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Specificity landscapes unmask submaximal binding site preferences of transcription factors

Bhimsaria, Devesh ; Rodríguez-Martínez, José A. ; Pan, Junkun ; [et al.]

Proceedings of the National Academy of Sciences ; 2018

In: Proceedings of the National Academy of Sciences Vol. 115, No. 45 ( 2018-11-06)

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In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 115, No. 45 ( 2018-11-06)

Abstract: We have developed Differential Specificity and Energy Landscape (DiSEL) analysis to comprehensively compare DNA–protein interactomes (DPIs) obtained by high-throughput experimental platforms and cutting edge computational methods. While high-affinity DNA binding sites are identified by most methods, DiSEL uncovered nuanced sequence preferences displayed by homologous transcription factors. Pairwise analysis of 726 DPIs uncovered homolog-specific differences at moderate- to low-affinity binding sites (submaximal sites). DiSEL analysis of variants of 41 transcription factors revealed that many disease-causing mutations result in allele-specific changes in binding site preferences. We focused on a set of highly homologous factors that have different biological roles but “read” DNA using identical amino acid side chains. Rather than direct readout, our results indicate that DNA noncontacting side chains allosterically contribute to sculpt distinct sequence preferences among closely related members of transcription factor families.

Type of Medium: Online Resource

ISSN: 0027-8424 , 1091-6490

URL: Article

DOI: 10.1073/pnas.1811431115

RVK:

TA 1000

RVK:

WA 15000

Language: English

Publisher: Proceedings of the National Academy of Sciences

Publication Date: 2018

detail.hit.zdb_id: 209104-5

detail.hit.zdb_id: 1461794-8

SSG: 11

SSG: 12

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Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB

Korkmaz, Elif Nihal ; Nussinov, Ruth ; Haliloğlu, Türkan ; [et al.]

Public Library of Science (PLoS) ; 2012

In: PLoS Computational Biology Vol. 8, No. 3 ( 2012-3-15), p. e1002420-

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In: PLoS Computational Biology, Public Library of Science (PLoS), Vol. 8, No. 3 ( 2012-3-15), p. e1002420-

Type of Medium: Online Resource

ISSN: 1553-7358

URL: Article

DOI: 10.1371/journal.pcbi.1002420

DOI: 10.1371/journal.pcbi.1002420.g001

DOI: 10.1371/journal.pcbi.1002420.g002

DOI: 10.1371/journal.pcbi.1002420.g003

DOI: 10.1371/journal.pcbi.1002420.g004

DOI: 10.1371/journal.pcbi.1002420.g005

DOI: 10.1371/journal.pcbi.1002420.g006

DOI: 10.1371/journal.pcbi.1002420.t001

DOI: 10.1371/journal.pcbi.1002420.s001

DOI: 10.1371/journal.pcbi.1002420.s002

DOI: 10.1371/journal.pcbi.1002420.s003

DOI: 10.1371/journal.pcbi.1002420.s004

DOI: 10.1371/journal.pcbi.1002420.s005

DOI: 10.1371/journal.pcbi.1002420.s006

DOI: 10.1371/journal.pcbi.1002420.s007

DOI: 10.1371/journal.pcbi.1002420.s008

DOI: 10.1371/journal.pcbi.1002420.s009

DOI: 10.1371/journal.pcbi.1002420.s010

DOI: 10.1371/journal.pcbi.1002420.s011

DOI: 10.1371/journal.pcbi.1002420.s012

DOI: 10.1371/journal.pcbi.1002420.s013

DOI: 10.1371/journal.pcbi.1002420.s014

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2012

detail.hit.zdb_id: 2193340-6

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Identification of the Ah-Receptor Structural Determinants for Ligand Preferences

Xing, Yongna ; Nukaya, Manabu ; Satyshur, Kenneth A. ; [et al.]

Oxford University Press (OUP) ; 2012

In: Toxicological Sciences Vol. 129, No. 1 ( 2012-9), p. 86-97

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In: Toxicological Sciences, Oxford University Press (OUP), Vol. 129, No. 1 ( 2012-9), p. 86-97

Type of Medium: Online Resource

ISSN: 1096-0929 , 1096-6080

URL: Article

DOI: 10.1093/toxsci/kfs194

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2012

detail.hit.zdb_id: 1471974-5

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Interplay of Electrostatics and Hydrophobic Effects in the Metamorphic Protein Human Lymphotactin

Korkmaz, Elif Nihal ; Volkman, Brian F. ; Cui, Qiang

American Chemical Society (ACS) ; 2015

In: The Journal of Physical Chemistry B Vol. 119, No. 30 ( 2015-07-30), p. 9547-9558

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In: The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol. 119, No. 30 ( 2015-07-30), p. 9547-9558

Type of Medium: Online Resource

ISSN: 1520-6106 , 1520-5207

URL: Article

DOI: 10.1021/acs.jpcb.5b02810

RVK:

VA5430.B

Language: English

Publisher: American Chemical Society (ACS)

Publication Date: 2015

detail.hit.zdb_id: 1357799-2

detail.hit.zdb_id: 2006039-7

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Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly

Taylor, Keenan C. ; Buvoli, Massimo ; Korkmaz, Elif Nihal ; [et al.]

Proceedings of the National Academy of Sciences ; 2015

In: Proceedings of the National Academy of Sciences Vol. 112, No. 29 ( 2015-07-21)

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In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 112, No. 29 ( 2015-07-21)

Abstract: The rod of sarcomeric myosins directs thick filament assembly and is characterized by the insertion of four skip residues that introduce discontinuities in the coiled-coil heptad repeats. We report here that the regions surrounding the first three skip residues share high structural similarity despite their low sequence homology. Near each of these skip residues, the coiled-coil transitions to a nonclose-packed structure inducing local relaxation of the superhelical pitch. Moreover, molecular dynamics suggest that these distorted regions can assume different conformationally stable states. In contrast, the last skip residue region constitutes a true molecular hinge, providing C-terminal rod flexibility. Assembly of myosin with mutated skip residues in cardiomyocytes shows that the functional importance of each skip residue is associated with rod position and reveals the unique role of the molecular hinge in promoting myosin antiparallel packing. By defining the biophysical properties of the rod, the structures and molecular dynamic calculations presented here provide insight into thick filament formation, and highlight the structural differences occurring between the coiled-coils of myosin and the stereotypical tropomyosin. In addition to extending our knowledge into the conformational and biological properties of coiled-coil discontinuities, the molecular characterization of the four myosin skip residues also provides a guide to modeling the effects of rod mutations causing cardiac and skeletal myopathies.

Type of Medium: Online Resource

ISSN: 0027-8424 , 1091-6490

URL: Article

DOI: 10.1073/pnas.1505813112

RVK:

TA 1000

RVK:

WA 15000

Language: English

Publisher: Proceedings of the National Academy of Sciences

Publication Date: 2015

detail.hit.zdb_id: 209104-5

detail.hit.zdb_id: 1461794-8

SSG: 11

SSG: 12

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Poster presentations

Aksu, Funda ; Topacoglu, Hakan ; Arman, Candan ; [et al.]

Springer Science and Business Media LLC ; 2009

In: Surgical and Radiologic Anatomy Vol. 31, No. S1 ( 2009-9), p. 95-229

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In: Surgical and Radiologic Anatomy, Springer Science and Business Media LLC, Vol. 31, No. S1 ( 2009-9), p. 95-229

Type of Medium: Online Resource

ISSN: 0930-1038 , 1279-8517

URL: Article

DOI: 10.1007/BF03371486

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2009

detail.hit.zdb_id: 1461974-X

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Effects of hospital facilities on patient outcomes after cancer surgery: an international, prospective, observational study

Knight, Stephen R ; Shaw, Catherine A ; Pius, Riinu ; [et al.]

Elsevier BV ; 2022

In: The Lancet Global Health Vol. 10, No. 7 ( 2022-07), p. e1003-e1011

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In: The Lancet Global Health, Elsevier BV, Vol. 10, No. 7 ( 2022-07), p. e1003-e1011

Type of Medium: Online Resource

ISSN: 2214-109X

URL: Article

DOI: 10.1016/S2214-109X(22)00168-1

Language: English

Publisher: Elsevier BV

Publication Date: 2022

detail.hit.zdb_id: 2723488-5

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Global variation in postoperative mortality and complications after cancer surgery: a multicentre, prospective cohort study in 82 countries

Knight, Stephen R ; Shaw, Catherine A ; Pius, Riinu ; [et al.]

Elsevier BV ; 2021

In: The Lancet Vol. 397, No. 10272 ( 2021-01), p. 387-397

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In: The Lancet, Elsevier BV, Vol. 397, No. 10272 ( 2021-01), p. 387-397

Type of Medium: Online Resource

ISSN: 0140-6736

URL: Article

DOI: 10.1016/S0140-6736(21)00001-5

RVK:

XA 10000

Language: English

Publisher: Elsevier BV

Publication Date: 2021

detail.hit.zdb_id: 2067452-1

detail.hit.zdb_id: 3306-6

detail.hit.zdb_id: 1476593-7

SSG: 5,21

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Eğitim ve Bilim Dergisinde Liderlik Alanında Yapılmış Makalelerin İncelenmesi ve Değerlendirilmesi

İLERİ, Gönül ; YÜCE, ALİ RAĞIP ; DUMAN, Nuriye Sanem ; [et al.]

ASOS Yayinevi ; 2023

In: Social Sciences Studies Journal Vol. 108, No. 108 ( 2023), p. 5332-5347

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In: Social Sciences Studies Journal, ASOS Yayinevi, Vol. 108, No. 108 ( 2023), p. 5332-5347

Type of Medium: Online Resource

ISSN: 2587-1587

URL: Article

DOI: 10.29228/sssj.67036

Language: Unknown

Publisher: ASOS Yayinevi

Publication Date: 2023

detail.hit.zdb_id: 2936460-7

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Incidence of Type 1 Diabetes in Children Aged Below 18 Years During 2013-2015 in Northwest Turkey

Poyrazoğlu, Şükran ; Bundak, Rüveyde ; Yavaş Abal, Zehra ; [et al.]

Galenos Yayinevi ; 2018

In: Journal of Clinical Research in Pediatric Endocrinology ( 2018-05-23)

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In: Journal of Clinical Research in Pediatric Endocrinology, Galenos Yayinevi, ( 2018-05-23)

Type of Medium: Online Resource

ISSN: 1308-5727 , 1308-5735

URL: Journal

URL: Article

DOI: 10.4274/jcrpe

DOI: 10.4274/jcrpe.0025

Language: Unknown

Publisher: Galenos Yayinevi

Publication Date: 2018

detail.hit.zdb_id: 2571625-6

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