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Journal articles on the topic 'LIM domains'

Author: Grafiati

Published: 20 February 2023

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1

Matthews, Jacqueline M., Mugdha Bhati, Vanessa J. Craig, et al. "Competition between LIM-binding domains." Biochemical Society Transactions 36, no. 6 (2008): 1393–97. http://dx.doi.org/10.1042/bst0361393.

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LMO (LIM-only) and LIM-HD (LIM-homeodomain) proteins form a family of proteins that is required for myriad developmental processes and which can contribute to diseases such as T-cell leukaemia and breast cancer. The four LMO and 12 LIM-HD proteins in mammals are expressed in a combinatorial manner in many cell types, forming a transcriptional ‘LIM code’. The proteins all contain a pair of closely spaced LIM domains near their N-termini that mediate protein–protein interactions, including binding to the ∼30-residue LID (LIM interaction domain) of the essential co-factor protein Ldb1 (LIM domain

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2

RABBITTS, T. H., and T. BOEHM. "LIM domains." Nature 346, no. 6283 (1990): 418. http://dx.doi.org/10.1038/346418a0.

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3

El Omari, Kamel, Sarah J. Hoosdally, Kapil Tuladhar, et al. "Structure of the leukemia oncogene LMO2: implications for the assembly of a hematopoietic transcription factor complex." Blood 117, no. 7 (2011): 2146–56. http://dx.doi.org/10.1182/blood-2010-07-293357.

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Abstract The LIM only protein 2 (LMO2) is a key regulator of hematopoietic stem cell development whose ectopic expression in T cells leads to the onset of acute lymphoblastic leukemia. Through its LIM domains, LMO2 is thought to function as the scaffold for a DNA-binding transcription regulator complex, including the basic helix-loop-helix proteins SCL/TAL1 and E47, the zinc finger protein GATA-1, and LIM-domain interacting protein LDB1. To understand the role of LMO2 in the formation of this complex and ultimately to dissect its function in normal and aberrant hematopoiesis, we solved the cry

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4

Breen, Joseph J., Alan D. Agulnick, Heiner Westphal, and Igor B. Dawid. "Interactions between LIM Domains and the LIM Domain-binding Protein Ldb1." Journal of Biological Chemistry 273, no. 8 (1998): 4712–17. http://dx.doi.org/10.1074/jbc.273.8.4712.

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SCHMEICHEL, Karen L., and Mary C. BECKERLE. "LIM domains of cysteine-rich protein 1 (CRP1) are essential for its zyxin-binding function." Biochemical Journal 331, no. 3 (1998): 885–92. http://dx.doi.org/10.1042/bj3310885.

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Previous studies have demonstrated that the adhesion-plaque protein, zyxin, interacts specifically with a 23 kDa protein, called the cysteine-rich protein 1 (CRP1), which has been implicated in myogenesis. Primary sequence analyses have revealed that both zyxin and CRP1 exhibit multiple copies of a structural motif called the LIM domain. LIM domains, which are defined by the consensus CX2CX16–23HX2CX2CX2CX16–23CX2–3(C,H,D), are found in a variety of proteins that are involved in cell growth and differentiation. Recent studies have established that LIM domains are zinc-binding structures that m

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Jurata, L. W., and G. N. Gill. "Functional analysis of the nuclear LIM domain interactor NLI." Molecular and Cellular Biology 17, no. 10 (1997): 5688–98. http://dx.doi.org/10.1128/mcb.17.10.5688.

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LIM homeodomain and LIM-only (LMO) transcription factors contain two tandemly arranged Zn2+-binding LIM domains capable of mediating protein-protein interactions. These factors have restricted patterns of expression, are found in invertebrates as well as vertebrates, and are required for cell type specification in a variety of developing tissues. A recently identified, widely expressed protein, NLI, binds with high affinity to the LIM domains of LIM homeodomain and LMO proteins in vitro and in vivo. In this study, a 38-amino-acid fragment of NLI was found to be sufficient for the association o

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Winkelman, Jonathan D., Caitlin A. Anderson, Cristian Suarez, David R. Kovar, and Margaret L. Gardel. "Evolutionarily diverse LIM domain-containing proteins bind stressed actin filaments through a conserved mechanism." Proceedings of the National Academy of Sciences 117, no. 41 (2020): 25532–42. http://dx.doi.org/10.1073/pnas.2004656117.

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The actin cytoskeleton assembles into diverse load-bearing networks, including stress fibers (SFs), muscle sarcomeres, and the cytokinetic ring to both generate and sense mechanical forces. The LIM (Lin11, Isl- 1, and Mec-3) domain family is functionally diverse, but most members can associate with the actin cytoskeleton with apparent force sensitivity. Zyxin rapidly localizes via its LIM domains to failing SFs in cells, known as strain sites, to initiate SF repair and maintain mechanical homeostasis. The mechanism by which these LIM domains associate with stress fiber strain sites (SFSS) is n

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8

O'Keefe, D. D., S. Thor, and J. B. Thomas. "Function and specificity of LIM domains in Drosophila nervous system and wing development." Development 125, no. 19 (1998): 3915–23. http://dx.doi.org/10.1242/dev.125.19.3915.

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LIM domains are found in a variety of proteins, including cytoplasmic and nuclear LIM-only proteins, LIM-homeodomain (LIM-HD) transcription factors and LIM-kinases. Although the ability of LIM domains to interact with other proteins has been clearly established in vitro and in cultured cells, their in vivo function is unknown. Here we use Drosophila to test the roles of the LIM domains of the LIM-HD family member Apterous (Ap) in wing and nervous system development. Using a rescuing assay of the ap mutant phenotype, we have found that the LIM domains are essential for Ap function. Furthermore,

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9

Thomas, Clément, Flora Moreau, Monika Dieterle, et al. "The LIM Domains of WLIM1 Define a New Class of Actin Bundling Modules." Journal of Biological Chemistry 282, no. 46 (2007): 33599–608. http://dx.doi.org/10.1074/jbc.m703691200.

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Actin filament bundling, i.e. the formation of actin cables, is an important process that relies on proteins able to directly bind and cross-link subunits of adjacent actin filaments. Animal cysteine-rich proteins and their plant counterparts are two LIM domain-containing proteins that were recently suggested to define a new family of actin cytoskeleton regulators involved in actin filament bundling. We here identified the LIM domains as responsible for F-actin binding and bundling activities of the tobacco WLIM1. The deletion of one of the two LIM domains reduced significantly, but did not en

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NAGATA, Kyoko, Kazumasa OHASHI, Neng YANG, and Kensaku MIZUNO. "The N-terminal LIM domain negatively regulates the kinase activity ofLIM-kinase 1." Biochemical Journal 343, no. 1 (1999): 99–105. http://dx.doi.org/10.1042/bj3430099.

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LIM-kinase 1 (LIMK1, where LIM is an acronym of the three gene products Lin-11, Isl-1 and Mec-3) is a serine/threonine kinase that phosphorylates cofilin and regulates actin cytoskeletal reorganization. LIMK1 contains two LIM domains and a PDZ (an acronym of the three proteins PSD-95, Dlg and ZO-1) domain in the N-terminal half and a kinase domain in the C-terminal half. In this study we examined the role of the extra-catalytic region in the regulation of kinase activity of LIMK1. Limited proteolysis of LIMK1 resulted in the production of the 35-40-kDa kinase core fragments with 3.5-5.5-fold i

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Guy, Pamela M., Daryn A. Kenny та Gordon N. Gill. "The PDZ Domain of the LIM Protein Enigma Binds to β-Tropomyosin". Molecular Biology of the Cell 10, № 6 (1999): 1973–84. http://dx.doi.org/10.1091/mbc.10.6.1973.

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PDZ and LIM domains are modular protein interaction motifs present in proteins with diverse functions. Enigma is representative of a family of proteins composed of a series of conserved PDZ and LIM domains. The LIM domains of Enigma and its most related family member, Enigma homology protein, bind to protein kinases, whereas the PDZ domains of Enigma and family member actin-associated LIM protein bind to actin filaments. Enigma localizes to actin filaments in fibroblasts via its PDZ domain, and actin-associated LIM protein binds to and colocalizes with the actin-binding protein α-actinin-2 at

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Johnson, J. D., W. Zhang, A. Rudnick, W. J. Rutter, and M. S. German. "Transcriptional synergy between LIM-homeodomain proteins and basic helix-loop-helix proteins: the LIM2 domain determines specificity." Molecular and Cellular Biology 17, no. 7 (1997): 3488–96. http://dx.doi.org/10.1128/mcb.17.7.3488.

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LIM-homeodomain proteins direct cellular differentiation by activating transcription of cell-type-specific genes, but this activation requires cooperation with other nuclear factors. The LIM-homeodomain protein Lmx1 cooperates with the basic helix-loop-helix (bHLH) protein E47/Pan-1 to activate the insulin promoter in transfected fibroblasts. In this study, we show that two proteins originally called Lmx1 are the closely related products of two distinct vertebrate genes, Lmx1.1 and Lmx1.2. We have used yeast genetic systems to delineate the functional domains of the Lmx1 proteins and to charac

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te Velthuis, Aartjan J. W., and Christoph P. Bagowski. "PDZ and LIM Domain-Encoding Genes: Molecular Interactions and their Role in Development." Scientific World JOURNAL 7 (2007): 1470–92. http://dx.doi.org/10.1100/tsw.2007.232.

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PDZ/LIM genes encode a group of proteins that play very important, but diverse, biological roles. They have been implicated in numerous vital processes, e.g., cytoskeleton organization, neuronal signaling, cell lineage specification, organ development, and oncogenesis.In mammals, there are ten genes that encode for both a PDZ domain, and one or several LIM domains: four genes of the ALP subfamily (ALP, Elfin, Mystique, and RIL), three of the Enigma subfamily (Enigma, Enigma Homolog, and ZASP), the two LIM kinases (LIMK1 and LIMK2), and the LIM only protein 7 (LMO7). Functionally, all PDZ and L

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Thomas, Clement, Monika Dieterle, Sabrina Gatti, et al. "Actin bundling via LIM domains." Plant Signaling & Behavior 3, no. 5 (2008): 320–21. http://dx.doi.org/10.4161/psb.3.5.5310.

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15

Gill, Gordon N. "The enigma of LIM domains." Structure 3, no. 12 (1995): 1285–89. http://dx.doi.org/10.1016/s0969-2126(01)00265-9.

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16

Brown, Michael C., Joseph A. Perrotta, and Christopher E. Turner. "Serine and Threonine Phosphorylation of the Paxillin LIM Domains Regulates Paxillin Focal Adhesion Localization and Cell Adhesion to Fibronectin." Molecular Biology of the Cell 9, no. 7 (1998): 1803–16. http://dx.doi.org/10.1091/mbc.9.7.1803.

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We have previously shown that the LIM domains of paxillin operate as the focal adhesion (FA)-targeting motif of this protein. In the current study, we have identified the capacity of paxillin LIM2 and LIM3 to serve as binding sites for, and substrates of serine/threonine kinases. The activities of the LIM2- and LIM3-associated kinases were stimulated after adhesion of CHO.K1 cells to fibronectin; consequently, a role for LIM domain phosphorylation in regulating the subcellular localization of paxillin after adhesion to fibronectin was investigated. An avian paxillin-CHO.K1 model system was use

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17

Li, Bo, Lei Zhuang, and Beat Trueb. "Zyxin Interacts with the SH3 Domains of the Cytoskeletal Proteins LIM-nebulette and Lasp-1." Journal of Biological Chemistry 279, no. 19 (2004): 20401–10. http://dx.doi.org/10.1074/jbc.m310304200.

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Zyxin is a versatile component of focal adhesions in eukaryotic cells. Here we describe a novel binding partner of zyxin, which we have named LIM-nebulette. LIM-nebulette is an alternative splice variant of the sarcomeric protein nebulette, which, in contrast to nebulette, is expressed in non-muscle cells. It displays a modular structure with an N-terminal LIM domain, three nebulin-like repeats, and a C-terminal SH3 domain and shows high similarity to another cytoskeletal protein, Lasp-1 (LIM and SH3 protein-1). Co-precipitation studies and results obtained with the two-hybrid system demonstra

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18

Seo, So Yeon, Bora Lee, and Seunghee Lee. "Critical Roles of the LIM Domains of Lhx3 in Recruiting Coactivators to the Motor Neuron-Specifying Isl1-Lhx3 Complex." Molecular and Cellular Biology 35, no. 20 (2015): 3579–89. http://dx.doi.org/10.1128/mcb.00335-15.

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During spinal cord development, the LIM domains of the LIM homeodomain factor Lhx3 bind to either the LIM cofactor nuclear LIM interactor (NLI) or another LIM homeodomain factor, Isl1, assembling the tetrameric V2 interneuron-specifying Lhx3 complex (2NLI:2Lhx3) or the hexameric motor neuron-specifying Isl1-Lhx3 complex (2NLI:2Isl1:2Lhx3). However, the detailed molecular basis by which the Lhx3-LIM domains contribute to motor neuron specification still remains poorly understood. Here, we show that the Lhx3-LIM domains are essential for recruiting transcriptional coactivators to the Isl1-Lhx3 c

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Rath, Nibedita, Zhishan Wang, Min Min Lu, and Edward E. Morrisey. "LMCD1/Dyxin Is a Novel Transcriptional Cofactor That Restricts GATA6 Function by Inhibiting DNA Binding." Molecular and Cellular Biology 25, no. 20 (2005): 8864–73. http://dx.doi.org/10.1128/mcb.25.20.8864-8873.2005.

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ABSTRACT The activity of GATA factors is regulated, in part, at the level of protein-protein interactions. LIM domain proteins, first defined by the zinc finger motifs found in the Lin11, Isl-1, and Mec-3 proteins, act as coactivators of GATA function in both hematopoietic and cardiovascular tissues. We have identified a novel GATA-LIM interaction between GATA6 and LMCD1/dyxin. The LIM domains and cysteine-rich domains in LMCD1/dyxin and the carboxy-terminal zinc finger of GATA6 mediate this interaction. Expression of LMCD1/dyxin is remarkably similar to that of GATA6, with high-level expressi

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Archer, V. E., J. Breton, I. Sanchez-Garcia, et al. "Cysteine-rich LIM domains of LIM-homeodomain and LIM-only proteins contain zinc but not iron." Proceedings of the National Academy of Sciences 91, no. 1 (1994): 316–20. http://dx.doi.org/10.1073/pnas.91.1.316.

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21

Liu, Yunshan, Gregory A. Hair, Scott D. Boden, Manjula Viggeswarapu, and Louisa Titus. "Overexpressed LIM Mineralization Proteins Do Not Require LIM Domains to Induce Bone." Journal of Bone and Mineral Research 17, no. 3 (2002): 406–14. http://dx.doi.org/10.1359/jbmr.2002.17.3.406.

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22

Schmeichel, K. L., and M. C. Beckerle. "Molecular dissection of a LIM domain." Molecular Biology of the Cell 8, no. 2 (1997): 219–30. http://dx.doi.org/10.1091/mbc.8.2.219.

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LIM domains are novel sequence elements that are found in more than 60 gene products, many of which function as key regulators of developmental pathways. The LIM domain, characterized by the cysteine-rich consensus CX2CX16-23HX2CX2CX2CX16-21 CX2-3(C/H/ D), is a specific mental-binding structure that consists of two distinct zinc-binding subdomains. We and others have recently demonstrated that the LIM domain mediates protein-protein interactions. However, the sequences that define the protein-binding specificity of the LIM domain had not yet been identified. Because structural studies have rev

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Goyal, Rakesh K., Phoebe Lin, Josna Kanungo, Aimee S. Payne, Anthony J. Muslin, and Gregory D. Longmore. "Ajuba, a Novel LIM Protein, Interacts with Grb2, Augments Mitogen-Activated Protein Kinase Activity in Fibroblasts, and Promotes Meiotic Maturation of Xenopus Oocytes in a Grb2- and Ras-Dependent Manner." Molecular and Cellular Biology 19, no. 6 (1999): 4379–89. http://dx.doi.org/10.1128/mcb.19.6.4379.

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ABSTRACT LIM domain-containing proteins contribute to cell fate determination, the regulation of cell proliferation and differentiation, and remodeling of the cell cytoskeleton. These proteins can be found in the cell nucleus, cytoplasm, or both. Whether and how cytoplasmic LIM proteins contribute to the cellular response to extracellular stimuli is an area of active investigation. We have identified and characterized a new LIM protein, Ajuba. Although predominantly a cytosolic protein, in contrast to other like proteins, it did not localize to sites of cellular adhesion to extracellular matri

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Cao, Tingyan, Minghui Qin, Shuai Zhu, and Yuanbao Li. "Silencing of a Cotton Actin-Binding Protein GhWLIM1C Decreases Resistance against Verticillium dahliae Infection." Plants 11, no. 14 (2022): 1828. http://dx.doi.org/10.3390/plants11141828.

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LIM proteins are widely spread in various types of plant cells and play diversely crucial cellular roles through actin cytoskeleton assembly and gene expression regulation. Till now, it has not been clear whether LIM proteins function in plant pathogen defense. In this study, we characterized a LIM protein, GhWLIM1C, in upland cotton (Gossypium hirsutum). We found that GhWLIM1C could bind and bundle the actin cytoskeleton, and it contains two LIM domains (LIM1 and LIM2). Both the two domains could bind directly to the actin filaments. Moreover, the LIM2 domain additionally bundles the actin cy

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Kanungo, Jyotshnabala, Stephen J. Pratt, Helene Marie, and Gregory D. Longmore. "Ajuba, a Cytosolic LIM Protein, Shuttles into the Nucleus and Affects Embryonal Cell Proliferation and Fate Decisions." Molecular Biology of the Cell 11, no. 10 (2000): 3299–313. http://dx.doi.org/10.1091/mbc.11.10.3299.

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Cellular adhesive events affect cell proliferation and differentiation decisions. How cell surface events mediating adhesion transduce signals to the nucleus is not well understood. After cell–cell or cell–substratum contact, cytosolic proteins are recruited to clustered adhesion receptor complexes. One such family of cytosolic proteins found at sites of cell adhesion is the Zyxin family of LIM proteins. Here we demonstrate that the family member Ajuba was recruited to the cell surface of embryonal cells, upon aggregate formation, at sites of cell–cell contact. Ajuba contained a functional nuc

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Jo, Kiwon, Bart Rutten, Robert C. Bunn, and David S. Bredt. "Actinin-Associated LIM Protein-Deficient Mice Maintain Normal Development and Structure of Skeletal Muscle." Molecular and Cellular Biology 21, no. 5 (2001): 1682–87. http://dx.doi.org/10.1128/mcb.21.5.1682-1687.2001.

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ABSTRACT The actinin-associated LIM protein, ALP, is the prototype of a large family of proteins containing an N-terminal PDZ domain and a C-terminal LIM domain. These PDZ-LIM proteins are components of the muscle cytoskeleton and occur along the Z lines owing to interaction of the PDZ domain with the spectrin-like repeats of α-actinin. Because PDZ and LIM domains are typically found in proteins that mediate cellular signaling, PDZ-LIM proteins are suspected to participate in muscle development. Interestingly the ALP gene occurs at 4q35 near the heterochromatic region mutated in facioscapulohu

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Yao, Shugang, and Hanne Ostergaard. "Leupaxin Regulates LFA-1 Related Function in Cytotoxic T Lymphocytes (CTL)." Journal of Immunology 196, no. 1_Supplement (2016): 119.1. http://dx.doi.org/10.4049/jimmunol.196.supp.119.1.

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Abstract Background Leupaxin is an adaptor protein that functions downstream of integrin receptor engagement. It contains N-terminal LD domains and C-terminal LIM domains. Although leupaxin is primarily expressed in leukocytes, it is very little known about the localization and function in leukocytes. Results Degranulation follows the formation of the immunological synapse (IS) and recruitment of MTOC to the IS. Leupaxin co-localizes with MTOC and microtubules, and is recruited to the IS during CTL degranulation. Through deletion of leupaxin domains, it shows that both LD2 and LD4 domains are

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Rauskolb, Cordelia, Ahri Han, Elmira Kirichenko, Consuelo Ibar, and Kenneth D. Irvine. "Analysis of the Drosophila Ajuba LIM protein defines functions for distinct LIM domains." PLOS ONE 17, no. 8 (2022): e0269208. http://dx.doi.org/10.1371/journal.pone.0269208.

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The Ajuba LIM protein Jub mediates regulation of Hippo signaling by cytoskeletal tension through interaction with the kinase Warts and participates in feedback regulation of junctional tension through regulation of the cytohesin Steppke. To investigate how Jub interacts with and regulates its distinct partners, we investigated the ability of Jub proteins missing different combinations of its three LIM domains to rescue jub phenotypes and to interact with α-catenin, Warts and Steppke. Multiple regions of Jub contribute to its ability to bind α-catenin and to localize to adherens junctions in Dr

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Staab, Erin M., Mara Terras, Pooja Dave, et al. "Measuring Perceived Level of Integration During the Process of Primary Care Behavioral Health Implementation." American Journal of Medical Quality 33, no. 3 (2017): 253–61. http://dx.doi.org/10.1177/1062860617736607.

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Provider- and staff-perceived levels of integration were measured during implementation of a primary care behavioral health clinic; these data were used to tailor and evaluate quality improvement strategies. Providers and staff at an urban, academic, adult primary care clinic completed the 32-item Level of Integration Measure (LIM) at baseline and 7 months. The LIM assesses 6 domains of integrated care. Overall and domain scores were calibrated from 0 to 100, with ≥80 representing a highly integrated clinic. Response rate was 79% (N = 46/58) at baseline and 83% (N = 52/63) at follow-up. Overal

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Robertson, Neil O., Ngaio C. Smith, Athina Manakas, et al. "Disparate binding kinetics by an intrinsically disordered domain enables temporal regulation of transcriptional complex formation." Proceedings of the National Academy of Sciences 115, no. 18 (2018): 4643–48. http://dx.doi.org/10.1073/pnas.1714646115.

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Intrinsically disordered regions are highly represented among mammalian transcription factors, where they often contribute to the formation of multiprotein complexes that regulate gene expression. An example of this occurs with LIM-homeodomain (LIM-HD) proteins in the developing spinal cord. The LIM-HD protein LHX3 and the LIM-HD cofactor LDB1 form a binary complex that gives rise to interneurons, whereas in adjacent cell populations, LHX3 and LDB1 form a rearranged ternary complex with the LIM-HD protein ISL1, resulting in motor neurons. The protein–protein interactions within these complexes

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van Meyel, D. J., D. D. O'Keefe, S. Thor, L. W. Jurata, G. N. Gill, and J. B. Thomas. "Chip is an essential cofactor for apterous in the regulation of axon guidance in Drosophila." Development 127, no. 9 (2000): 1823–31. http://dx.doi.org/10.1242/dev.127.9.1823.

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LIM-homeodomain transcription factors are expressed in subsets of neurons and are required for correct axon guidance and neurotransmitter identity. The LIM-homeodomain family member Apterous requires the LIM-binding protein Chip to execute patterned outgrowth of the Drosophila wing. To determine whether Chip is a general cofactor for diverse LIM-homeodomain functions in vivo, we studied its role in the embryonic nervous system. Loss-of-function Chip mutations cause defects in neurotransmitter production that mimic apterous and islet mutants. Chip is also required cell-autonomously by Apterous-

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Dobbs, David E., and Marco Fontana. "Inverse limits of integral domains arising from iterated Nagata composition." MATHEMATICA SCANDINAVICA 88, no. 1 (2001): 17. http://dx.doi.org/10.7146/math.scand.a-14312.

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By iterating the type of pullback constructions in which $P^rVD$s arise by Nagata composition, we are led to study a class of inverse limits $A=\underleftarrow{\lim}A_n$ of integral domains indexed by $\boldsymbol N$. After identifying the prime spectrum, the localizations, and the integral closure of $A$, we then characterize when, i.a., such (typically infinite-dimensional) $A$ is a Prüfer domain, Bezout domain, divided domain, or $P^rVD$.

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Carroll, Stefanie L., Amy H. Herrera, and Robert Horowits. "Targeting and functional role of N-RAP, a nebulin-related LIM protein, during myofibril assembly in cultured chick cardiomyocytes." Journal of Cell Science 114, no. 23 (2001): 4229–38. http://dx.doi.org/10.1242/jcs.114.23.4229.

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Targeting and functional effects of N-RAP domains were studied by expression as GFP-tagged fusion proteins in cultured embryonic chick cardiomyocytes. GFP-tagged N-RAP was targeted to myofibril precursors, myofibril ends and cell contacts, expression patterns that are similar to endogenous N-RAP. The GFP-tagged N-RAP LIM domain (GFP-N-RAP-LIM) was targeted to the membrane in cells with myofibril precursors and cell-cell contacts. The GFP-tagged super repeats (N-RAP-SR) and the GFP-tagged domain normally found in between the super repeats and the LIM domain (N-RAP-IB) were each observed at site

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Sadler, I., A. W. Crawford, J. W. Michelsen, and M. C. Beckerle. "Zyxin and cCRP: two interactive LIM domain proteins associated with the cytoskeleton." Journal of Cell Biology 119, no. 6 (1992): 1573–87. http://dx.doi.org/10.1083/jcb.119.6.1573.

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Interaction with extracellular matrix can trigger a variety of responses by cells including changes in specific gene expression and cell differentiation. The mechanism by which cell surface events are coupled to the transcriptional machinery is not understood, however, proteins localized at sites of cell-substratum contact are likely to function as signal transducers. We have recently purified and characterized a low abundance adhesion plaque protein called zyxin (Crawford, A. W., and M. C. Beckerle. 1991. J. Biol. Chem. 266:5847-5853; Crawford, A. W., J. W. Michelsen, and M. C. Beckerle. 1992

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Akazawa, Hiroshi, Sumiyo Kudoh, Naoki Mochizuki, et al. "A novel LIM protein Cal promotes cardiac differentiation by association with CSX/NKX2-5." Journal of Cell Biology 164, no. 3 (2004): 395–405. http://dx.doi.org/10.1083/jcb.200309159.

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The cardiac homeobox transcription factor CSX/NKX2-5 plays an important role in vertebrate heart development. Using a yeast two-hybrid screening, we identified a novel LIM domain–containing protein, named CSX-associated LIM protein (Cal), that interacts with CSX/NKX2-5. CSX/NKX2-5 and Cal associate with each other both in vivo and in vitro, and the LIM domains of Cal and the homeodomain of CSX/NKX2-5 were necessary for mutual binding. Cal itself possessed the transcription-promoting activity, and cotransfection of Cal enhanced CSX/NKX2-5–induced activation of atrial natriuretic peptide gene pr

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Shimojo, Masahito, and Louis B. Hersh. "REST/NRSF-Interacting LIM Domain Protein, a Putative Nuclear Translocation Receptor." Molecular and Cellular Biology 23, no. 24 (2003): 9025–31. http://dx.doi.org/10.1128/mcb.23.24.9025-9031.2003.

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ABSTRACT The transcriptional repressor REST/NRSF (RE-1 silencing transcription factor/neuron-restrictive silencer factor) and the transcriptional regulator REST4 share an N-terminal zinc finger domain structure involved in nuclear targeting. Using this domain as bait in a yeast two-hybrid screen, a novel protein that contains three LIM domains, putative nuclear localization sequences, protein kinase A phosphorylation sites, and a CAAX prenylation motif was isolated. This protein, which is localized around the nucleus, is involved in determining the nuclear localization of REST4 and REST/NRSF.

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Brown, Imogen D. Coghill, Meagan J., Susan. "Role of LIM Domains in Mediating Signaling Protein Interactions." IUBMB Life (International Union of Biochemistry and Molecular Biology: Life) 51, no. 6 (2001): 359–64. http://dx.doi.org/10.1080/152165401753366113.

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Siddiqui, M., Maulik Badmalia, and Trushar Patel. "Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins." International Journal of Molecular Sciences 22, no. 5 (2021): 2647. http://dx.doi.org/10.3390/ijms22052647.

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Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and functions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of Lxx

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Tu, Yizeng, Fugang Li, and Chuanyue Wu. "Nck-2, a Novel Src Homology2/3-containing Adaptor Protein That Interacts with the LIM-only Protein PINCH and Components of Growth Factor Receptor Kinase-signaling Pathways." Molecular Biology of the Cell 9, no. 12 (1998): 3367–82. http://dx.doi.org/10.1091/mbc.9.12.3367.

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Many of the protein–protein interactions that are essential for eukaryotic intracellular signal transduction are mediated by protein binding modules including SH2, SH3, and LIM domains. Nck is a SH3- and SH2-containing adaptor protein implicated in coordinating various signaling pathways, including those of growth factor receptors and cell adhesion receptors. We report here the identification, cloning, and characterization of a widely expressed, Nck-related adaptor protein termed Nck-2. Nck-2 comprises primarily three N-terminal SH3 domains and one C-terminal SH2 domain. We show that Nck-2 int

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Gadd, Morgan S., David A. Jacques, J. Mitchell Guss, and Jacqueline M. Matthews. "Crystallization and diffraction of an Isl1–Ldb1 complex." Acta Crystallographica Section F Structural Biology and Crystallization Communications 68, no. 11 (2012): 1398–401. http://dx.doi.org/10.1107/s1744309112040031.

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A stable intramolecular complex comprising the LIM domains of the LIM-homeodomain protein Isl1 tethered to a peptide region of Ldb1 has been engineered, purified and crystallized. The orthorhombic crystals belonged to space groupP2221, with unit-cell parametersa= 57.2,b= 56.7,c= 179.8 Å, and diffracted to 3.10 Å resolution.

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Jeleń, Filip, Arkadiusz Oleksy, Katarzyna Smietana, and Jacek Otlewski. "PDZ domains - common players in the cell signaling." Acta Biochimica Polonica 50, no. 4 (2003): 985–1017. http://dx.doi.org/10.18388/abp.2003_3628.

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PDZ domains are ubiquitous protein interaction modules that play a key role in cellular signaling. Their binding specificity involves recognition of the carboxyl-terminus of various proteins, often belonging to receptor and ion channel families. PDZ domains also mediate more complicated molecular networks through PDZ-PDZ interactions, recognition of internal protein sequences or phosphatidylinositol moieties. The domains often form a tandem of multiple copies, but equally often such tandems or single PDZ domain occur in combination with other signaling domains (for example SH3, DH/PH, GUK, LIM

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Brown, M. C., J. A. Perrotta, and C. E. Turner. "Identification of LIM3 as the principal determinant of paxillin focal adhesion localization and characterization of a novel motif on paxillin directing vinculin and focal adhesion kinase binding." Journal of Cell Biology 135, no. 4 (1996): 1109–23. http://dx.doi.org/10.1083/jcb.135.4.1109.

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Paxillin is a 68-kD focal adhesion phosphoprotein that interacts with several proteins including members of the src family of tyrosine kinases, the transforming protein v-crk, and the cytoskeletal proteins vinculin and the tyrosine kinase, focal adhesion kinase (FAK). This suggests a function for paxillin as a molecular adaptor, responsible for the recruitment of structural and signaling molecules to focal adhesions. The current study defines the vinculin- and FAK-interaction domains on paxillin and identifies the principal paxillin focal adhesion targeting motif. Using truncation and deletion

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Chen, G. C., L. Zheng, and C. S. Chan. "The LIM domain-containing Dbm1 GTPase-activating protein is required for normal cellular morphogenesis in Saccharomyces cerevisiae." Molecular and Cellular Biology 16, no. 4 (1996): 1376–90. http://dx.doi.org/10.1128/mcb.16.4.1376.

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Normal cell growth in the yeast Saccharomyces cerevisiae involves the selection of genetically determined bud sites where most growth is localized. Previous studies have shown that BEM2, which encodes a GTPase-activating protein (GAP) that is specific for the Rho-type GTPase Rho1p in vitro, is required for proper bud site selection and bud emergence. We show here that DBM1, which encodes another putative Rho-type GAP with two tandemly arranged cysteine-rich LIM domains, also is needed for proper bud site selection, as haploid cells lacking Dbm1p bud predominantly in a bipolar, rather than the

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Qadota, Hiroshi, Kristina B. Mercer, Rachel K. Miller, Kozo Kaibuchi, and Guy M. Benian. "Two LIM Domain Proteins and UNC-96 Link UNC-97/PINCH to Myosin Thick Filaments in Caenorhabditis elegans Muscle." Molecular Biology of the Cell 18, no. 11 (2007): 4317–26. http://dx.doi.org/10.1091/mbc.e07-03-0278.

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By yeast two-hybrid screening, we found three novel interactors (UNC-95, LIM-8, and LIM-9) for UNC-97/PINCH in Caenorhabditis elegans. All three proteins contain LIM domains that are required for binding. Among the three interactors, LIM-8 and LIM-9 also bind to UNC-96, a component of sarcomeric M-lines. UNC-96 and LIM-8 also bind to the C-terminal portion of a myosin heavy chain (MHC), MHC A, which resides in the middle of thick filaments in the proximity of M-lines. All interactions identified by yeast two-hybrid assays were confirmed by in vitro binding assays using purified proteins. All t

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Doğan, Tunca, Ece Akhan Güzelcan, Marcus Baumann, et al. "Protein domain-based prediction of drug/compound–target interactions and experimental validation on LIM kinases." PLOS Computational Biology 17, no. 11 (2021): e1009171. http://dx.doi.org/10.1371/journal.pcbi.1009171.

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Predictive approaches such as virtual screening have been used in drug discovery with the objective of reducing developmental time and costs. Current machine learning and network-based approaches have issues related to generalization, usability, or model interpretability, especially due to the complexity of target proteins’ structure/function, and bias in system training datasets. Here, we propose a new method “DRUIDom” (DRUg Interacting Domain prediction) to identify bio-interactions between drug candidate compounds and targets by utilizing the domain modularity of proteins, to overcome probl

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Renko, Miha, Marc Fiedler, Trevor J. Rutherford, Jonas V. Schaefer, Andreas Plückthun, and Mariann Bienz. "Rotational symmetry of the structured Chip/LDB-SSDP core module of the Wnt enhanceosome." Proceedings of the National Academy of Sciences 116, no. 42 (2019): 20977–83. http://dx.doi.org/10.1073/pnas.1912705116.

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The Chip/LIM-domain binding protein (LDB)–single-stranded DNA-binding protein (SSDP) (ChiLS) complex controls numerous cell-fate decisions in animal cells, by mediating transcription of developmental control genes via remote enhancers. ChiLS is recruited to these enhancers by lineage-specific LIM-domain proteins that bind to its Chip/LDB subunit. ChiLS recently emerged as the core module of the Wnt enhanceosome, a multiprotein complex that primes developmental control genes for timely Wnt responses. ChiLS binds to NPFxD motifs within Pygopus (Pygo) and the Osa/ARID1A subunit of the BAF chromat

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Razzell, William, Maria E. Bustillo, and Jennifer A. Zallen. "The force-sensitive protein Ajuba regulates cell adhesion during epithelial morphogenesis." Journal of Cell Biology 217, no. 10 (2018): 3715–30. http://dx.doi.org/10.1083/jcb.201801171.

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The reorganization of cells in response to mechanical forces converts simple epithelial sheets into complex tissues of various shapes and dimensions. Epithelial integrity is maintained throughout tissue remodeling, but the mechanisms that regulate dynamic changes in cell adhesion under tension are not well understood. In Drosophila melanogaster, planar polarized actomyosin forces direct spatially organized cell rearrangements that elongate the body axis. We show that the LIM-domain protein Ajuba is recruited to adherens junctions in a tension-dependent fashion during axis elongation. Ajuba loc

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Nakazawa, Naotaka, Aneesh R. Sathe, G. V. Shivashankar, and Michael P. Sheetz. "Matrix mechanics controls FHL2 movement to the nucleus to activate p21 expression." Proceedings of the National Academy of Sciences 113, no. 44 (2016): E6813—E6822. http://dx.doi.org/10.1073/pnas.1608210113.

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Substrate rigidity affects many physiological processes through mechanochemical signals from focal adhesion (FA) complexes that subsequently modulate gene expression. We find that shuttling of the LIM domain (domain discovered in the proteins, Lin11, Isl-1, and Mec-3) protein four-and-a-half LIM domains 2 (FHL2) between FAs and the nucleus depends on matrix mechanics. In particular, on soft surfaces or after the loss of force, FHL2 moves from FAs into the nucleus and concentrates at RNA polymerase (Pol) II sites, where it acts as a transcriptional cofactor, causing an increase in p21 gene expr

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Sun, Xiaoyu, Donovan Y. Z. Phua, Lucas Axiotakis, et al. "Mechanosensing through Direct Binding of Tensed F-Actin by LIM Domains." Developmental Cell 55, no. 4 (2020): 468–82. http://dx.doi.org/10.1016/j.devcel.2020.09.022.

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Zhang, Jianhua, John M. Erikson, and Merry L. Lindsey. "Going Out on a LIM and Cysteine-Rich Domains 1 Limb." Hypertension 55, no. 2 (2010): 231–32. http://dx.doi.org/10.1161/hypertensionaha.109.142521.

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