1
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González Wusener AE, González Á, Perez Collado ME, Maza MR, General IJ, Arregui CO. Protein tyrosine phosphatase 1B targets focal adhesion kinase and paxillin in cell-matrix adhesions. J Cell Sci 2021; 134:272564. [PMID: 34553765 DOI: 10.1242/jcs.258769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/14/2021] [Indexed: 11/20/2022] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B, also known as PTPN1) is an established regulator of cell-matrix adhesion and motility. However, the nature of substrate targets at adhesion sites remains to be validated. Here, we used bimolecular fluorescence complementation assays, in combination with a substrate trapping mutant of PTP1B, to directly examine whether relevant phosphotyrosines on paxillin and focal adhesion kinase (FAK, also known as PTK2) are substrates of the phosphatase in the context of cell-matrix adhesion sites. We found that the formation of catalytic complexes at cell-matrix adhesions requires intact tyrosine residues Y31 and Y118 on paxillin, and the localization of FAK at adhesion sites. Additionally, we found that PTP1B specifically targets Y925 on the focal adhesion targeting (FAT) domain of FAK at adhesion sites. Electrostatic analysis indicated that dephosphorylation of this residue promotes the closed conformation of the FAT 4-helix bundle and its interaction with paxillin at adhesion sites.
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Affiliation(s)
- Ana E González Wusener
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires 1650, Argentina
| | - Ángela González
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires 1650, Argentina
| | - María E Perez Collado
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires 1650, Argentina
| | - Melina R Maza
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martin, Instituto de Ciencias Físicas and CONICET, San Martin, Buenos Aires 1650, Argentina
| | - Ignacio J General
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martin, Instituto de Ciencias Físicas and CONICET, San Martin, Buenos Aires 1650, Argentina
| | - Carlos O Arregui
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires 1650, Argentina
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2
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Sivaraman T, Richa T. Cryptic intermediates and metastable states of proteins as predicted by OneG computational method. J Biomol Struct Dyn 2021; 40:7899-7914. [PMID: 33764262 DOI: 10.1080/07391102.2021.1904288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Understanding structural excursions of proteins under folding conditions is crucial to map energy landscapes of proteins. In the present study, OneG computational tool has been used for analyzing possible existence of cryptic intermediates and metastable states of 26 proteins for which three prerequisite inputs of the OneG such as atomic coordinates of proteins, free energy of unfolding (ΔGU) and free energy of exchange (ΔGHX) determined in the absence of denaturant were available during the course of the study. The veraciousness of the tool on predicting the partially folded states of the proteins has been comprehensively described using experimental data available for 15 of the 26 proteins. Meanwhile, possible existence of partially structured states in the folding pathways of 11 other proteins has also been delineated as predicted by the OneG. In addition to mapping the folding pathways of proteins, the salient merits of the tool on systematically addressing the discrepancy between the ΔGU and the ΔGHX of the proteins have also been dealt.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Thirunavukkarasu Sivaraman
- Drug Design and Discovery Lab, Department of Biotechnology, Karpagam Academy of Higher Education (Deemed to be University), Coimbatore, Tamil Nadu, India
| | - Tambi Richa
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
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3
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FAK Structure and Regulation by Membrane Interactions and Force in Focal Adhesions. Biomolecules 2020; 10:biom10020179. [PMID: 31991559 PMCID: PMC7072507 DOI: 10.3390/biom10020179] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 12/21/2022] Open
Abstract
Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase with key roles in the regulation of cell adhesion migration, proliferation and survival. In cancer FAK is a major driver of invasion and metastasis and its upregulation is associated with poor patient prognosis. FAK is autoinhibited in the cytosol, but activated upon localisation into a protein complex, known as focal adhesion complex. This complex forms upon cell adhesion to the extracellular matrix (ECM) at the cytoplasmic side of the plasma membrane at sites of ECM attachment. FAK is anchored to the complex via multiple sites, including direct interactions with specific membrane lipids and connector proteins that attach focal adhesions to the actin cytoskeleton. In migrating cells, the contraction of actomyosin stress fibres attached to the focal adhesion complex apply a force to the complex, which is likely transmitted to the FAK protein, causing stretching of the FAK molecule. In this review we discuss the current knowledge of the FAK structure and how specific structural features are involved in the regulation of FAK signalling. We focus on two major regulatory mechanisms known to contribute to FAK activation, namely interactions with membrane lipids and stretching forces applied to FAK, and discuss how they might induce structural changes that facilitate FAK activation.
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4
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Xu S, Liu Y, Li X, Liu Y, Meijers R, Zhang Y, Wang JH. The binding of DCC-P3 motif and FAK-FAT domain mediates the initial step of netrin-1/DCC signaling for axon attraction. Cell Discov 2018; 4:8. [PMID: 29479476 PMCID: PMC5818605 DOI: 10.1038/s41421-017-0008-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 12/17/2017] [Accepted: 12/22/2017] [Indexed: 01/05/2023] Open
Abstract
Netrin-1 plays a key role in axon guidance through binding to its receptor, Deleted in Colorectal Cancer (DCC). The initial step of signaling inside the cell after netrin-1/DCC ligation is the binding of DCC cytoplasmic P3 motif to focal adhesion targeting (FAT) domain of focal adhesion kinase (FAK). Here we report the crystal structure of P3/FAT complex. The helical P3 peptide interacts with a helix-swapped FAT dimer in a 2:2 ratio. Dimeric FAT binding is P3-specific and stabilized by a calcium ion. Biochemical studies showed that DCC-P3 motif and calcium ion could facilitate FAT dimerization in solution. Axon guidance assays confirm that the DCC/FAK complex is essential for netrin-1-induced chemoattraction. We propose that netrin-1/DCC engagement creates a small cluster of P3/FAT for FAK recruitment close to the cell membrane, which exerts a concerted effect with PIP2 for FAK signaling. We also compare P3/FAT binding with paxillin/FAT binding and discuss their distinct recognition specificity on a common FAT domain for axon attraction versus integrin signaling, respectively.
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Affiliation(s)
- Shutong Xu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- Department of Medical Oncology, and Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
| | - Yiqiong Liu
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, 100871 China
- PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871 China
| | - Xiaolong Li
- Department of Medical Oncology, and Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
| | - Ying Liu
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, 100871 China
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Yan Zhang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, 100871 China
- PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871 China
| | - Jia-huai Wang
- Department of Medical Oncology, and Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
- Department of Pediatrics, and Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215 USA
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5
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Cardoso AC, Pereira AHM, Ambrosio ALB, Consonni SR, Rocha de Oliveira R, Bajgelman MC, Dias SMG, Franchini KG. FAK Forms a Complex with MEF2 to Couple Biomechanical Signaling to Transcription in Cardiomyocytes. Structure 2016; 24:1301-1310. [PMID: 27427476 DOI: 10.1016/j.str.2016.06.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 05/06/2016] [Accepted: 06/04/2016] [Indexed: 11/27/2022]
Abstract
Focal adhesion kinase (FAK) has emerged as a mediator of mechanotransduction in cardiomyocytes, regulating gene expression during hypertrophic remodeling. However, how FAK signaling is relayed onward to the nucleus is unclear. Here, we show that FAK interacts with and regulates myocyte enhancer factor 2 (MEF2), a master cardiac transcriptional regulator. In cardiomyocytes exposed to biomechanical stimulation, FAK accumulates in the nucleus, binds to and upregulates the transcriptional activity of MEF2 through an interaction with the FAK focal adhesion targeting (FAT) domain. In the crystal structure (2.9 Å resolution), FAT binds to a stably folded groove in the MEF2 dimer, known to interact with regulatory cofactors. FAK cooperates with MEF2 to enhance the expression of Jun in cardiomyocytes, an important component of hypertrophic response to mechanical stress. These findings underscore a connection between the mechanotransduction involving FAK and transcriptional regulation by MEF2, with potential relevance to the pathogenesis of cardiac disease.
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Affiliation(s)
- Alisson Campos Cardoso
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Ana Helena Macedo Pereira
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Andre Luis Berteli Ambrosio
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Silvio Roberto Consonni
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Renata Rocha de Oliveira
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Marcio Chain Bajgelman
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Sandra Martha Gomes Dias
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil
| | - Kleber Gomes Franchini
- Brazilian National Laboratory for Biosciences, Center for Research in Energy and Materials, Campinas, São Paulo 13084-971, Brazil; Department of Internal Medicine, School of Medicine, University of Campinas, Campinas, São Paulo 13081-970, Brazil.
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6
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Mohanty P, Bhatnagar S. Structural basis of focal adhesion targeting domain-mediated signaling in cardiac hypertrophy. J Recept Signal Transduct Res 2016; 37:38-50. [DOI: 10.3109/10799893.2016.1155067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Pallavi Mohanty
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
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7
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Vanarotti MS, Finkelstein DB, Guibao CD, Nourse A, Miller DJ, Zheng JJ. Structural Basis for the Interaction between Pyk2-FAT Domain and Leupaxin LD Repeats. Biochemistry 2016; 55:1332-45. [PMID: 26866573 PMCID: PMC4843776 DOI: 10.1021/acs.biochem.5b01274] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Proline-rich
tyrosine kinase 2 (Pyk2) is a nonreceptor tyrosine
kinase and belongs to the focal adhesion kinase (FAK) family. Like
FAK, the C-terminal focal adhesion-targeting (FAT) domain of Pyk2
binds to paxillin, a scaffold protein in focal adhesions; however,
the interaction between the FAT domain of Pyk2 and paxillin is dynamic
and unstable. Leupaxin is another member in the paxillin family and
was suggested to be the native binding partner of Pyk2; Pyk2 gene
expression is strongly correlated with that of leupaxin in many tissues
including primary breast cancer. Here, we report that leupaxin interacts
with Pyk2-FAT. Leupaxin has four leucine–aspartate (LD) motifs.
The first and third LD motifs of leupaxin preferably target the two
LD-binding sites on the Pyk2-FAT domain, respectively. Moreover, the
full-length leupaxin binds to Pyk2-FAT as a stable one-to-one complex.
Together, we propose that there is an underlying selectivity between
leupaxin and paxillin for Pyk2, which may influence the differing
behavior of the two proteins at focal adhesion sites.
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Affiliation(s)
| | | | | | | | | | - Jie J Zheng
- Stein Eye Institute, Department of Ophthalmology, David Geffen School of Medicine at UCLA , Los Angeles, California 90095, United States
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8
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Lee HJ, Shi DL, Zheng JJ. Conformational change of Dishevelled plays a key regulatory role in the Wnt signaling pathways. eLife 2015; 4:e08142. [PMID: 26297804 PMCID: PMC4577825 DOI: 10.7554/elife.08142] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 08/21/2015] [Indexed: 01/02/2023] Open
Abstract
The intracellular signaling molecule Dishevelled (Dvl) mediates canonical and non-canonical Wnt signaling via its PDZ domain. Different pathways diverge at this point by a mechanism that remains unclear. Here we show that the peptide-binding pocket of the Dvl PDZ domain can be occupied by Dvl's own highly conserved C-terminus, inducing a closed conformation. In Xenopus, Wnt-regulated convergent extension (CE) is readily affected by Dvl mutants unable to form the closed conformation than by wild-type Dvl. We also demonstrate that while Dvl cooperates with other Wnt pathway elements to activate canonical Wnt signaling, the open conformation of Dvl more effectively activates Jun N-terminal kinase (JNK). These results suggest that together with other players in the Wnt signaling pathway, the conformational change of Dvl regulates Wnt stimulated JNK activity in the non-canonical Wnt signaling. DOI:http://dx.doi.org/10.7554/eLife.08142.001 The development of an animal embryo depends on a number of signaling pathways that pass information from the outside of the cell to the inside. These pathways include Wnt signaling, which also regulates cell growth. The pathways must be precisely controlled; abnormal Wnt activity has been implicated in several human diseases, ranging from heart disease to cancer. Wnt signaling is complex, and actually comprises two major pathways: the canonical pathway (which depends on a protein called β-catenin) and the PCP pathway (which doesn't depend on β-catenin). Both pathways are triggered when Wnt molecules bind to receptors on the outside of the cell. These receptors pass the signal into the cell and to a protein called ‘Dishevelled’ (or ‘Dvl’ for short). This protein then passes the signal on through either the canonical or PCP pathway. Nevertheless it is not clear how the Dishevelled protein can direct the signal specifically down either one of these pathways. Lee et al. now show that the Dishevelled protein can take on at least two different shapes. When it is ‘closed’, one end of the protein is tucked inside a pocket elsewhere on the protein's surface. But when Dishevelled is ‘open’, this end of the protein moves out of this pocket. Further experiments using frogs (called Xenopus, which are commonly used in research) reveal that mutant versions of Dishevelled that were unable to take on the closed form strongly affected an aspect of the frog's development that involves the PCP pathway. Lee et al. then demonstrate that while Dishevelled cooperates with several other Wnt pathway components to activate the canonical pathway, the open form of Dishevelled activates the PCP pathway. The next challenge following on from this work is to find out how Wnt molecules binding to the receptor trigger the shape change in Dishevelled. DOI:http://dx.doi.org/10.7554/eLife.08142.002
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Affiliation(s)
- Ho-Jin Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - De-Li Shi
- Laboratoire de biologie du développement, Institut de Biologie Paris-Seine, Sorbonne Universités, Paris, France
| | - Jie J Zheng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, United States
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9
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Walkiewicz KW, Girault JA, Arold ST. How to awaken your nanomachines: Site-specific activation of focal adhesion kinases through ligand interactions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:60-71. [PMID: 26093249 DOI: 10.1016/j.pbiomolbio.2015.06.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 06/07/2015] [Accepted: 06/14/2015] [Indexed: 01/12/2023]
Abstract
The focal adhesion kinase (FAK) and the related protein-tyrosine kinase 2-beta (Pyk2) are highly versatile multidomain scaffolds central to cell adhesion, migration, and survival. Due to their key role in cancer metastasis, understanding and inhibiting their functions are important for the development of targeted therapy. Because FAK and Pyk2 are involved in many different cellular functions, designing drugs with partial and function-specific inhibitory effects would be desirable. Here, we summarise recent progress in understanding the structural mechanism of how the tug-of-war between intramolecular and intermolecular interactions allows these protein 'nanomachines' to become activated in a site-specific manner.
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Affiliation(s)
- Katarzyna W Walkiewicz
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Jean-Antoine Girault
- Inserm, UMR-S 839, F-75005 Paris, France; Université Pierre & Marie Curie (UPMC), Sorbonne Universités, F-75005 Paris, France; Institut du Fer à Moulin, F-75005 Paris, France
| | - Stefan T Arold
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia.
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10
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Kadaré G, Gervasi N, Brami-Cherrier K, Blockus H, El Messari S, Arold ST, Girault JA. Conformational dynamics of the focal adhesion targeting domain control specific functions of focal adhesion kinase in cells. J Biol Chem 2014; 290:478-91. [PMID: 25391654 DOI: 10.1074/jbc.m114.593632] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Focal adhesion (FA) kinase (FAK) regulates cell survival and motility by transducing signals from membrane receptors. The C-terminal FA targeting (FAT) domain of FAK fulfils multiple functions, including recruitment to FAs through paxillin binding. Phosphorylation of FAT on Tyr(925) facilitates FA disassembly and connects to the MAPK pathway through Grb2 association, but requires dissociation of the first helix (H1) of the four-helix bundle of FAT. We investigated the importance of H1 opening in cells by comparing the properties of FAK molecules containing wild-type or mutated FAT with impaired or facilitated H1 openings. These mutations did not alter the activation of FAK, but selectively affected its cellular functions, including self-association, Tyr(925) phosphorylation, paxillin binding, and FA targeting and turnover. Phosphorylation of Tyr(861), located between the kinase and FAT domains, was also enhanced by the mutation that opened the FAT bundle. Similarly phosphorylation of Ser(910) by ERK in response to bombesin was increased by FAT opening. Although FAK molecules with the mutation favoring FAT opening were poorly recruited at FAs, they efficiently restored FA turnover and cell shape in FAK-deficient cells. In contrast, the mutation preventing H1 opening markedly impaired FAK function. Our data support the biological importance of conformational dynamics of the FAT domain and its functional interactions with other parts of the molecule.
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Affiliation(s)
- Gress Kadaré
- From the INSERM, UMR-S 839, F-75005 Paris, France, the Université Pierre & Marie Curie (UPMC), Sorbonne Universités, F-75005 Paris, France, the Institut du Fer à Moulin, F-75005 Paris, France
| | - Nicolas Gervasi
- From the INSERM, UMR-S 839, F-75005 Paris, France, the Université Pierre & Marie Curie (UPMC), Sorbonne Universités, F-75005 Paris, France, the Institut du Fer à Moulin, F-75005 Paris, France
| | - Karen Brami-Cherrier
- From the INSERM, UMR-S 839, F-75005 Paris, France, the Université Pierre & Marie Curie (UPMC), Sorbonne Universités, F-75005 Paris, France, the Institut du Fer à Moulin, F-75005 Paris, France
| | - Heike Blockus
- From the INSERM, UMR-S 839, F-75005 Paris, France, the Université Pierre & Marie Curie (UPMC), Sorbonne Universités, F-75005 Paris, France, the Institut du Fer à Moulin, F-75005 Paris, France
| | - Said El Messari
- From the INSERM, UMR-S 839, F-75005 Paris, France, the Université Pierre & Marie Curie (UPMC), Sorbonne Universités, F-75005 Paris, France, the Institut du Fer à Moulin, F-75005 Paris, France
| | - Stefan T Arold
- the King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia, and the Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier I & II, Montpellier, France
| | - Jean-Antoine Girault
- From the INSERM, UMR-S 839, F-75005 Paris, France, the Université Pierre & Marie Curie (UPMC), Sorbonne Universités, F-75005 Paris, France, the Institut du Fer à Moulin, F-75005 Paris, France,
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11
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How to find a leucine in a haystack? Structure, ligand recognition and regulation of leucine-aspartic acid (LD) motifs. Biochem J 2014; 460:317-29. [PMID: 24870021 DOI: 10.1042/bj20140298] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
LD motifs (leucine-aspartic acid motifs) are short helical protein-protein interaction motifs that have emerged as key players in connecting cell adhesion with cell motility and survival. LD motifs are required for embryogenesis, wound healing and the evolution of multicellularity. LD motifs also play roles in disease, such as in cancer metastasis or viral infection. First described in the paxillin family of scaffolding proteins, LD motifs and similar acidic LXXLL interaction motifs have been discovered in several other proteins, whereas 16 proteins have been reported to contain LDBDs (LD motif-binding domains). Collectively, structural and functional analyses have revealed a surprising multivalency in LD motif interactions and a wide diversity in LDBD architectures. In the present review, we summarize the molecular basis for function, regulation and selectivity of LD motif interactions that has emerged from more than a decade of research. This overview highlights the intricate multi-level regulation and the inherently noisy and heterogeneous nature of signalling through short protein-protein interaction motifs.
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12
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Abstract
Kinetic folding of the large two-domain maltose binding protein (MBP; 370 residues) was studied at high structural resolution by an advanced hydrogen-exchange pulse-labeling mass-spectrometry method (HX MS). Dilution into folding conditions initiates a fast molecular collapse into a polyglobular conformation (<20 ms), determined by various methods including small angle X-ray scattering. The compaction produces a structurally heterogeneous state with widespread low-level HX protection and spectroscopic signals that match the equilibrium melting posttransition-state baseline. In a much slower step (7-s time constant), all of the MBP molecules, although initially heterogeneously structured, form the same distinct helix plus sheet folding intermediate with the same time constant. The intermediate is composed of segments that are distant in the MBP sequence but adjacent in the native protein where they close the longest residue-to-residue contact. Segments that are most HX protected in the early molecular collapse do not contribute to the initial intermediate, whereas the segments that do participate are among the less protected. The 7-s intermediate persists through the rest of the folding process. It contains the sites of three previously reported destabilizing mutations that greatly slow folding. These results indicate that the intermediate is an obligatory step on the MBP folding pathway. MBP then folds to the native state on a longer time scale (~100 s), suggestively in more than one step, the first of which forms structure adjacent to the 7-s intermediate. These results add a large protein to the list of proteins known to fold through distinct native-like intermediates in distinct pathways.
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13
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NMR as a tool to identify and characterize protein folding intermediates. Arch Biochem Biophys 2013; 531:90-9. [DOI: 10.1016/j.abb.2012.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 11/20/2022]
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14
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Skinner JJ, Lim WK, Bédard S, Black BE, Englander SW. Protein dynamics viewed by hydrogen exchange. Protein Sci 2012; 21:996-1005. [PMID: 22544544 DOI: 10.1002/pro.2081] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 04/09/2012] [Indexed: 01/19/2023]
Abstract
To examine the relationship between protein structural dynamics and measurable hydrogen exchange (HX) data, the detailed exchange behavior of most of the backbone amide hydrogens of Staphylococcal nuclease was compared with that of their neighbors, with their structural environment, and with other information. Results show that H-bonded hydrogens are protected from exchange, with HX rate effectively zero, even when they are directly adjacent to solvent. The transition to exchange competence requires a dynamic structural excursion that removes H-bond protection and allows exposure to solvent HX catalyst. The detailed data often make clear the nature of the dynamic excursion required. These range from whole molecule unfolding, through smaller cooperative unfolding reactions of secondary structural elements, and down to local fluctuations that involve as little as a single peptide group or side chain or water molecule. The particular motion that dominates the exchange of any hydrogen is the one that allows the fastest HX rate. The motion and the rate it produces are determined by surrounding structure and not by nearness to solvent or the strength of the protecting H-bond itself or its acceptor type (main chain, side chain, structurally bound water). Many of these motions occur over time scales that are appropriate for biochemical function.
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Affiliation(s)
- John J Skinner
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA.
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15
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Cable J, Prutzman K, Gunawardena HP, Schaller MD, Chen X, Campbell SL. In vitro phosphorylation of the focal adhesion targeting domain of focal adhesion kinase by Src kinase. Biochemistry 2012; 51:2213-23. [PMID: 22372511 DOI: 10.1021/bi300123a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Focal adhesion kinase (FAK), a key regulator of cell adhesion and migration, is overexpressed in many types of cancer. The C-terminal focal adhesion targeting (FAT) domain of FAK is necessary for proper localization of FAK to focal adhesions and subsequent activation. Phosphorylation of Y926 in the FAT domain by the tyrosine kinase Src has been shown to promote metastasis and invasion in vivo by linking the FAT domain to the MAPK pathway via its interaction with growth factor receptor-bound protein 2. Several groups have reported that inherent conformational dynamics in the FAT domain likely regulate phosphorylation of Y926; however, what regulates these dynamics is unknown. In this paper, we demonstrate that there are two sites of in vitro Src-mediated phosphorylation in the FAT domain: Y926, which has been shown to affect FAK function in vivo, and Y1008, which has no known biological role. The phosphorylation of these two tyrosine residues is pH-dependent, but this does not reflect the pH dependence of Src kinase activity. Circular dichroism and nuclear magnetic resonance data indicate that the stability and conformational dynamics of the FAT domain are sensitive to changes in pH over a physiological pH range. In particular, regions of the FAT domain previously shown to regulate phosphorylation of Y926 as well as regions near Y1008 show pH-dependent dynamics on the microsecond to millisecond time scale.
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Affiliation(s)
- Jennifer Cable
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Arold ST. How focal adhesion kinase achieves regulation by linking ligand binding, localization and action. Curr Opin Struct Biol 2011; 21:808-13. [PMID: 22030387 DOI: 10.1016/j.sbi.2011.09.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 09/27/2011] [Accepted: 09/29/2011] [Indexed: 12/20/2022]
Abstract
Focal adhesion kinase (FAK) has an astonishing number of ligands and functions, which enable it to contribute to embryonic development and human health. FAK can promote different effects in similar cellular environments or similar effects in different cellular environments. Recent advances in structural and cellular analysis of FAK are starting to reveal the interrelationships between the conformations, localizations, interactions, and functions of FAK. This review focuses on our emerging understanding of how the structural framework of FAK mechanistically allows it to integrate manifold stimuli into environment-specific functions.
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Affiliation(s)
- Stefan T Arold
- Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
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Vicatos S, Roca M, Warshel A. Effective approach for calculations of absolute stability of proteins using focused dielectric constants. Proteins 2010; 77:670-84. [PMID: 19856460 DOI: 10.1002/prot.22481] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The ability to predict the absolute stability of proteins based on their corresponding sequence and structure is a problem of great fundamental and practical importance. In this work, we report an extensive, refinement and validation of our recent approach (Roca et al., FEBS Lett 2007;581:2065-2071) for predicting absolute values of protein stability DeltaG(fold). This approach employs the semimacroscopic protein dipole Langevin dipole method in its linear response approximation version (PDLD/S-LRA) while using the best fitted values of the dielectric constants epsilon'(p) and epsilon'(eff) for the self energy and charge-charge interactions, respectively. The method is validated on a diverse set of 45 proteins. It is found that the best fitted values of both dielectric constants are around 40. However, the self energy of internal residues and the charge-charge interactions of Lys have to be treated with care, using a somewhat lower values of epsilon'(p) and epsilon'(eff). The predictions of DeltaG(fold) reported here, have an average error of only 1.8 kcal/mole compared to the observed values, making our method very promising for estimating protein stability. It also provides valuable insight into the complex electrostatic phenomena taking place in folded proteins.
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Affiliation(s)
- Spyridon Vicatos
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms. Nat Struct Mol Biol 2009; 16:582-8. [DOI: 10.1038/nsmb.1592] [Citation(s) in RCA: 205] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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The high-resolution NMR structure of the early folding intermediate of the Thermus thermophilus ribonuclease H. J Mol Biol 2008; 384:531-9. [PMID: 18848567 DOI: 10.1016/j.jmb.2008.09.044] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 09/16/2008] [Accepted: 09/17/2008] [Indexed: 11/23/2022]
Abstract
Elucidation of the high-resolution structures of folding intermediates is a necessary but difficult step toward the ultimate understanding of the mechanism of protein folding. Here, using hydrogen-exchange-directed protein engineering, we populated the folding intermediate of the Thermus thermophilus ribonuclease H, which forms before the rate-limiting transition state, by removing the unfolded regions of the intermediate, including an alpha-helix and two beta-strands (51 folded residues). Using multidimensional NMR, we solved the structure of this intermediate mimic to an atomic resolution (backbone rmsd, 0.51 A). It has a native-like backbone topology and shows some local deviations from the native structure, revealing that the structure of the folded region of an early folding intermediate can be as well defined as the native structure. The topological parameters calculated from the structures of the intermediate mimic and the native state predict that the intermediate should fold on a millisecond time scale or less and form much faster than the native state. Other factors that may lead to the slow folding of the native state and the accumulation of the intermediate before the rate-limiting transition state are also discussed.
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Chen Y, Ding F, Nie H, Serohijos AW, Sharma S, Wilcox KC, Yin S, Dokholyan NV. Protein folding: then and now. Arch Biochem Biophys 2008; 469:4-19. [PMID: 17585870 PMCID: PMC2173875 DOI: 10.1016/j.abb.2007.05.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Revised: 05/11/2007] [Accepted: 05/21/2007] [Indexed: 01/19/2023]
Abstract
Over the past three decades the protein folding field has undergone monumental changes. Originally a purely academic question, how a protein folds has now become vital in understanding diseases and our abilities to rationally manipulate cellular life by engineering protein folding pathways. We review and contrast past and recent developments in the protein folding field. Specifically, we discuss the progress in our understanding of protein folding thermodynamics and kinetics, the properties of evasive intermediates, and unfolded states. We also discuss how some abnormalities in protein folding lead to protein aggregation and human diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Nikolay V. Dokholyan
- † To whom correspondence should be addressed: Nikolay V. Dokholyan, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina 27599. Fax: 919-966-2852.
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Abstract
Two fundamentally different views of how proteins fold are now being debated. Do proteins fold through multiple unpredictable routes directed only by the energetically downhill nature of the folding landscape or do they fold through specific intermediates in a defined pathway that systematically puts predetermined pieces of the target native protein into place? It has now become possible to determine the structure of protein folding intermediates, evaluate their equilibrium and kinetic parameters, and establish their pathway relationships. Results obtained for many proteins have serendipitously revealed a new dimension of protein structure. Cooperative structural units of the native protein, called foldons, unfold and refold repeatedly even under native conditions. Much evidence obtained by hydrogen exchange and other methods now indicates that cooperative foldon units and not individual amino acids account for the unit steps in protein folding pathways. The formation of foldons and their ordered pathway assembly systematically puts native-like foldon building blocks into place, guided by a sequential stabilization mechanism in which prior native-like structure templates the formation of incoming foldons with complementary structure. Thus the same propensities and interactions that specify the final native state, encoded in the amino-acid sequence of every protein, determine the pathway for getting there. Experimental observations that have been interpreted differently, in terms of multiple independent pathways, appear to be due to chance misfolding errors that cause different population fractions to block at different pathway points, populate different pathway intermediates, and fold at different rates. This paper summarizes the experimental basis for these three determining principles and their consequences. Cooperative native-like foldon units and the sequential stabilization process together generate predetermined stepwise pathways. Optional misfolding errors are responsible for 3-state and heterogeneous kinetic folding.
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Affiliation(s)
- S Walter Englander
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia 19104-6059, USA.
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Brockwell DJ, Radford SE. Intermediates: ubiquitous species on folding energy landscapes? Curr Opin Struct Biol 2007; 17:30-7. [PMID: 17239580 PMCID: PMC2706323 DOI: 10.1016/j.sbi.2007.01.003] [Citation(s) in RCA: 172] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2006] [Revised: 12/07/2006] [Accepted: 01/09/2007] [Indexed: 11/23/2022]
Abstract
Although intermediates have long been recognised as fascinating species that form during the folding of large proteins, the role that intermediates play in the folding of small, single-domain proteins has been widely debated. Recent discoveries using new, sensitive methods of detection and studies combining simulation and experiment have now converged on a common vision for folding, involving intermediates as ubiquitous stepping stones en route to the native state. The results suggest that the folding energy landscapes of even the smallest proteins possess significant ruggedness in which intermediates stabilized by both native and non-native interactions are common features.
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