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Sheng R, Jung DJ, Silkov A, Kim H, Singaram I, Wang ZG, Xin Y, Kim E, Park MJ, Thiagarajan-Rosenkranz P, Smrt S, Honig B, Baek K, Ryu S, Lorieau J, Kim YM, Cho W. Lipids Regulate Lck Protein Activity through Their Interactions with the Lck Src Homology 2 Domain. J Biol Chem 2016; 291:17639-50. [PMID: 27334919 DOI: 10.1074/jbc.m116.720284] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Indexed: 11/06/2022] Open
Abstract
Lymphocyte-specific protein-tyrosine kinase (Lck) plays an essential role in T cell receptor (TCR) signaling and T cell development, but its activation mechanism is not fully understood. To explore the possibility that plasma membrane (PM) lipids control TCR signaling activities of Lck, we measured the membrane binding properties of its regulatory Src homology 2 (SH2) and Src homology 3 domains. The Lck SH2 domain binds anionic PM lipids with high affinity but with low specificity. Electrostatic potential calculation, NMR analysis, and mutational studies identified the lipid-binding site of the Lck SH2 domain that includes surface-exposed basic, aromatic, and hydrophobic residues but not the phospho-Tyr binding pocket. Mutation of lipid binding residues greatly reduced the interaction of Lck with the ζ chain in the activated TCR signaling complex and its overall TCR signaling activities. These results suggest that PM lipids, including phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate, modulate interaction of Lck with its binding partners in the TCR signaling complex and its TCR signaling activities in a spatiotemporally specific manner via its SH2 domain.
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Affiliation(s)
- Ren Sheng
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Da-Jung Jung
- the Division of Integrative Biosciences and Biotechnology and
| | - Antonina Silkov
- the Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York 11032, and
| | - Hyunjin Kim
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Indira Singaram
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Zhi-Gang Wang
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Yao Xin
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Eui Kim
- the Division of Integrative Biosciences and Biotechnology and
| | - Mi-Jeong Park
- the Division of Integrative Biosciences and Biotechnology and
| | | | - Sean Smrt
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Barry Honig
- the Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York 11032, and
| | - Kwanghee Baek
- the Department of Genetic Engineering, Kyung Hee University, Yongin 446-701, Korea
| | - Sungho Ryu
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Justin Lorieau
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - You-Me Kim
- the Division of Integrative Biosciences and Biotechnology and Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea,
| | - Wonhwa Cho
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, the Department of Genetic Engineering, Kyung Hee University, Yongin 446-701, Korea
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2
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SH2 Domains Serve as Lipid-Binding Modules for pTyr-Signaling Proteins. Mol Cell 2016; 62:7-20. [PMID: 27052731 DOI: 10.1016/j.molcel.2016.01.027] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/21/2015] [Accepted: 01/26/2016] [Indexed: 01/26/2023]
Abstract
The Src-homology 2 (SH2) domain is a protein interaction domain that directs myriad phosphotyrosine (pY)-signaling pathways. Genome-wide screening of human SH2 domains reveals that ∼90% of SH2 domains bind plasma membrane lipids and many have high phosphoinositide specificity. They bind lipids using surface cationic patches separate from pY-binding pockets, thus binding lipids and the pY motif independently. The patches form grooves for specific lipid headgroup recognition or flat surfaces for non-specific membrane binding and both types of interaction are important for cellular function and regulation of SH2 domain-containing proteins. Cellular studies with ZAP70 showed that multiple lipids bind its C-terminal SH2 domain in a spatiotemporally specific manner and thereby exert exquisite spatiotemporal control over its protein binding and signaling activities in T cells. Collectively, this study reveals how lipids control SH2 domain-mediated cellular protein-protein interaction networks and suggest a new strategy for therapeutic modulation of pY-signaling pathways.
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Chintapalli SV, Bhardwaj G, Patel R, Shah N, Patterson RL, van Rossum DB, Anishkin A, Adams SH. Molecular dynamic simulations reveal the structural determinants of Fatty Acid binding to oxy-myoglobin. PLoS One 2015; 10:e0128496. [PMID: 26030763 PMCID: PMC4451517 DOI: 10.1371/journal.pone.0128496] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 04/27/2015] [Indexed: 11/18/2022] Open
Abstract
The mechanism(s) by which fatty acids are sequestered and transported in muscle have not been fully elucidated. A potential key player in this process is the protein myoglobin (Mb). Indeed, there is a catalogue of empirical evidence supporting direct interaction of globins with fatty acid metabolites; however, the binding pocket and regulation of the interaction remains to be established. In this study, we employed a computational strategy to elucidate the structural determinants of fatty acids (palmitic & oleic acid) binding to Mb. Sequence analysis and docking simulations with a horse (Equus caballus) structural Mb reference reveals a fatty acid-binding site in the hydrophobic cleft near the heme region in Mb. Both palmitic acid and oleic acid attain a "U" shaped structure similar to their conformation in pockets of other fatty acid-binding proteins. Specifically, we found that the carboxyl head group of palmitic acid coordinates with the amino group of Lys45, whereas the carboxyl group of oleic acid coordinates with both the amino groups of Lys45 and Lys63. The alkyl tails of both fatty acids are supported by surrounding hydrophobic residues Leu29, Leu32, Phe33, Phe43, Phe46, Val67, Val68 and Ile107. In the saturated palmitic acid, the hydrophobic tail moves freely and occasionally penetrates deeper inside the hydrophobic cleft, making additional contacts with Val28, Leu69, Leu72 and Ile111. Our simulations reveal a dynamic and stable binding pocket in which the oxygen molecule and heme group in Mb are required for additional hydrophobic interactions. Taken together, these findings support a mechanism in which Mb acts as a muscle transporter for fatty acid when it is in the oxygenated state and releases fatty acid when Mb converts to deoxygenated state.
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Affiliation(s)
- Sree V. Chintapalli
- Arkansas Children’s Nutrition Center, and Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- * E-mail: (SVC); (SHA)
| | - Gaurav Bhardwaj
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Reema Patel
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America
- Department of Physiology and Membrane Biology, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Natasha Shah
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America
- Department of Physiology and Membrane Biology, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Randen L. Patterson
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America
- Department of Physiology and Membrane Biology, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Damian B. van Rossum
- Center for Computational Proteomics, The Pennsylvania State University, State College, Pennsylvania, United States of America
- Department of Biology, The Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
| | - Sean H. Adams
- Arkansas Children’s Nutrition Center, and Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- * E-mail: (SVC); (SHA)
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Hedgepeth SC, Garcia MI, Wagner LE, Rodriguez AM, Chintapalli SV, Snyder RR, Hankins GDV, Henderson BR, Brodie KM, Yule DI, van Rossum DB, Boehning D. The BRCA1 tumor suppressor binds to inositol 1,4,5-trisphosphate receptors to stimulate apoptotic calcium release. J Biol Chem 2015; 290:7304-13. [PMID: 25645916 DOI: 10.1074/jbc.m114.611186] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The inositol 1,4,5-trisphosphate receptor (IP3R) is a ubiquitously expressed endoplasmic reticulum (ER)-resident calcium channel. Calcium release mediated by IP3Rs influences many signaling pathways, including those regulating apoptosis. IP3R activity is regulated by protein-protein interactions, including binding to proto-oncogenes and tumor suppressors to regulate cell death. Here we show that the IP3R binds to the tumor suppressor BRCA1. BRCA1 binding directly sensitizes the IP3R to its ligand, IP3. BRCA1 is recruited to the ER during apoptosis in an IP3R-dependent manner, and, in addition, a pool of BRCA1 protein is constitutively associated with the ER under non-apoptotic conditions. This is likely mediated by a novel lipid binding activity of the first BRCA1 C terminus domain of BRCA1. These findings provide a mechanistic explanation by which BRCA1 can act as a proapoptotic protein.
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Affiliation(s)
- Serena C Hedgepeth
- From the Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas 77030, the Cell Biology Graduate Program and
| | - M Iveth Garcia
- From the Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas 77030, the Cell Biology Graduate Program and
| | - Larry E Wagner
- the Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, New York 14642
| | - Ana M Rodriguez
- the Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, Texas 77555
| | - Sree V Chintapalli
- the Department of Biology, Penn State University, University Park, Pennsylvania, 16802, and
| | - Russell R Snyder
- the Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, Texas 77555
| | - Gary D V Hankins
- the Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, Texas 77555
| | - Beric R Henderson
- the Centre for Cancer Research, Westmead Millennium Institute at Westmead Hospital, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Kirsty M Brodie
- the Centre for Cancer Research, Westmead Millennium Institute at Westmead Hospital, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - David I Yule
- the Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, New York 14642
| | - Damian B van Rossum
- the Department of Biology, Penn State University, University Park, Pennsylvania, 16802, and
| | - Darren Boehning
- From the Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, Texas 77030,
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Kaneko T, Joshi R, Feller SM, Li SS. Phosphotyrosine recognition domains: the typical, the atypical and the versatile. Cell Commun Signal 2012; 10:32. [PMID: 23134684 PMCID: PMC3507883 DOI: 10.1186/1478-811x-10-32] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 10/09/2012] [Indexed: 12/21/2022] Open
Abstract
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 some of their members, also recognise pTyr residues in a sequence-specific context. This superfamily of pTyr recognition modules, which includes substantial fractions of the PTB domains, as well as much smaller, or even single member fractions like the HYB domain, the PKCδ and PKCθ C2 domains and RKIP, represents a fascinating, medically relevant and hence intensely studied part of the cellular signaling architecture of metazoans. Protein tyrosine phosphorylation clearly serves a plethora of functions and pTyr recognition domains are used in a similarly wide range of interaction modes, which encompass, for example, partner protein switching, tandem recognition functionalities and the interaction with catalytically active protein domains. If looked upon closely enough, virtually no pTyr recognition and regulation event is an exact mirror image of another one in the same cell. Thus, the more we learn about the biology and ultrastructural details of pTyr recognition domains, the more does it become apparent that nature cleverly combines and varies a few basic principles to generate a sheer endless number of sophisticated and highly effective recognition/regulation events that are, under normal conditions, elegantly orchestrated in time and space. This knowledge is also valuable when exploring pTyr reader domains as diagnostic tools, drug targets or therapeutic reagents to combat human diseases.
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Affiliation(s)
- Tomonori Kaneko
- Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.
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Basu MK, Selengut JD, Haft DH. ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. BMC Bioinformatics 2011; 12:434. [PMID: 22070167 PMCID: PMC3226654 DOI: 10.1186/1471-2105-12-434] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 11/09/2011] [Indexed: 12/02/2022] Open
Abstract
Background Phylogenetic profiling is a technique of scoring co-occurrence between a protein family and some other trait, usually another protein family, across a set of taxonomic groups. In spite of several refinements in recent years, the technique still invites significant improvement. To be its most effective, a phylogenetic profiling algorithm must be able to examine co-occurrences among protein families whose boundaries are uncertain within large homologous protein superfamilies. Results Partial Phylogenetic Profiling (PPP) is an iterative algorithm that scores a given taxonomic profile against the taxonomic distribution of families for all proteins in a genome. The method works through optimizing the boundary of each protein family, rather than by relying on prebuilt protein families or fixed sequence similarity thresholds. Double Partial Phylogenetic Profiling (DPPP) is a related procedure that begins with a single sequence and searches for optimal granularities for its surrounding protein family in order to generate the best query profiles for PPP. We present ProPhylo, a high-performance software package for phylogenetic profiling studies through creating individually optimized protein family boundaries. ProPhylo provides precomputed databases for immediate use and tools for manipulating the taxonomic profiles used as queries. Conclusion ProPhylo results show universal markers of methanogenesis, a new DNA phosphorothioation-dependent restriction enzyme, and efficacy in guiding protein family construction. The software and the associated databases are freely available under the open source Perl Artistic License from ftp://ftp.jcvi.org/pub/data/ppp/.
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Affiliation(s)
- Malay K Basu
- J. Craig Venter Institute, Rockville, MD 20850, USA.
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Hong Y, Kang J, Lee D, van Rossum DB. Adaptive GDDA-BLAST: fast and efficient algorithm for protein sequence embedding. PLoS One 2010; 5:e13596. [PMID: 21042584 PMCID: PMC2962639 DOI: 10.1371/journal.pone.0013596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 09/28/2010] [Indexed: 11/28/2022] Open
Abstract
A major computational challenge in the genomic era is annotating structure/function to the vast quantities of sequence information that is now available. This problem is illustrated by the fact that most proteins lack comprehensive annotations, even when experimental evidence exists. We previously theorized that embedded-alignment profiles (simply "alignment profiles" hereafter) provide a quantitative method that is capable of relating the structural and functional properties of proteins, as well as their evolutionary relationships. A key feature of alignment profiles lies in the interoperability of data format (e.g., alignment information, physio-chemical information, genomic information, etc.). Indeed, we have demonstrated that the Position Specific Scoring Matrices (PSSMs) are an informative M-dimension that is scored by quantitatively measuring the embedded or unmodified sequence alignments. Moreover, the information obtained from these alignments is informative, and remains so even in the "twilight zone" of sequence similarity (<25% identity). Although our previous embedding strategy was powerful, it suffered from contaminating alignments (embedded AND unmodified) and high computational costs. Herein, we describe the logic and algorithmic process for a heuristic embedding strategy named "Adaptive GDDA-BLAST." Adaptive GDDA-BLAST is, on average, up to 19 times faster than, but has similar sensitivity to our previous method. Further, data are provided to demonstrate the benefits of embedded-alignment measurements in terms of detecting structural homology in highly divergent protein sequences and isolating secondary structural elements of transmembrane and ankyrin-repeat domains. Together, these advances allow further exploration of the embedded alignment data space within sufficiently large data sets to eventually induce relevant statistical inferences. We show that sequence embedding could serve as one of the vehicles for measurement of low-identity alignments and for incorporation thereof into high-performance PSSM-based alignment profiles.
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Affiliation(s)
- Yoojin Hong
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Center for Computational Proteomics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jaewoo Kang
- Department of Computer Science and Engineering, Korea University, Seoul, Korea
- Department of Biostatistics, College of Medicine, Korea University, Seoul, Korea
| | - Dongwon Lee
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- College of Information Sciences and Technology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Damian B. van Rossum
- Center for Computational Proteomics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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Kiselyov K, van Rossum DB, Patterson RL. TRPC Channels in Pheromone Sensing. VITAMINS & HORMONES 2010; 83:197-213. [DOI: 10.1016/s0083-6729(10)83008-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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