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Phylogenetic Profiles Reveal Structural and Functional Determinants of Lipid-binding.

Journal of proteomics & bioinformatics

Hong Y, Chalkia D, Ko KD, Bhardwaj G, Chang GS, van Rossum DB, Patterson RL.
PMID: 19946567
J Proteomics Bioinform. 2009 Mar 21;2:139-149. doi: 10.4172/jpb.1000071.

One of the major challenges in the genomic era is annotating structure/function to the vast quantities of sequence information now available. Indeed, most of the protein sequence database lacks comprehensive annotation, even when experimental evidence exists. Further, within structurally...

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Hong Y, Chalkia D, Ko KD, et al. Phylogenetic Profiles Reveal Structural and Functional Determinants of Lipid-binding. J Proteomics Bioinform. 2009;2:139-149doi: 10.4172/jpb.1000071.
Hong, Y., Chalkia, D., Ko, K. D., Bhardwaj, G., Chang, G. S., van Rossum, D. B., & Patterson, R. L. (2009). Phylogenetic Profiles Reveal Structural and Functional Determinants of Lipid-binding. Journal of proteomics & bioinformatics, 2139-149. https://doi.org/10.4172/jpb.1000071
Hong, Yoojin, et al. "Phylogenetic Profiles Reveal Structural and Functional Determinants of Lipid-binding." Journal of proteomics & bioinformatics vol. 2 (2009): 139-149. doi: https://doi.org/10.4172/jpb.1000071
Hong Y, Chalkia D, Ko KD, Bhardwaj G, Chang GS, van Rossum DB, Patterson RL. Phylogenetic Profiles Reveal Structural and Functional Determinants of Lipid-binding. J Proteomics Bioinform. 2009 Mar 21;2:139-149. doi: 10.4172/jpb.1000071. PMID: 19946567; PMCID: PMC2782862.
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Size matters: side chain length affects SH2 substrate binding.

Chemistry & biology

Becker CF.
PMID: 20338512
Chem Biol. 2010 Mar 26;17(3):211-2. doi: 10.1016/j.chembiol.2010.03.001.

The incorporation of lysine analogs in Src Homology 2 (SH2) domain variants by Virdee et al. (2010) reveals the length-dependent contribution of a single amino acid side chain in recognition of phosphotyrosine-containing substrate peptides and a change in specificity...

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Becker CF. Size matters: side chain length affects SH2 substrate binding. Chem Biol. 2010;17(3):211-2doi: 10.1016/j.chembiol.2010.03.001.
Becker, C. F. (2010). Size matters: side chain length affects SH2 substrate binding. Chemistry & biology, 17(3), 211-2. https://doi.org/10.1016/j.chembiol.2010.03.001
Becker, Christian F W. "Size matters: side chain length affects SH2 substrate binding." Chemistry & biology vol. 17,3 (2010): 211-2. doi: https://doi.org/10.1016/j.chembiol.2010.03.001
Becker CF. Size matters: side chain length affects SH2 substrate binding. Chem Biol. 2010 Mar 26;17(3):211-2. doi: 10.1016/j.chembiol.2010.03.001. PMID: 20338512.
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Phosphotyrosine Kinase Assays as a Prescreen for Inhibitors of EGFr.

Methods in molecular medicine

Edwards J, Bartlett JM.
PMID: 21340815
Methods Mol Med. 2001;39:577-81. doi: 10.1385/1-59259-071-3:577.

The epidermal growth factor receptor (EGFr) is a 170-kDa glycosylated transmembrane protein found in a wide variety of tissues (1). It is the receptor for epidermal growth factor (EGF), transforming growth factor α (TGFα), and other related growth factor...

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Edwards J, Bartlett JM. Phosphotyrosine Kinase Assays as a Prescreen for Inhibitors of EGFr. Methods Mol Med. 2001;39:577-81doi: 10.1385/1-59259-071-3:577.
Edwards, J., & Bartlett, J. M. (2001). Phosphotyrosine Kinase Assays as a Prescreen for Inhibitors of EGFr. Methods in molecular medicine, 39577-81. https://doi.org/10.1385/1-59259-071-3:577
Edwards, J, and Bartlett, J M. "Phosphotyrosine Kinase Assays as a Prescreen for Inhibitors of EGFr." Methods in molecular medicine vol. 39 (2001): 577-81. doi: https://doi.org/10.1385/1-59259-071-3:577
Edwards J, Bartlett JM. Phosphotyrosine Kinase Assays as a Prescreen for Inhibitors of EGFr. Methods Mol Med. 2001;39:577-81. doi: 10.1385/1-59259-071-3:577. PMID: 21340815.
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Tyrosine kinases in disease: overview of kinase inhibitors as therapeutic agents and current drugs in clinical trials.

Expert opinion on investigational drugs

Strawn LM, Shawver LK.
PMID: 15991993
Expert Opin Investig Drugs. 1998 Apr;7(4):553-73. doi: 10.1517/13543784.7.4.553.

Tyrosine kinases, first described as oncogenes, have been shown to play a role in normal cellular processes. Aberrations in tyrosine kinase activity lead to disease states. For fifteen years it has been postulated that the inhibition of tyrosine kinases...

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Strawn LM, Shawver LK. Tyrosine kinases in disease: overview of kinase inhibitors as therapeutic agents and current drugs in clinical trials. Expert Opin Investig Drugs. 1998;7(4):553-73doi: 10.1517/13543784.7.4.553.
Strawn, L. M., & Shawver, L. K. (1998). Tyrosine kinases in disease: overview of kinase inhibitors as therapeutic agents and current drugs in clinical trials. Expert opinion on investigational drugs, 7(4), 553-73. https://doi.org/10.1517/13543784.7.4.553
Strawn, L M, and Shawver, L K. "Tyrosine kinases in disease: overview of kinase inhibitors as therapeutic agents and current drugs in clinical trials." Expert opinion on investigational drugs vol. 7,4 (1998): 553-73. doi: https://doi.org/10.1517/13543784.7.4.553
Strawn LM, Shawver LK. Tyrosine kinases in disease: overview of kinase inhibitors as therapeutic agents and current drugs in clinical trials. Expert Opin Investig Drugs. 1998 Apr;7(4):553-73. doi: 10.1517/13543784.7.4.553. PMID: 15991993.
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Phosphotyrosine recognition domains: the typical, the atypical and the versatile.

Cell communication and signaling : CCS

Kaneko T, Joshi R, Feller SM, Li SS.
PMID: 23134684
Cell Commun Signal. 2012 Nov 07;10(1):32. doi: 10.1186/1478-811X-10-32.

SH2 domains are long known prominent players in the field of phosphotyrosine recognition within signaling protein networks. However, over the years they have been joined by an increasing number of other protein domain families that can, at least with...

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Kaneko T, Joshi R, Feller SM, et al. Phosphotyrosine recognition domains: the typical, the atypical and the versatile. Cell Commun Signal. 2012;10(1):32doi: 10.1186/1478-811X-10-32.
Kaneko, T., Joshi, R., Feller, S. M., & Li, S. S. (2012). Phosphotyrosine recognition domains: the typical, the atypical and the versatile. Cell communication and signaling : CCS, 10(1), 32. https://doi.org/10.1186/1478-811X-10-32
Kaneko, Tomonori, et al. "Phosphotyrosine recognition domains: the typical, the atypical and the versatile." Cell communication and signaling : CCS vol. 10,1 (2012): 32. doi: https://doi.org/10.1186/1478-811X-10-32
Kaneko T, Joshi R, Feller SM, Li SS. Phosphotyrosine recognition domains: the typical, the atypical and the versatile. Cell Commun Signal. 2012 Nov 07;10(1):32. doi: 10.1186/1478-811X-10-32. PMID: 23134684; PMCID: PMC3507883.
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STATs get their move on.

JAK-STAT

Reich NC.
PMID: 24470978
JAKSTAT. 2013 Oct 01;2(4):e27080. doi: 10.4161/jkst.27080. Epub 2013 Nov 13.

Understanding the mechanisms that regulate dynamic localization of a protein within a cell can provide critical insight to its functional molecular interactions. Signal transducers and activators of transcription (STATs) play essential roles in development, proliferation, and immune defense. However...

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Reich NC. STATs get their move on. JAKSTAT. 2013;2(4):e27080doi: 10.4161/jkst.27080.
Reich, N. C. (2013). STATs get their move on. JAK-STAT, 2(4), e27080. https://doi.org/10.4161/jkst.27080
Reich, Nancy C. "STATs get their move on." JAK-STAT vol. 2,4 (2013): e27080. doi: https://doi.org/10.4161/jkst.27080
Reich NC. STATs get their move on. JAKSTAT. 2013 Oct 01;2(4):e27080. doi: 10.4161/jkst.27080. Epub 2013 Nov 13. PMID: 24470978; PMCID: PMC3891633.
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WITHDRAWN: Intrinsic molecular characteristics of inhibiting STAT3 activation and dimerization through targeting the phosphotyrosine binding site within the SH2 domain-A molecular dynamics study.

Journal of structural biology

Fan Y, Kong R, Tweardy DJ, Wong ST.
PMID: 23428430
J Struct Biol. 2013 Feb 18; doi: 10.1016/j.jsb.2013.02.005. Epub 2013 Feb 18.

This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.

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Fan Y, Kong R, Tweardy DJ, et al. WITHDRAWN: Intrinsic molecular characteristics of inhibiting STAT3 activation and dimerization through targeting the phosphotyrosine binding site within the SH2 domain-A molecular dynamics study. J Struct Biol. 2013;doi: 10.1016/j.jsb.2013.02.005.
Fan, Y., Kong, R., Tweardy, D. J., & Wong, S. T. (2013). WITHDRAWN: Intrinsic molecular characteristics of inhibiting STAT3 activation and dimerization through targeting the phosphotyrosine binding site within the SH2 domain-A molecular dynamics study. Journal of structural biology, . https://doi.org/10.1016/j.jsb.2013.02.005
Fan, Yubo, et al. "WITHDRAWN: Intrinsic molecular characteristics of inhibiting STAT3 activation and dimerization through targeting the phosphotyrosine binding site within the SH2 domain-A molecular dynamics study." Journal of structural biology vol. (2013). doi: https://doi.org/10.1016/j.jsb.2013.02.005
Fan Y, Kong R, Tweardy DJ, Wong ST. WITHDRAWN: Intrinsic molecular characteristics of inhibiting STAT3 activation and dimerization through targeting the phosphotyrosine binding site within the SH2 domain-A molecular dynamics study. J Struct Biol. 2013 Feb 18; doi: 10.1016/j.jsb.2013.02.005. Epub 2013 Feb 18. PMID: 23428430.
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STAT3 expression is associated with poor survival in non-elderly adult patients with newly diagnosed multiple myeloma.

Blood research

Jung SH, Ahn SY, Choi HW, Shin MG, Lee SS, Yang DH, Ahn JS, Kim YK, Kim HJ, Lee JJ.
PMID: 29333406
Blood Res. 2017 Dec;52(4):293-299. doi: 10.5045/br.2017.52.4.293. Epub 2017 Dec 26.

BACKGROUND: Signal transducer and activator of transcription 3 (STAT3) is not only a key signaling molecule in the regulation of growth but is also involved in malignant transformation. We investigated the prognostic significance of STAT3 expression in 94 non-elderly...

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Jung SH, Ahn SY, Choi HW, et al. STAT3 expression is associated with poor survival in non-elderly adult patients with newly diagnosed multiple myeloma. Blood Res. 2017;52(4):293-299doi: 10.5045/br.2017.52.4.293.
Jung, S. H., Ahn, S. Y., Choi, H. W., Shin, M. G., Lee, S. S., Yang, D. H., Ahn, J. S., Kim, Y. K., Kim, H. J., & Lee, J. J. (2017). STAT3 expression is associated with poor survival in non-elderly adult patients with newly diagnosed multiple myeloma. Blood research, 52(4), 293-299. https://doi.org/10.5045/br.2017.52.4.293
Jung, Sung-Hoon, et al. "STAT3 expression is associated with poor survival in non-elderly adult patients with newly diagnosed multiple myeloma." Blood research vol. 52,4 (2017): 293-299. doi: https://doi.org/10.5045/br.2017.52.4.293
Jung SH, Ahn SY, Choi HW, Shin MG, Lee SS, Yang DH, Ahn JS, Kim YK, Kim HJ, Lee JJ. STAT3 expression is associated with poor survival in non-elderly adult patients with newly diagnosed multiple myeloma. Blood Res. 2017 Dec;52(4):293-299. doi: 10.5045/br.2017.52.4.293. Epub 2017 Dec 26. PMID: 29333406; PMCID: PMC5762740.
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Role of the N-terminal lid in regulating the interaction of phosphorylated MDMX with p53.

Oncotarget

Chan JV, Ping Koh DX, Liu Y, Joseph TL, Lane DP, Verma CS, Tan YS.
PMID: 29348869
Oncotarget. 2017 Dec 01;8(68):112825-112840. doi: 10.18632/oncotarget.22829. eCollection 2017 Dec 22.

Murine double minute 4 protein (MDMX) is crucial for the regulation of the tumor suppressor protein p53. Phosphorylation of the N-terminal domain of MDMX is thought to affect its binding with the transactivation domain of p53, thus playing a...

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Chan JV, Ping Koh DX, Liu Y, et al. Role of the N-terminal lid in regulating the interaction of phosphorylated MDMX with p53. Oncotarget. 2017;8(68):112825-112840doi: 10.18632/oncotarget.22829.
Chan, J. V., Ping Koh, D. X., Liu, Y., Joseph, T. L., Lane, D. P., Verma, C. S., & Tan, Y. S. (2017). Role of the N-terminal lid in regulating the interaction of phosphorylated MDMX with p53. Oncotarget, 8(68), 112825-112840. https://doi.org/10.18632/oncotarget.22829
Chan, Jane Vin, et al. "Role of the N-terminal lid in regulating the interaction of phosphorylated MDMX with p53." Oncotarget vol. 8,68 (2017): 112825-112840. doi: https://doi.org/10.18632/oncotarget.22829
Chan JV, Ping Koh DX, Liu Y, Joseph TL, Lane DP, Verma CS, Tan YS. Role of the N-terminal lid in regulating the interaction of phosphorylated MDMX with p53. Oncotarget. 2017 Dec 01;8(68):112825-112840. doi: 10.18632/oncotarget.22829. eCollection 2017 Dec 22. PMID: 29348869; PMCID: PMC5762554.
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Deregulation of tyrosine kinases in a rat macrophage tumor - ectopic expression of lck.

International journal of oncology

Sridhar T, Rema V, Swarup G, Khar A.
PMID: 21556564
Int J Oncol. 1995 Feb;6(2):487-92.

AK-5, a spontaneous rat macrophage tumor has 2-3 fold higher membrane-associated tyrosine kinase (TK) activity than normal peritoneal macrophages. lck, the lymphoid-specific TK, is expressed ectopically in AK-5. p56(lck), the protein product of lck, was detected in AK-5 by...

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Sridhar T, Rema V, Swarup G, et al. Deregulation of tyrosine kinases in a rat macrophage tumor - ectopic expression of lck. Int J Oncol. 1995;6(2):487-92
Sridhar, T., Rema, V., Swarup, G., & Khar, A. (1995). Deregulation of tyrosine kinases in a rat macrophage tumor - ectopic expression of lck. International journal of oncology, 6(2), 487-92.
Sridhar, T, et al. "Deregulation of tyrosine kinases in a rat macrophage tumor - ectopic expression of lck." International journal of oncology vol. 6,2 (1995): 487-92.
Sridhar T, Rema V, Swarup G, Khar A. Deregulation of tyrosine kinases in a rat macrophage tumor - ectopic expression of lck. Int J Oncol. 1995 Feb;6(2):487-92. PMID: 21556564.
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Structure Modeling of Human Tyrosyl-DNA Phosphodiesterase 1 and Screening for Its Inhibitors.

Acta naturae

Gushchina IV, Nilov DK, Zakharenko AL, Lavrik OI, Švedas VK.
PMID: 28740727
Acta Naturae. 2017 Apr-Jun;9(2):59-66.

The DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (Tdp1) represents a potential molecular target for anticancer therapy. A human Tdp1 model has been constructed using the methods of quantum and molecular mechanics, taking into account the ionization states of the...

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Gushchina IV, Nilov DK, Zakharenko AL, et al. Structure Modeling of Human Tyrosyl-DNA Phosphodiesterase 1 and Screening for Its Inhibitors. Acta Naturae. 2017;9(2):59-66
Gushchina, I. V., Nilov, D. K., Zakharenko, A. L., Lavrik, O. I., & Švedas, V. K. (2017). Structure Modeling of Human Tyrosyl-DNA Phosphodiesterase 1 and Screening for Its Inhibitors. Acta naturae, 9(2), 59-66.
Gushchina, I V, et al. "Structure Modeling of Human Tyrosyl-DNA Phosphodiesterase 1 and Screening for Its Inhibitors." Acta naturae vol. 9,2 (2017): 59-66.
Gushchina IV, Nilov DK, Zakharenko AL, Lavrik OI, Švedas VK. Structure Modeling of Human Tyrosyl-DNA Phosphodiesterase 1 and Screening for Its Inhibitors. Acta Naturae. 2017 Apr-Jun;9(2):59-66. PMID: 28740727; PMCID: PMC5509001.
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Specificity and regulation of phosphotyrosine signaling through SH2 domains.

Journal of structural biology: X

Marasco M, Carlomagno T.
PMID: 32647828
J Struct Biol X. 2020 May 27;4:100026. doi: 10.1016/j.yjsbx.2020.100026. eCollection 2020.

Phosphotyrosine (pY) signaling is instrumental to numerous cellular processes. pY recognition occurs through specialized protein modules, among which the Src-homology 2 (SH2) domain is the most common. SH2 domains are small protein modules with an invariant fold, and are...

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Marasco M, Carlomagno T. Specificity and regulation of phosphotyrosine signaling through SH2 domains. J Struct Biol X. 2020;4:100026doi: 10.1016/j.yjsbx.2020.100026.
Marasco, M., & Carlomagno, T. (2020). Specificity and regulation of phosphotyrosine signaling through SH2 domains. Journal of structural biology: X, 4100026. https://doi.org/10.1016/j.yjsbx.2020.100026
Marasco, Michelangelo, and Carlomagno, Teresa. "Specificity and regulation of phosphotyrosine signaling through SH2 domains." Journal of structural biology: X vol. 4 (2020): 100026. doi: https://doi.org/10.1016/j.yjsbx.2020.100026
Marasco M, Carlomagno T. Specificity and regulation of phosphotyrosine signaling through SH2 domains. J Struct Biol X. 2020 May 27;4:100026. doi: 10.1016/j.yjsbx.2020.100026. eCollection 2020. PMID: 32647828; PMCID: PMC7337045.
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Showing 13 to 24 of 200 entries