Three-Dimensional Models of Immune Cell Surface Proteins and Identification of Binding Sites

J&#x000FC;rgen Bajorath

doi:10.1007/s008940050066

Interaction of single-chain urokinase with its receptor induces the appearance and disappearance of binding epitopes within the resultant complex for other cell surface proteins

Blood ◽

10.1182/blood.v88.2.542.bloodjournal882542 ◽

1996 ◽

Vol 88 (2) ◽

pp. 542-551 ◽

Cited By ~ 39

Author(s):

AA Higazi ◽

RH Upson ◽

RL Cohen ◽

J Manuppello ◽

J Bognacki ◽

...

Keyword(s):

Signal Transduction ◽

Cell Surface ◽

Binding Sites ◽

Ldl Receptor ◽

Cell Types ◽

Surface Proteins ◽

Single Chain ◽

Cell Surface Proteins ◽

Functional Changes ◽

And Migration

Binding of urokinase-type plasminogen activator (uPA) to its glycosylphosphatidylinositol-anchored receptor (uPAR) initiates signal transduction, adhesion, and migration in certain cell types. To determine whether some of these activities may be mediated by associations between the uPA/uPAR complex and other cell surface proteins, we studied the binding of complexes composed of recombinant, soluble uPA receptor (suPAR) and single chain uPA (scuPA) to a cell line (LM-TK- fibroblasts) that does not express glycosylphosphatidylinositol (GPI)-anchored proteins to eliminate potential competition by endogenous uPA receptors. scuPA induced the binding of suPAR to LM-TK- cells. Binding of labeled suPAR/scuPA was inhibited by unlabeled complex, but not by scuPA or suPAR added separately, indicating cellular binding sites had been formed that are not present in either component. Binding of the complex was inhibited by low molecular weight uPA (LMW-uPA) indicating exposure of an epitope found normally in the isolated B chain of two chain uPA (tcuPA), but hidden in soluble scuPA. Binding of LMW-uPA was independent of its catalytic site and was associated with retention of its enzymatic activity. Additional cell binding epitopes were generated within suPAR itself by the aminoterminal fragment of scuPA, which itself does not bind to LM-TK- cells. When scuPA bound to suPAR, a binding site for alpha 2-macroglobulin receptor/LDL receptor-related protein (alpha 2 MR/LRP) was lost, while binding sites for cell-associated vitronectin and thrombospondin were induced. In accord with this, the internalization and degradation of cell-associated tcuPA and tcuPA-PAI- 1 complexes proceeded less efficiently in the presence of suPAR. Further, little degradation of suPAR was detected, suggesting that cell- bound complex dissociated during the initial stages of endocytosis. Thus, the interaction of scuPA with its receptor causes multiple functional changes within the complex including the dis-appearance of an epitope in scuPA involved in its clearance from the cell surface and the generation of novel epitopes that promote its binding to proteins involved in cell adhesion and signal transduction.

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Interaction of Lp(a) with Plasminogen Binding Sites on Cells

Thrombosis and Haemostasis ◽

10.1055/s-0038-1653797 ◽

1995 ◽

Vol 73 (03) ◽

pp. 458-465 ◽

Cited By ~ 42

Author(s):

Lindsey A Miles ◽

Gunther M Fless ◽

Angelo M Scanu ◽

Patricia Baynham ◽

Matthew T Sebald ◽

...

Keyword(s):

Endothelial Cells ◽

Cell Surface ◽

Binding Sites ◽

Surface Proteins ◽

Time Dependent ◽

Temperature Sensitive ◽

U937 Cells ◽

Cell Surface Proteins ◽

Sensitive Characteristics ◽

Lipoprotein Binding

SummaryLp(a) competes with plasminogen for binding to cells but it is not known whether this competition is due to the ability of Lp(a) to interact directly with plasminogen receptors. In the present study, we demonstrate that Lp(a) can interact directly with plasminogen binding sites on monocytoid U937 cells and endothelial cells. The interaction of Lp(a) with these sites was time dependent, specific, saturable, divalent ion independent and temperature sensitive, characteristics of plasminogen binding to these sites. The affinity of plasminogen and Lp(a) for these sites also was similar (Kd = 1-3 μM), but Lp(a) bound to fewer sites (̴10-fold less). Both gangliosides and cell surface proteins with car- boxy-terminal lysyl residues, including enolase, a candidate plasminogen receptor, inhibited Lp(a) binding to U937 cells. Additionally, Lp(a) interacted with low affinity lipoprotein binding sites on these cells which also recognized LDL and HDL. The ability of Lp(a) to interact with sites on cells that recognize plasminogen may contribute to the pathogenetic consequences of high levels of circulating Lp(a).

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Prediction of the Iron–Sulfur Binding Sites in Proteins Using the Highly Accurate Three-Dimensional Models Calculated by AlphaFold and RoseTTAFold

Inorganics ◽

10.3390/inorganics10010002 ◽

2021 ◽

Vol 10 (1) ◽

pp. 2

Author(s):

Béatrice Golinelli-Pimpaneau

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Conformational Changes ◽

Binding Sites ◽

Three Dimensional ◽

Amino Acid Sequences ◽

Iron Sulfur ◽

Dimensional Models ◽

Three Dimensional Models ◽

Substrate Inhibitor

AlphaFold and RoseTTAFold are deep learning-based approaches that predict the structure of proteins from their amino acid sequences. Remarkable success has recently been achieved in the prediction accuracy of not only the fold of the target protein but also the position of its amino acid side chains. In this article, I question the accuracy of these methods to predict iron–sulfur binding sites. I analyze three-dimensional models calculated by AlphaFold and RoseTTAFold of Fe–S–dependent enzymes, for which no structure of a homologous protein has been solved experimentally. In all cases, the amino acids that presumably coordinate the cluster were gathered together and facing each other, which led to a quite accurate model of the Fe–S cluster binding site. Yet, cysteine candidates were often involved in intramolecular disulfide bonds, and the number and identity of the protein amino acids that should ligate the cluster were not always clear. The experimental structure determination of the protein with its Fe–S cluster and in complex with substrate/inhibitor/product is still needed to unambiguously visualize the coordination state of the cluster and understand the conformational changes occurring during catalysis.

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What do nanometer molecular trajectories tell us about heterogeneous cell surface domaines?

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100140300 ◽

1995 ◽

Vol 53 ◽

pp. 786-787

Author(s):

Watt W. Webb

Keyword(s):

Cell Surface ◽

Lipid Membranes ◽

Surface Proteins ◽

Protein Diffusion ◽

Coated Pits ◽

Cell Surface Proteins ◽

Membrane Heterogeneity ◽

Fluorescence Photobleaching Recovery ◽

Photobleaching Recovery ◽

Plasma Membrane Heterogeneity

Plasma membrane heterogeneity is implicit in the existence of specialized cell surface organelles which are necessary for cellular function; coated pits, post and pre-synaptic terminals, microvillae, caveolae, tight junctions, focal contacts and endothelial polarization are examples. The persistence of these discrete molecular aggregates depends on localized restraint of the constituent molecules within specific domaines in the cell surface by strong intermolecular bonds and/or anchorage to extended cytoskeleton. The observed plasticity of many of organelles and the dynamical modulation of domaines induced by cellular signaling evidence evanescent intermolecular interactions even in conspicuous aggregates. There is also strong evidence that universal restraints on the mobility of cell surface proteins persist virtually everywhere in cell surfaces, not only in the discrete organelles. Diffusion of cell surface proteins is slowed by several orders of magnitude relative to corresponding protein diffusion coefficients in isolated lipid membranes as has been determined by various ensemble average methods of measurement such as fluorescence photobleaching recovery(FPR).

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