without utilising the three-dimensional structure is challenging. Deep Learning has been used in a variety of biochemical tasks and has been hugely successful. In this paper, a Residual Neural Network (leveraging skip connections) is implemented to predict a protein's most active binding site. An Annotated Database of Druggable Binding Sites from the Protein DataBank, sc-PDB, is used for training the network. Features extracted from the Multiple Sequence Alignments (MSAs) of the protein generated using DeepMSA, such as Position-Specific Scoring Matrix (PSSM), Secondary Structure (SS3), and Relative Solvent Accessibility (RSA), are provided as input to the network. A weighted binary cross-entropy loss function is used to counter the substantial imbalance in the two classes of binding and non-binding residues. The network performs very well on single-chain proteins, providing a pocket that has good interactions with a ligand.

scholarly journals The Ins(1,4,5)P3 binding site of bovine adrenocortical microsomes: function and regulation

1989 ◽  
Vol 260 (2) ◽  
pp. 593-596 ◽  
Author(s):  
S Palmer ◽  
M J O Wakelam
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Specific Binding ◽  
Cell Signalling ◽  
Single Population ◽  
Lower Affinity ◽  
Specific Binding Sites ◽  
Kinase C ◽  
And Function ◽  
Gamma S

Adrenocortical microsomes possess a single population of Ins(1,4,5)P3-specific binding sites [IC50 5.9 +/- 0.9 nM; Palmer, Hughes, Lee & Wakelam (1988) Cell. Signalling 1, 147-156]. Competition studies showed that Ins(1:2-cyclic,4,5)P3 exhibits a 21-fold lower affinity for the site than Ins(1,4,5)P3 (IC50 124 +/- 16 nM). The affinity of the binding sites for Ins(1,4,5)P3 was not influenced by the non-hydrolysable GTP analogues GTP gamma S and Gpp[NH]p or by preincubation of the binding protein with a preparation of partially purified protein kinase C in the presence of ATP and TPA (12-O-tetradecanoylphorbol 13-acetate). These observations are discussed with reference to the identify and function of the Ins(1,4,5)P3 binding site.

C/EBPalpha Is a Key Transcriptional Regulator of the Triggering Receptor on Myeloid Cells-2 Gene

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 4762-4762
Author(s):  
Maria Michela Mancarelli ◽  
Lily Catherine Frusciante ◽  
Gabrielle Francoise Cauvi ◽  
Charles De Rossi ◽  
Bruce Edward Torbett
Keyword(s):  
Gene Regulation ◽  
Binding Site ◽  
Binding Sites ◽  
Transcriptional Control ◽  
Transcriptional Activity ◽  
Myeloid Cells ◽  
Myeloid Cell ◽  
Fold Increase ◽  
Full Length ◽  
And Function

Abstract Triggering receptor on myeloid cells-2 (TREM-2) is a member of the innate immune signaling receptor TREM family. After differentiation of monocytes, TREM-2 is expressed on the cell surface of macrophages, monocyte-derived dendritic cells, microglia, and osteoclasts. TREM-2 is necessary for modulation of cellular activation and function, and loss of TREM-2 results in the decrease of phagocytosis of apoptotic neurons and cells and an increase in inflammation response of macrophage-lineage cells. To better understand TREM-2 gene regulation during monocyte differentiation we isolated and then analyzed the putative human TREM-2 promoter to identify transcriptional control. The 1131 bp TREM- 2 promoter contains binding sites for C/EBPα and PU.1 transcription factors, known for regulation of myeloid cell differentiation and function. A series of 5 promoter reporter deletion mutants were generated to dissect transcription regulation. We progressively deleted the full-length promoter, −1002/+129, of HIF1, STAT5, GATA1, YY1F, C/EBPα binding sites generating −866/+129, −632/+129, −526/+129, −258/+129, +37/+129 promoter reporters, respectively. All TREM-2 promoter reporters showed minimal transcriptional activity when transfected in 293T-HEK cells. In contrast, C/EBPα was necessary and sufficient for TREM-2 promoter reporter activity in co-transfection studies, demonstrating a 5-fold induction of transcriptional activity as compared to controls. Consistent with the TREM-2 reporter findings showing C/EBPα mediated activity, EMSA assays demonstrated specific C/EBPα binding to sites within the TREM-2 promoter. To determine if both C/EBPα binding sites in TREM-2 were necessary for activity we generated loss of C/EBPα binding site reporters and observed that only the −43/−28 C/EBPα binding site was essential for activity. To clarify if +73/+93 PU.1 binding site had a role in TREM-2 regulation, we co-transfected the full-length promoter with PU.1 and C/EBPα and observed a 10-fold increase of induction of TREM-2 transcriptional activity. However, PU.1 alone did not activate the full-length TREM-2 promoter or bind to the PU.1 consensus site, and loss of the PU.1 binding site did not alter transcriptional activity. These results suggest a key role for direct C/EBPα and indirect PU.1 participation in regulation of TREM-2. Studies are underway to precisely understand TREM-2 gene regulation and how TREM-2 controls macrophage-mediated phagocytosis and inflammation.

scholarly journals Identification of HSP47 Binding Site on Native Collagen and Its Implications for the Development of HSP47 Inhibitors

Biomolecules ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 983
Author(s):  
Haiyan Cai ◽  
Parvathy Sasikumar ◽  
Gemma Little ◽  
Dominique Bihan ◽  
Samir W. Hamaia ◽  
...  
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Binding Mode ◽  
Amino Acid Sequences ◽  
Helical Conformation ◽  
Energy Calculation ◽  
Collagen Peptides ◽  
Binding Energy Calculation ◽  
And Function ◽  
Neighboring Area

HSP47 (heat shock protein 47) is a collagen-specific molecular chaperone that is essential for procollagen folding and function. Previous studies have shown that HSP47 binding requires a critical Arg residue at the Y position of the (Gly-Xaa-Yaa) repeats of collagen; however, the exact binding sites of HSP47 on native collagens are not fully defined. To address this, we mapped the HSP47 binding sites on collagens through an ELISA binding assay using collagen toolkits, synthetic collagen peptides covering the entire amino acid sequences of collagen types II and III assembled in triple-helical conformation. Our results showed that HSP47 binds to only a few of the GXR motifs in collagen, with most of the HSP47 binding sites identified located near the N-terminal part of the triple-helical region. Molecular modelling and binding energy calculation indicated that residues flanking the key Arg in the collagen sequence also play an important role in defining the high-affinity HSP47 binding site of collagen. Based on this binding mode of HSP47 to collagen, virtual screening targeting both the Arg binding site and its neighboring area on the HSP47 surface, and a subsequent bioassay, we identified two novel compounds with blocking activity towards HSP47 binding of collagen. Overall, our study revealed the native HSP47 binding sites on collagen and provided novel information for the design of small-molecule inhibitors of HSP47.

scholarly journals Analysis of the FBXO7 promoter reveals overlapping Pax5 and c-Myb binding sites functioning in B cells

2019 ◽  
Author(s):  
Suzanne Randle ◽  
Heike Laman
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
B Cells ◽  
Blood Cell ◽  
Binding Sites ◽  
Cell Types ◽  
Sequence Alignments ◽  
Multiple Transcription Factor ◽  
And Function ◽  
Insight Into

AbstractFbxo7 is a key player in the differentiation and function of numerous blood cell types, and in neurons, oligodendrocytes and spermatocytes. In an effort to gain insight into the physiological and pathological settings where Fbxo7 is likely to play a key role, we sought to define the transcription factors which direct FBXO7 expression. Using sequence alignments across 28 species, we defined the human FBXO7 promoter and found that it contains two conserved regions enriched for multiple transcription factor binding sites. Many of these have roles in either neuronal or haematopoietic development. Using various FBXO7 promoter reporters, we found ELF4, Pax5 and c-Myb have functional binding sites that activate transcription. Overlap of Pax5 and c-Myb binding sites suggest that these factors bind cooperatively to transactivate the FBXO7 promoter. Although endogenous Pax5 is bound to the FBXO7 promoter in B cells, c-Myb is also required for FBXO7 expression. Our data suggest the interplay of multiple transcription factors regulate the FBXO7 promoter.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Covalent-Fragment Screening of Brd4 Identifies a Ligandable Site Orthogonal to the Acetyl-Lysine Binding Sites

2019 ◽  
Author(s):  
Michael Olp ◽  
Daniel Sprague ◽  
Stefan Kathman ◽  
Ziyang Xu ◽  
Alexandar Statsyuk ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Binding Site ◽  
Binding Sites ◽  
Computational Prediction ◽  
Chemical Probes ◽  
Computational Docking ◽  
Fragment Screening ◽  
Covalent Inhibitors ◽  
Bet Protein ◽  
Proof Of Principle

<p>Brd4, a member of the bromodomain and extraterminal domain (BET) family, has emerged as a promising epigenetic target in cancer and inflammatory disorders. All reported BET family ligands bind within the bromodomain acetyl-lysine binding sites and competitively inhibit BET protein interaction with acetylated chromatin. Alternative chemical probes that act orthogonally to the highly-conserved acetyl-lysine binding sites may exhibit selectivity within the BET family and avoid recently reported toxicity in clinical trials of BET bromodomain inhibitors. Here, we report the first identification of a ligandable site on a bromodomain outside the acetyl-lysine binding site. Inspired by our computational prediction of hotspots adjacent to non-homologous cysteine residues within the <i>C</i>-terminal Brd4 bromodomain (Brd4-BD2), we performed a mid-throughput mass spectrometry screen to identify cysteine-reactive fragments that covalently and selectively modify Brd4. Subsequent mass spectrometry, NMR and computational docking analyses of electrophilic fragment hits revealed a novel ligandable site near Cys356 that is unique to Brd4 among all human bromodomains. This site is orthogonal to the Brd4-BD2 acetyl-lysine binding site as Cys356 modification did not impact binding of the pan-BET bromodomain inhibitor JQ1 in fluorescence polarization assays. Finally, we tethered covalent fragments to JQ1 and performed NanoBRET assays to provide proof of principle that this orthogonal site can be covalently targeted in intact human cells. Overall, we demonstrate the potential of targeting sites orthogonal to bromodomain acetyl-lysine binding sites to develop bivalent and covalent inhibitors that displace Brd4 from chromatin.</p>

Effects of Multiple Binding Sites on Studies of Hydrogen Bonding between Nitroxide Radicals and Solvent Molecules

1993 ◽  
Vol 58 (1) ◽  
pp. 47-52 ◽  
Author(s):  
Imad Al-Bala'a ◽  
Richard D. Bates
Keyword(s):  
Hydrogen Bonding ◽  
Magnetic Resonance ◽  
Binding Site ◽  
Binding Sites ◽  
Hyperfine Coupling Constant ◽  
Hydrogen Donor ◽  
Complex Formation Constants ◽  
Multiple Binding Sites ◽  
Multiple Binding ◽  
Solvent Molecules

The role of more than one binding site on a nitroxide free radical in magnetic resonance determinations of the properties of the complex formed with a hydrogen donor is examined. The expression that relates observed hyperfine couplings in EPR spectra to complex formation constants and concentrations of each species in solution becomes much more complex when multiple binding sites are present, but reduces to a simpler form when binding at the two sites occurs independently and the binding at the non-nitroxide site does not produce significant differences in the hyperfine coupling constant in the complexed radical. Effects on studies of hydrogen bonding between multiple binding site nitroxides and hydrogen donor solvent molecules by other magnetic resonance methods are potentially more extreme.

Tuning of Electronic Properties in Conducting Polymers

2001 ◽  
Vol 66 (8) ◽  
pp. 1208-1218 ◽  
Author(s):  
Guofeng Li ◽  
Mira Josowicz ◽  
Jiří Janata
Keyword(s):  
Hydrogen Bonding ◽  
Binding Site ◽  
Binding Sites ◽  
Polymer Chains ◽  
Electronic Transitions ◽  
Weakly Bound ◽  
Ordered Structures ◽  
Doped Polymer ◽  
Positively Charged ◽  
Repeated Cycling

Structural and electronic transitions in poly(thiophenyleneiminophenylene), usually referred to as poly(phenylenesulfidephenyleneamine) (PPSA) upon electrochemical doping with LiClO4 have been investigated. The unusual electrochemical behavior of PPSA indicates that the dopant anions are bound in two energetically different sites. In the so-called "binding site", the ClO4- anion is Coulombically attracted to the positively charged S or N sites on one chain and simultaneously hydrogen-bonded with the N-H group on a neighboring polymer chain. This strong interaction causes a re-organization of the polymer chains, resulting in the formation of a networked structure linked together by these ClO4- Coulombic/hydrogen bonding "bridges". However, in the "non-binding site", the ClO4- anion is very weakly bound, involves only the electrostatic interaction and can be reversibly exchanged when the doped polymer is reduced. In the repeated cycling, the continuous and alternating influx and expulsion of ClO4- ions serves as a self-organizing process for such networked structures, giving rise to a diminishing number of available "non-binding" sites. The occurrence of these ordered structures has a major impact on the electrochemical activity and the morphology of the doped polymer. Also due to stabilization of the dopant ions, the doped polymer can be kept in a stable and desirable oxidation state, thus both work function and conductivity of the polymer can be electrochemically controlled.

scholarly journals Genes encoding components of the olfactory signal transduction cascade contain a DNA binding site that may direct neuronal expression.

1993 ◽  
Vol 13 (9) ◽  
pp. 5805-5813 ◽  
Author(s):  
M M Wang ◽  
R Y Tsai ◽  
K A Schrader ◽  
R R Reed
Keyword(s):  
Signal Transduction ◽  
Dna Binding ◽  
Binding Site ◽  
Binding Sites ◽  
Consensus Sequence ◽  
Initiation Site ◽  
Olfactory Neuron ◽  
Promoter Regions ◽  
Transcriptional Initiation ◽  
Genes Encoding

Genes which mediate odorant signal transduction are expressed at high levels in neurons of the olfactory epithelium. The molecular mechanism governing the restricted expression of these genes likely involves tissue-specific DNA binding proteins which coordinately activate transcription through sequence-specific interactions with olfactory promoter regions. We have identified binding sites for the olfactory neuron-specific transcription factor, Olf-1, in the sequences surrounding the transcriptional initiation site of five olfactory neuron-specific genes. The Olf-1 binding sites described define the consensus sequence YTCCCYRGGGAR. In addition, we have identified a second binding site, the U site, in the olfactory cyclic nucleotide gated channel and type III cyclase promoters, which binds factors present in all tissue examined. These experiments support a model in which expression of Olf-1 in the sensory neurons coordinately activates a set of olfactory neuron-specific genes. Furthermore, expression of a subset of these genes may be modulated by additional binding factors.

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