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Crystal structure of chemically synthesized [N33A] stromal cell-derived factor 1α, a potent ligand for the HIV-1 “fusin” coreceptor

Dealwis, Chris ; Fernandez, Elias J. ; Thompson, Darren A. ; [et al.]

Proceedings of the National Academy of Sciences ; 1998

In: Proceedings of the National Academy of Sciences Vol. 95, No. 12 ( 1998-06-09), p. 6941-6946

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In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 95, No. 12 ( 1998-06-09), p. 6941-6946

Abstract: Stromal cell-derived factor-1α (SDF-1α ) is a member of the chemokine superfamily and functions as a growth factor and chemoattractant through activation of CXCR4/LESTR/Fusin, a G protein-coupled receptor. This receptor also functions as a coreceptor for T-tropic syncytium-inducing strains of HIV-1. SDF-1α antagonizes infectivity of these strains by competing with gp120 for binding to the receptor. The crystal structure of a variant SDF-1α ([N33A]SDF-1α ) prepared by total chemical synthesis has been refined to 2.2-Å resolution. Although SDF-1α adopts a typical chemokine β-β-β-α topology, the packing of the α-helix against the β-sheet is strikingly different. Comparison of SDF-1α with other chemokine structures confirms the hypothesis that SDF-1α may be either an ancestral protein from which all other chemokines evolved or the chemokine that is the least divergent from a primordial chemokine. The structure of SDF-1α reveals a positively charged surface ideal for binding to the negatively charged extracellular loops of the CXCR4 HIV-1 coreceptor. This ionic complementarity is likely to promote the interaction of the mobile N-terminal segment of SDF-1α with interhelical sites of the receptor, resulting in a biological response.

Type of Medium: Online Resource

ISSN: 0027-8424 , 1091-6490

URL: Article

DOI: 10.1073/pnas.95.12.6941

RVK:

TA 1000

RVK:

WA 15000

Language: English

Publisher: Proceedings of the National Academy of Sciences

Publication Date: 1998

detail.hit.zdb_id: 209104-5

detail.hit.zdb_id: 1461794-8

SSG: 11

SSG: 12

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Comparison of the Structure of vMIP-II with Eotaxin-1, RANTES, and MCP-3 Suggests a Unique Mechanism for CCR3 Activation ,

Fernandez, Elias J. ; Wilken, Jill ; Thompson, Darren A. ; [et al.]

American Chemical Society (ACS) ; 2000

In: Biochemistry Vol. 39, No. 42 ( 2000-10-01), p. 12837-12844

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In: Biochemistry, American Chemical Society (ACS), Vol. 39, No. 42 ( 2000-10-01), p. 12837-12844

Type of Medium: Online Resource

ISSN: 0006-2960 , 1520-4995

URL: Article

DOI: 10.1021/bi001166f

RVK:

WA 15000

Language: English

Publisher: American Chemical Society (ACS)

Publication Date: 2000

detail.hit.zdb_id: 1472258-6

SSG: 12

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Structure, Function, and Inhibition of Chemokines

Fernandez, Elias J. ; Lolis, Elias

Annual Reviews ; 2002

In: Annual Review of Pharmacology and Toxicology Vol. 42, No. 1 ( 2002-04), p. 469-499

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In: Annual Review of Pharmacology and Toxicology, Annual Reviews, Vol. 42, No. 1 ( 2002-04), p. 469-499

Abstract: Chemokines are the largest family of cytokines in human immunophysiology. These proteins are defined by four invariant cysteines and are categorized based on the sequence around the first two cysteines, which leads to two major and two minor subfamilies. Chemokines function by activating specific G protein–coupled receptors, which results in, among other functions, the migration of inflammatory and noninflammatory cells to the appropriate tissues or compartments within tissues. Some of these proteins and receptors have been implicated or shown to be involved in inflammation, autoimmune diseases, and infection by HIV-1. The three-dimensional structure of each monomer is virtually identical, but the quaternary structure of chemokines is different for each subfamily. Structure-function studies reveal several regions of chemokines to be involved in function, with the N-terminal region playing a dominant role. A number of proteins and small-molecule antagonists have been identified that inhibit chemokine activities. In this review, we discuss aspects of the structure, function, and inhibition of chemokines.

Type of Medium: Online Resource

ISSN: 0362-1642 , 1545-4304

URL: Issue

URL: Article

DOI: 10.1146/pharmtox.2002.42.issue-1

DOI: 10.1146/annurev.pharmtox.42.091901.115838

RVK:

VT 2500

Language: English

Publisher: Annual Reviews

Publication Date: 2002

detail.hit.zdb_id: 1474461-2

SSG: 15,3

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A cryocooling technique for protein crystals grown by dialysis from volatile solvents

Fernandez, Elias J. ; Joachimiak, Andrzej ; Lolis, Elias

International Union of Crystallography (IUCr) ; 2000

In: Journal of Applied Crystallography Vol. 33, No. 1 ( 2000-02-01), p. 168-171

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In: Journal of Applied Crystallography, International Union of Crystallography (IUCr), Vol. 33, No. 1 ( 2000-02-01), p. 168-171

Abstract: The transfer of protein crystals from the original crystallization environment to cryoprotectants, heavy-atom solutions, or quartz capillary tubes, exposes crystal droplets to conditions that can cause evaporation of the droplet and damage to the crystal. This problem is particularly acute for crystals grown from volatile solvents or that are otherwise air-sensitive. Here a method that overcomes this problem is applied to crystals of macrophage inflammatory protein II encoded by herpesvirus-8. The method is based on dialysis and makes use of a dialysis adaptor that can be used with 24-well crystallization plates. This method permits the transfer of crystals to cryoprotectant conditions with greater ease and lowers the risk of mechanical damage relative to other available methods.

Type of Medium: Online Resource

ISSN: 0021-8898

URL: Article

DOI: 10.1107/S0021889899012406

RVK:

VA 4540

Language: Unknown

Publisher: International Union of Crystallography (IUCr)

Publication Date: 2000

detail.hit.zdb_id: 2020879-0

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Nanosecond Dynamics Regulate the MIF‐Induced Activity of CD74

Pantouris, Georgios ; Ho, Junming ; Shah, Dilip ; [et al.]

Wiley ; 2018

In: Angewandte Chemie Vol. 130, No. 24 ( 2018-06-11), p. 7234-7237

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In: Angewandte Chemie, Wiley, Vol. 130, No. 24 ( 2018-06-11), p. 7234-7237

Abstract: Macrophage migration inhibitory factor (MIF) activates CD74, which leads to severe disorders including inflammation, autoimmune diseases and cancer under pathological conditions. Molecular dynamics (MD) simulations up to one microsecond revealed dynamical correlation between a residue located at the opening of one end of the MIF solvent channel, previously thought to be a consequence of homotrimerization, and residues in a distal region responsible for CD74 activation. Experiments verified the allosteric regulatory site and identified a pathway to this site via the MIF β‐strands. The reported findings provide fundamental insights on a dynamic mechanism that controls the MIF‐induced activation of CD74.

Type of Medium: Online Resource

ISSN: 0044-8249 , 1521-3757

URL: Issue

URL: Article

DOI: 10.1002/ange.v130.24

DOI: 10.1002/ange.201803191

RVK:

VA 2100

RVK:

VN 5020

Language: English

Publisher: Wiley

Publication Date: 2018

detail.hit.zdb_id: 505868-5

detail.hit.zdb_id: 506609-8

detail.hit.zdb_id: 514305-6

detail.hit.zdb_id: 505872-7

detail.hit.zdb_id: 1479266-7

detail.hit.zdb_id: 505867-3

detail.hit.zdb_id: 506259-7

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Nanosecond Dynamics Regulate the MIF‐Induced Activity of CD74

Pantouris, Georgios ; Ho, Junming ; Shah, Dilip ; [et al.]

Wiley ; 2018

In: Angewandte Chemie International Edition Vol. 57, No. 24 ( 2018-06-11), p. 7116-7119

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In: Angewandte Chemie International Edition, Wiley, Vol. 57, No. 24 ( 2018-06-11), p. 7116-7119

Type of Medium: Online Resource

ISSN: 1433-7851 , 1521-3773

URL: Issue

URL: Article

DOI: 10.1002/anie.v57.24

DOI: 10.1002/anie.201803191

RVK:

VA 2100

Language: English

Publisher: Wiley

Publication Date: 2018

detail.hit.zdb_id: 2011836-3

detail.hit.zdb_id: 123227-7

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DataSheet1.pdf

Skeens, Erin ; Pantouris, Georgios ; Shah, Dilip ; [et al.]

Frontiers Media SA ; 2022

In: Frontiers in Molecular Biosciences Vol. 9 ( 2022-2-8)

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In: Frontiers in Molecular Biosciences, Frontiers Media SA, Vol. 9 ( 2022-2-8)

Abstract: Macrophage migration inhibitory factor (MIF) is an inflammatory protein with various non-overlapping functions. It is not only conserved in mammals, but it is found in parasites, fish, and plants. Human MIF is a homotrimer with an enzymatic cavity between two subunits with Pro1 as a catalytic base, activates the receptors CD74, CXCR2, and CXCR4, has functional interactions in the cytosol, and is reported to be a nuclease. There is a solvent channel down its 3-fold axis with a recently identified gating residue as an allosteric site important for regulating, to different extents, the enzymatic activity and CD74 binding and signaling. In this study we explore the consequence of converting the allosteric residue Tyr99 to cysteine (Y99C) and characterize its crystallographic structure, NMR dynamics, stability, CD74 function, and enzymatic activity. In addition to the homotrimeric variant, we develop strategies for expressing and purifying a heterotrimeric variant consisting of mixed wild type and Y99C for characterization of the allosteric site to provide more insight.

Type of Medium: Online Resource

ISSN: 2296-889X

URL: Article

DOI: 10.3389/fmolb.2022.783669

DOI: 10.3389/fmolb.2022.783669.s001

Language: Unknown

Publisher: Frontiers Media SA

Publication Date: 2022

detail.hit.zdb_id: 2814330-9

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Unraveling the mechanism of recognition of the 3’ splice site of the adenovirus major late promoter intron by the alternative splicing factor PUF60

Hsiao, Hsin-hao T. ; Crichlow, Gregg V. ; Murphy, James W. ; [et al.]

Public Library of Science (PLoS) ; 2020

In: PLOS ONE Vol. 15, No. 11 ( 2020-11-30), p. e0242725-

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In: PLOS ONE, Public Library of Science (PLoS), Vol. 15, No. 11 ( 2020-11-30), p. e0242725-

Abstract: Pre-mRNA splicing is critical for achieving required amounts of a transcript at a given time and for regulating production of encoded protein. A given pre-mRNA may be spliced in many ways, or not at all, giving rise to multiple gene products. Numerous splicing factors are recruited to pre-mRNA splice sites to ensure proper splicing. One such factor, the 60 kDa poly(U)-binding splicing factor (PUF60), is recruited to sites that are not always spliced, but rather function as alternative splice sites. In this study, we characterized the interaction of PUF60 with a splice site from the adenovirus major late promoter (the AdML 3' splice site, AdML 3’). We found that the PUF60– AdML 3’ dissociation constants are in the micromolar range, with the binding affinity predominantly provided by PUF60’s two central RNA recognition motifs (RRMs). A 1.95 Å crystal structure of the two PUF60 RRMs in complex with AdML 3’ revealed a dimeric organization placing two stretches of nucleic acid tracts in opposing directionalities, which can cause looping of nucleic acid and explain how PUF60 affects pre-mRNA geometry to effect splicing. Solution characterization of this complex by light-scattering and UV/Vis spectroscopy suggested a potential 2:1 (PUF60 2 : AdML 3’) stoichiometry, consistent with the crystal structure. This work defines the sequence specificity of the alternative splicing factor PUF60 at the pre-mRNA 3’ splice site. Our observations suggest that control of pre-mRNA directionality is important in the early stage of spliceosome assembly, and advance our understanding of the molecular mechanism by which alternative and constitutive splicing factors differentiate among 3’ splice sites.

Type of Medium: Online Resource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0242725

DOI: 10.1371/journal.pone.0242725.g001

DOI: 10.1371/journal.pone.0242725.g002

DOI: 10.1371/journal.pone.0242725.g003

DOI: 10.1371/journal.pone.0242725.g004

DOI: 10.1371/journal.pone.0242725.g005

DOI: 10.1371/journal.pone.0242725.g006

DOI: 10.1371/journal.pone.0242725.g007

DOI: 10.1371/journal.pone.0242725.g008

DOI: 10.1371/journal.pone.0242725.g009

DOI: 10.1371/journal.pone.0242725.g010

DOI: 10.1371/journal.pone.0242725.s001

DOI: 10.1371/journal.pone.0242725.s002

DOI: 10.1371/journal.pone.0242725.s003

DOI: 10.1371/journal.pone.0242725.s004

DOI: 10.1371/journal.pone.0242725.s005

DOI: 10.1371/journal.pone.0242725.s006

DOI: 10.1371/journal.pone.0242725.s007

DOI: 10.1371/journal.pone.0242725.s008

DOI: 10.1371/journal.pone.0242725.s009

DOI: 10.1371/journal.pone.0242725.s010

DOI: 10.1371/journal.pone.0242725.s011

DOI: 10.1371/journal.pone.0242725.s012

DOI: 10.1371/journal.pone.0242725.s013

DOI: 10.1371/journal.pone.0242725.s014

DOI: 10.1371/journal.pone.0242725.s015

DOI: 10.1371/journal.pone.0242725.s016

DOI: 10.1371/journal.pone.0242725.s017

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2020

detail.hit.zdb_id: 2267670-3

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MIF intersubunit disulfide mutant antagonist supports activation of CD74 by endogenous MIF trimer at physiologic concentrations

Fan, Chengpeng ; Rajasekaran, Deepa ; Syed, Mansoor Ali ; [et al.]

Proceedings of the National Academy of Sciences ; 2013

In: Proceedings of the National Academy of Sciences Vol. 110, No. 27 ( 2013-07-02), p. 10994-10999

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In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 110, No. 27 ( 2013-07-02), p. 10994-10999

Abstract: Macrophage migration inhibitory factor (MIF) is a proinflammatory cytokine. In addition to its known receptor-mediated biological activities, MIF possesses a catalytic site of unknown function between subunits of a homotrimer. Each subunit contributes three β-strands to adjacent subunits to form a core seven-stranded β-sheet for each monomer. MIF monomers, dimers, or trimers have been reported, but the active form that binds and activates the MIF receptor (CD74) is still a matter of debate. A cysteine mutant (N110C) that covalently locks MIF into a trimer by forming a disulfide with Cys-80 of an adjacent subunit is used to study this issue. Partial catalytic activity and receptor binding to CD74 are retained by N110C (locked trimer), but there is no cellular signaling. Wild-type MIF-induced cellular signaling, in vivo lung neutrophil accumulation, and alveolar permeability are inhibited with a fivefold excess of N110C. NMR and size-exclusion chromatography with light scattering reveal that N110C can form a higher-order oligomer in equilibrium with a single locked trimer. The X-ray structure confirms a local conformational change that disrupts the subunit interface and results in global changes responsible for the oligomeric form. The structure also confirms these changes are consistent for the partial catalytic and receptor binding activities. The absence of any potential monomer and the retention of partial catalytic and receptor binding activities despite changes in conformation (and dynamics) in the mutant support an endogenous MIF trimer that binds and activates CD74 at nanomolar concentrations. This conclusion has implications for therapeutic development.

Type of Medium: Online Resource

ISSN: 0027-8424 , 1091-6490

URL: Article

DOI: 10.1073/pnas.1221817110

RVK:

TA 1000

RVK:

WA 15000

Language: English

Publisher: Proceedings of the National Academy of Sciences

Publication Date: 2013

detail.hit.zdb_id: 209104-5

detail.hit.zdb_id: 1461794-8

SSG: 11

SSG: 12

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Allosteric inhibition of macrophage migration inhibitory factor revealed by ibudilast

Cho, Yoonsang ; Crichlow, Gregg V. ; Vermeire, Jon J. ; [et al.]

Proceedings of the National Academy of Sciences ; 2010

In: Proceedings of the National Academy of Sciences Vol. 107, No. 25 ( 2010-06-22), p. 11313-11318

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In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 107, No. 25 ( 2010-06-22), p. 11313-11318

Abstract: AV411 (ibudilast; 3-isobutyryl-2-isopropylpyrazolo-[1,5-a]pyridine) is an antiinflammatory drug that was initially developed for the treatment of bronchial asthma but which also has been used for cerebrovascular and ocular indications. It is a nonselective inhibitor of various phosphodiesterases (PDEs) and has varied antiinflammatory activity. More recently, AV411 has been studied as a possible therapeutic for the treatment of neuropathic pain and opioid withdrawal through its actions on glial cells. As described herein, the PDE inhibitor AV411 and its PDE-inhibition-compromised analog AV1013 inhibit the catalytic and chemotactic functions of the proinflammatory protein, macrophage migration inhibitory factor (MIF). Enzymatic analysis indicates that these compounds are noncompetitive inhibitors of the p -hydroxyphenylpyruvate (HPP) tautomerase activity of MIF and an allosteric binding site of AV411 and AV1013 is detected by NMR. The allosteric inhibition mechanism is further elucidated by X-ray crystallography based on the MIF/AV1013 binary and MIF/AV1013/HPP ternary complexes. In addition, our antibody experiments directed against MIF receptors indicate that CXCR2 is the major receptor for MIF-mediated chemotaxis of peripheral blood mononuclear cells.

Type of Medium: Online Resource

ISSN: 0027-8424 , 1091-6490

URL: Article

DOI: 10.1073/pnas.1002716107

RVK:

TA 1000

RVK:

WA 15000

Language: English

Publisher: Proceedings of the National Academy of Sciences

Publication Date: 2010

detail.hit.zdb_id: 209104-5

detail.hit.zdb_id: 1461794-8

SSG: 11

SSG: 12

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