1
|
Tušar L, Usenik A, Turk B, Turk D. Mechanisms Applied by Protein Inhibitors to Inhibit Cysteine Proteases. Int J Mol Sci 2021; 22:ijms22030997. [PMID: 33498210 PMCID: PMC7863939 DOI: 10.3390/ijms22030997] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/13/2021] [Accepted: 01/16/2021] [Indexed: 02/07/2023] Open
Abstract
Protein inhibitors of proteases are an important tool of nature to regulate and control proteolysis in living organisms under physiological and pathological conditions. In this review, we analyzed the mechanisms of inhibition of cysteine proteases on the basis of structural information and compiled kinetic data. The gathered structural data indicate that the protein fold is not a major obstacle for the evolution of a protease inhibitor. It appears that nature can convert almost any starting fold into an inhibitor of a protease. In addition, there appears to be no general rule governing the inhibitory mechanism. The structural data make it clear that the “lock and key” mechanism is a historical concept with limited validity. However, the analysis suggests that the shape of the active site cleft of proteases imposes some restraints. When the S1 binding site is shaped as a pocket buried in the structure of protease, inhibitors can apply substrate-like binding mechanisms. In contrast, when the S1 binding site is in part exposed to solvent, the substrate-like inhibition cannot be employed. It appears that all proteases, with the exception of papain-like proteases, belong to the first group of proteases. Finally, we show a number of examples and provide hints on how to engineer protein inhibitors.
Collapse
Affiliation(s)
- Livija Tušar
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Aleksandra Usenik
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Faculty of Chemistry, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
- Institute of Regenerative Medicine, I.M. Sechenov First Moscow State Medical University, Bol’shaya Pirogovskaya Ulitsa, 19c1, 119146 Moscow, Russia
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
- Correspondence: ; Tel.: +386-1477-3857
| |
Collapse
|
2
|
Grigoryev SA, Popova EY. Attraction of Likenesses: Mechanisms of Self-Association and Compartmentalization of Eukaryotic Chromatin. Mol Biol 2019. [DOI: 10.1134/s0026893319060050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
3
|
Chen J, Kuhn LA. Deciphering the three-domain architecture in schlafens and the structures and roles of human schlafen12 and serpinB12 in transcriptional regulation. J Mol Graph Model 2019; 90:59-76. [PMID: 31026779 PMCID: PMC6657700 DOI: 10.1016/j.jmgm.2019.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 12/22/2022]
Abstract
Schlafen proteins are important in cell differentiation and defense against viruses, and yet this family of vertebrate proteins is just beginning to be understood at the molecular level. Here, the three-dimensional architecture and molecular interfaces of human schlafen12 (hSLFN12), which promotes intestinal stem cell differentiation, are analyzed by sequence conservation and structural modeling in light of the functions of its homologs and binding partners. Our analysis shows that the schlafen or divergent AAA ATPase domain described in the N-terminal region of schlafens in databases and the literature is a misannotation. This N-terminal region is conclusively an AlbA_2 DNA/RNA binding domain, forming the conserved core of schlafens and their sequence homologs from bacteria through mammals. Group III schlafens additionally contain a AAA NTPase domain in their C-terminal helicase region. In hSLFN12, we have uncovered a domain matching rho GTPases, which directly follows the AlbA_2 domain in all group II-III schlafens. Potential roles for the GTPase-like domain include antiviral activity and cytoskeletal interactions that contribute to nucleocytoplasmic shuttling and cell polarization during differentiation. Based on features conserved with rSlfn13, the AlbA_2 region in hSLFN12 is likely to bind RNA, possibly as a ribonuclease. We hypothesize that RNA binding by hSLFN12 contributes to an RNA-induced transcriptional silencing/E3 ligase complex, given the functions of hSLFN12's partners, SUV39H1, JMJD6, and PDLIM7. hSLFN12's partner hSerpinB12 may contribute to heterochromatin formation, based on its homology to MENT, or directly regulate transcription via its binding to RNA polymerase II. The analysis presented here provides clear architectural and transcriptional regulation hypotheses to guide experimental design for hSLFN12 and the thousands of schlafens that share its motifs.
Collapse
Affiliation(s)
- Jiaxing Chen
- Protein Structural Analysis and Design Lab, Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI, 48824-1319, USA
| | - Leslie A Kuhn
- Protein Structural Analysis and Design Lab, Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI, 48824-1319, USA.
| |
Collapse
|
4
|
Li M, Christen JM, Dittmer NT, Cao X, Zhang X, Jiang H, Kanost MR. The Manduca sexta serpinome: Analysis of serpin genes and proteins in the tobacco hornworm. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 102:21-30. [PMID: 30237077 PMCID: PMC6249112 DOI: 10.1016/j.ibmb.2018.09.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/14/2018] [Accepted: 09/16/2018] [Indexed: 06/02/2023]
Abstract
Members of the serpin superfamily of proteins occur in animals, plants, bacteria, archaea and some viruses. They adopt a variety of physiological functions, including regulation of immune system, modulation of apoptosis, hormone transport and acting as storage proteins. Most members of the serpin family are inhibitors of serine proteinases. In this study, we searched the genome of Manduca sexta and identified 32 serpin genes. We analyzed the structure of these genes and the sequences of their encoded proteins. Three M. sexta genes (serpin-1, serpin-15, and serpin-28) have mutually exclusive alternatively spliced exons encoding the carboxyl-terminal reactive center loop of the protein, which is the site of interaction with target proteases. We discovered that MsSerpin-1 has 14 splicing isoforms, including two undiscovered in previous studies. Twenty-eight of the 32 M. sexta serpins include a putative secretion signal peptide and are predicted to be extracellular proteins. Phylogenetic analysis of serpins in M. sexta and Bombyx mori indicates that 17 are orthologous pairs, perhaps carrying out essential physiological functions. Analysis of the reactive center loop and hinge regions of the protein sequences indicates that 16 of the serpin genes encode proteins that may lack proteinase inhibitor activity. Our annotation and analysis of these serpin genes and their transcript profiles should lead to future advances in experimental study of their functions in insect biochemistry.
Collapse
Affiliation(s)
- Miao Li
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Jayne M Christen
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Neal T Dittmer
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Xiaolong Cao
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Xiufeng Zhang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Haobo Jiang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Michael R Kanost
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA.
| |
Collapse
|
5
|
Meekins DA, Zhang X, Battaile KP, Lovell S, Michel K. 1.45 Å resolution structure of SRPN18 from the malaria vector Anopheles gambiae. Acta Crystallogr F Struct Biol Commun 2016; 72:853-862. [PMID: 27917832 PMCID: PMC5137461 DOI: 10.1107/s2053230x16017854] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/08/2016] [Indexed: 12/28/2022] Open
Abstract
Serine protease inhibitors (serpins) in insects function within development, wound healing and immunity. The genome of the African malaria vector, Anopheles gambiae, encodes 23 distinct serpin proteins, several of which are implicated in disease-relevant physiological responses. A. gambiae serpin 18 (SRPN18) was previously categorized as non-inhibitory based on the sequence of its reactive-center loop (RCL), a region responsible for targeting and initiating protease inhibition. The crystal structure of A. gambiae SRPN18 was determined to a resolution of 1.45 Å, including nearly the entire RCL in one of the two molecules in the asymmetric unit. The structure reveals that the SRPN18 RCL is extremely short and constricted, a feature associated with noncanonical inhibitors or non-inhibitory serpin superfamily members. Furthermore, the SRPN18 RCL does not contain a suitable protease target site and contains a large number of prolines. The SRPN18 structure therefore reveals a unique RCL architecture among the highly conserved serpin fold.
Collapse
Affiliation(s)
| | - Xin Zhang
- Division of Biology, Kansas State University, USA
| | - Kevin P. Battaile
- IMCA–CAT, Hauptman–Woodward Medical Research Institute, Argonne National Laboratory, USA
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, USA
| | | |
Collapse
|
6
|
Caccia S, Ricagno S, Bolognesi M. Molecular bases of neuroserpin function and pathology. Biomol Concepts 2015; 1:117-30. [PMID: 25961991 DOI: 10.1515/bmc.2010.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Serpins build a large and evolutionary widespread protein superfamily, hosting members that are mainly Ser-protease inhibitors. Typically, serpins display a conserved core domain composed of three main β-sheets and 9-10 α-helices, for a total of approximately 350 amino acids. Neuroserpin (NS) is mostly expressed in neurons and in the central and peripheral nervous systems, where it targets tissue-type plasminogen activator. NS activity is relevant for axogenesis, synaptogenesis and synaptic plasticity. Five (single amino acid) NS mutations are associated with severe neurodegenerative disease in man, leading to early onset dementia, epilepsy and neuronal death. The functional aspects of NS protease inhibition are linked to the presence of a long exposed loop (reactive center loop, RCL) that acts as bait for the incoming partner protease. Large NS conformational changes, associated with the cleavage of the RCL, trap the protease in an acyl-enzyme complex. Contrary to other serpins, this complex has a half-life of approximately 10 min. Conformational flexibility is held to be at the bases of NS polymerization leading to Collins bodies intracellular deposition and neuronal damage in the pathological NS variants. Two main general mechanisms of serpin polymerization are currently discussed. Both models require the swapping of the RCL among neighboring serpin molecules. Specific differences in the size of swapped regions, as well as differences in the folding stage at which polymerization can occur, distinguish the two models. The results provided by recent crystallographic and biophysical studies allow rationalization of the functional and pathological roles played by NS based on the analysis of four three-dimensional structures.
Collapse
|
7
|
Tan L, Perez J, Mela M, Miranda E, Burling KA, Rouhani FN, DeMeo DL, Haq I, Irving JA, Ordóñez A, Dickens JA, Brantly M, Marciniak SJ, Alexander GJM, Gooptu B, Lomas DA. Characterising the association of latency with α(1)-antitrypsin polymerisation using a novel monoclonal antibody. Int J Biochem Cell Biol 2014; 58:81-91. [PMID: 25462157 PMCID: PMC4305080 DOI: 10.1016/j.biocel.2014.11.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 10/13/2014] [Accepted: 11/04/2014] [Indexed: 11/27/2022]
Abstract
α1-Antitrypsin is primarily synthesised in the liver, circulates to the lung and protects pulmonary tissues from proteolytic damage. The Z mutant (Glu342Lys) undergoes inactivating conformational change and polymerises. Polymers are retained within the hepatocyte endoplasmic reticulum (ER) in homozygous (PiZZ) individuals, predisposing the individuals to hepatic cirrhosis and emphysema. Latency is an analogous process of inactivating, intra-molecular conformational change and may co-occur with polymerisation. However, the relationship between latency and polymerisation remained unexplored in the absence of a suitable probe. We have developed a novel monoclonal antibody specific for latent α1-antitrypsin and used it in combination with a polymer-specific antibody, to assess the association of both conformers in vitro, in disease and during augmentation therapy. In vitro kinetics analysis showed polymerisation dominated the pathway but latency could be promoted by stabilising monomeric α1-antitrypsin. Polymers were extensively produced in hepatocytes and a cell line expressing Z α1-antitrypsin but the latent protein was not detected despite manipulation of the secretory pathway. However, α1-antitrypsin augmentation therapy contains latent α1-antitrypsin, as did the plasma of 63/274 PiZZ individuals treated with augmentation therapy but 0/264 who were not receiving this medication (p<10(-14)). We conclude that latent α1-antitrypsin is a by-product of the polymerisation pathway, that the intracellular folding environment is resistant to formation of the latent conformer but that augmentation therapy introduces latent α1-antitrypsin into the circulation. A suite of monoclonal antibodies and methodologies developed in this study can characterise α1-antitrypsin folding and conformational transitions, and screen methods to improve augmentation therapy.
Collapse
Affiliation(s)
- Lu Tan
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, UK; Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Juan Perez
- Department of Cell Biology, Genetics and Physiology, University of Málaga, Málaga, Spain
| | - Marianna Mela
- Division of Gastroenterology & Hepatology, University Department of Medicine, Cambridge University Hospitals, Cambridge, UK
| | - Elena Miranda
- Department of Biology and Biotechnologies Charles Darwin and Pasteur Institute-Cenci Bolognetti Foundation-University of Rome La Sapienza, Rome, Italy
| | - Keith A Burling
- Core Biochemical Assay Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Farshid N Rouhani
- Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Imran Haq
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - James A Irving
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Adriana Ordóñez
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, UK
| | - Jennifer A Dickens
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, UK
| | - Mark Brantly
- Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Stefan J Marciniak
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, UK
| | - Graeme J M Alexander
- Division of Gastroenterology & Hepatology, University Department of Medicine, Cambridge University Hospitals, Cambridge, UK
| | - Bibek Gooptu
- Division of Asthma, Allergy and Lung Biology, King's College London, Guy's Hospital, 5th Floor, Tower Wing, London, UK.
| | - David A Lomas
- Wolfson Institute for Biomedical Research, University College London, London, UK.
| |
Collapse
|
8
|
Lomas DA. Twenty Years of Polymers: A Personal Perspective on Alpha-1 Antitrypsin Deficiency. COPD 2013; 10 Suppl 1:17-25. [DOI: 10.3109/15412555.2013.764401] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
9
|
Collepardo-Guevara R, Schlick T. Crucial role of dynamic linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes. Nucleic Acids Res 2012; 40:8803-17. [PMID: 22790986 PMCID: PMC3467040 DOI: 10.1093/nar/gks600] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Monte Carlo simulations of a mesoscale model of oligonucleosomes are analyzed to examine the role of dynamic-linker histone (LH) binding/unbinding in high monovalent salt with divalent ions, and to further interpret noted chromatin fiber softening by dynamic LH in monovalent salt conditions. We find that divalent ions produce a fiber stiffening effect that competes with, but does not overshadow, the dramatic softening triggered by dynamic-LH behavior. Indeed, we find that in typical in vivo conditions, dynamic-LH binding/unbinding reduces fiber stiffening dramatically (by a factor of almost 5, as measured by the elasticity modulus) compared with rigidly fixed LH, and also the force needed to initiate chromatin unfolding, making it consistent with those of molecular motors. Our data also show that, during unfolding, divalent ions together with LHs induce linker-DNA bending and DNA–DNA repulsion screening, which guarantee formation of heteromorphic superbeads-on-a-string structures that combine regions of loose and compact fiber independently of the characteristics of the LH–core bond. These structures might be important for gene regulation as they expose regions of the DNA selectively. Dynamic control of LH binding/unbinding, either globally or locally, in the presence of divalent ions, might constitute a mechanism for regulation of gene expression.
Collapse
|
10
|
Sjakste N, Bielskiene K, Bagdoniene L, Labeikyte D, Gutcaits A, Vassetzky Y, Sjakste T. Tightly bound to DNA proteins: Possible universal substrates for intranuclear processes. Gene 2012; 492:54-64. [PMID: 22001404 DOI: 10.1016/j.gene.2011.09.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 09/08/2011] [Accepted: 09/22/2011] [Indexed: 01/05/2023]
Affiliation(s)
- N Sjakste
- Faculty of Medicine, University of Latvia, Šarlotes 1a, LV1001, Riga, Latvia
| | | | | | | | | | | | | |
Collapse
|
11
|
Goulet B, Kennette W, Ablack A, Postenka CO, Hague MN, Mymryk JS, Tuck AB, Giguère V, Chambers AF, Lewis JD. Nuclear localization of maspin is essential for its inhibition of tumor growth and metastasis. J Transl Med 2011; 91:1181-7. [PMID: 21502940 DOI: 10.1038/labinvest.2011.66] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Maspin (mammary serine protease inhibitor or SerpinB5) acts as a tumor suppressor when overexpressed in aggressive cancer cell lines. However, its role in human cancer is controversial. Maspin expression has been associated with a poor prognosis in some studies, whereas in others, with favorable outcome. The clinical data suggest, however, that nuclear-localized maspin is associated with improved survival. We hypothesized that the tumor suppressor activity of maspin may require nuclear localization, and that the discordance between clinical and experimental reports is a consequence of the variable subcellular distribution of maspin. Furthermore, we surmized that nuclear maspin could function as a tumor suppressor through the regulation of genes involved in tumor growth and invasion. Maspin or maspin fused to a nuclear export signal were expressed in metastatic human breast and epidermoid carcinoma cell lines. We found that pan-cellular localized maspin inhibited in vivo tumor growth and metastasis when assessed in xenograft chicken embryo and murine mammary fat pad injection models. However, when maspin was excluded from the nucleus via a nuclear exclusion signal, it no longer functioned as a metastasis suppressor. Using chromatin immunoprecipitation, we show that nuclear maspin was enriched at the promoter of colony-stimulating factor-1 (CSF-1) and associated with diminished levels of CSF-1 mRNA. Our findings demonstrate that the nuclear localization of maspin is required for its tumor and metastasis suppressor functions in vivo, and suggest that its mechanism of action involves, in part, direct association of maspin with target genes.
Collapse
|
12
|
Roussel BD, Irving JA, Ekeowa UI, Belorgey D, Haq I, Ordóñez A, Kruppa AJ, Duvoix A, Rashid ST, Crowther DC, Marciniak SJ, Lomas DA. Unravelling the twists and turns of the serpinopathies. FEBS J 2011; 278:3859-67. [DOI: 10.1111/j.1742-4658.2011.08201.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
13
|
Kowalski A, Pałyga J. Chromatin compaction in terminally differentiated avian blood cells: the role of linker histone H5 and non-histone protein MENT. Chromosome Res 2011; 19:579-90. [PMID: 21656257 PMCID: PMC3139888 DOI: 10.1007/s10577-011-9218-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Revised: 05/04/2011] [Accepted: 05/06/2011] [Indexed: 10/28/2022]
Abstract
Chromatin has a tendency to shift from a relatively decondensed (active) to condensed (inactive) state during cell differentiation due to interactions of specific architectural and/or regulatory proteins with DNA. A promotion of chromatin folding in terminally differentiated avian blood cells requires the presence of either histone H5 in erythrocytes or non-histone protein, myeloid and erythroid nuclear termination stage-specific protein (MENT), in white blood cells (lymphocytes and granulocytes). These highly abundant proteins assist in folding of nucleosome arrays and self-association of chromatin fibers into compacted chromatin structures. Here, we briefly review structural aspects and molecular mode of action by which these unrelated proteins can spread condensed chromatin to form inactivated regions in the genome.
Collapse
Affiliation(s)
- Andrzej Kowalski
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, ul. Świętokrzyska 15, 25-406 Kielce, Poland.
| | | |
Collapse
|
14
|
Alvarez-Alfageme F, Maharramov J, Carrillo L, Vandenabeele S, Vercammen D, Van Breusegem F, Smagghe G. Potential use of a serpin from Arabidopsis for pest control. PLoS One 2011; 6:e20278. [PMID: 21655276 PMCID: PMC3104999 DOI: 10.1371/journal.pone.0020278] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 04/25/2011] [Indexed: 12/20/2022] Open
Abstract
Although genetically modified (GM) plants expressing toxins from Bacillus thuringiensis (Bt) protect agricultural crops against lepidopteran and coleopteran pests, field-evolved resistance to Bt toxins has been reported for populations of several lepidopteran species. Moreover, some important agricultural pests, like phloem-feeding insects, are not susceptible to Bt crops. Complementary pest control strategies are therefore necessary to assure that the benefits provided by those insect-resistant transgenic plants are not compromised and to target those pests that are not susceptible. Experimental GM plants producing plant protease inhibitors have been shown to confer resistance against a wide range of agricultural pests. In this study we assessed the potential of AtSerpin1, a serpin from Arabidopsis thaliana (L). Heynh., for pest control. In vitro assays were conducted with a wide range of pests that rely mainly on either serine or cysteine proteases for digestion and also with three non-target organisms occurring in agricultural crops. AtSerpin1 inhibited proteases from all pest and non-target species assayed. Subsequently, the cotton leafworm Spodoptera littoralis Boisduval and the pea aphid Acyrthosiphon pisum (Harris) were fed on artificial diets containing AtSerpin1, and S. littoralis was also fed on transgenic Arabidopsis plants overproducing AtSerpin1. AtSerpin1 supplied in the artificial diet or by transgenic plants reduced the growth of S. littoralis larvae by 65% and 38%, respectively, relative to controls. Nymphs of A. pisum exposed to diets containing AtSerpin1 suffered high mortality levels (LC50 = 637 µg ml−1). The results indicate that AtSerpin1 is a good candidate for exploitation in pest control.
Collapse
Affiliation(s)
- Fernando Alvarez-Alfageme
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
- * E-mail: (F-AA); (GS)
| | - Jafar Maharramov
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Laura Carrillo
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Steven Vandenabeele
- VIB Department of Plant Systems Biology, Ghent University, Gent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, Gent, Belgium
| | - Dominique Vercammen
- VIB Department of Plant Systems Biology, Ghent University, Gent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, Gent, Belgium
| | - Frank Van Breusegem
- VIB Department of Plant Systems Biology, Ghent University, Gent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, Gent, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
- * E-mail: (F-AA); (GS)
| |
Collapse
|
15
|
Structural basis for the recognition and cleavage of histone H3 by cathepsin L. Nat Commun 2011; 2:197. [PMID: 21326229 PMCID: PMC3105313 DOI: 10.1038/ncomms1204] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 01/20/2011] [Indexed: 11/23/2022] Open
Abstract
Proteolysis of eukaryotic histone tails has emerged as an important factor in the modulation of cell-cycle progression and cellular differentiation. The recruitment of lysosomal cathepsin L to the nucleus where it mediates proteolysis of the mouse histone H3 tail has been described recently. Here, we report the three-dimensional crystal structures of a mature, inactive mutant of human cathepsin L alone and in complex with a peptide derived from histone H3. Canonical substrate–cathepsin L interactions are observed in the complex between the protease and the histone H3 peptide. Systematic analysis of the impact of posttranslational modifications at histone H3 on substrate selectivity suggests cathepsin L to be highly accommodating of all modified peptides. This is the first report of cathepsin L–histone H3 interaction and the first structural description of cathepsin L in complex with a substrate. Cathepsin L mediates proteolysis of the histone H3 tail and is a factor in cell-cycle progression and cellular differentiation. Adams-Cioaba et al. report crystal structures of an inactive mutant of the protease complexed with substrate peptides, and find that it is highly accommodating of modified substrates.
Collapse
|
16
|
Huntington JA, Whisstock JC. Molecular contortionism - on the physical limits of serpin 'loop-sheet' polymers. Biol Chem 2011; 391:973-82. [PMID: 20731544 DOI: 10.1515/bc.2010.085] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Members of the serpin (serine protease inhibitor) superfamily fold into a metastable conformation that is crucial for proper function. As a consequence, serpins are susceptible to mutations that cause misfolding and the intracellular accumulation of pathogenic polymers. The mechanism of serpin polymerisation remains to be resolved, however, over the past two decades the 'loop-sheet' hypothesis has gained wide acceptance. In this mechanism the reactive centre loop of one serpin monomer inserts into the beta-sheet A of another (in trans), in a manner similar to what is seen for reactive centre loop-cleaved and latent conformations (in cis). The hypothesis has been refined in response to certain experimental data, but it has proved difficult to assess the various propositions without creating molecular models. Here we evaluate the loop-sheet mechanism by creating models of pentamers of the archetypal serpin alpha(1)-antitrypsin. We conclude that an inescapable consequence of the loop-sheet mechanism is polymer compaction and rigidity, properties that are inconsistent with the 'beads-on-a-string' morphology of polymers obtained from human tissue. The recent crystal structure of a domain-swapped serpin dimer suggests an alternative mechanism that is consistent with known polymer properties, including the requirement of partial unfolding to induce polymer formation in vitro, and polymerisation from a folding intermediate in vivo.
Collapse
Affiliation(s)
- James A Huntington
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, UK.
| | | |
Collapse
|
17
|
Abstract
A balance between proteolytic activity and protease inhibition is required to maintain the appropriate function of biological systems in which proteases play a role. The Myeloid and Erythroid Nuclear Termination protein, MENT, is a nonhistone heterochromatin-associated serpin that is an effective inhibitor of the papain-like cysteine proteases. Our laboratories have extensively investigated the dual functions of this protein, namely, chromatin condensation and protease inhibition. Unlike other serpins to date, MENT contains a unique insertion between the C- and D-helices known as the "M-loop." This loop contains two critical functional motifs that allow the nuclear function of MENT, namely, nuclear localization and DNA binding. However, the nuclear function of MENT is not restricted to the activities of the M-loop alone. In vitro, MENT brings about the dramatic remodeling of chromatin into higher-order structures by forming protein bridges via its reactive center loop. Further, we have determined that in a protease-mediated effect, DNA can act as a cofactor to accelerate the rate at which MENT can inhibit its target proteases. In this chapter, we discuss the isolation of MENT from native chicken blood as well as recombinant protein produced in Escherichia coli. Various techniques including in vitro functional assays and biophysical characterization are explained that can be used to elucidate the ability of the protein to interact with DNA and other deoxynucleoprotein complexes. In situ chromatin precipitation using natively purified MENT is also detailed.
Collapse
Affiliation(s)
- Sergei Grigoryev
- Department of Biochemistry & Molecular Biology, Penn State University College of Medicine, Milton S. Hershey Medical Center, University Drive, Hershey, Pennsylvania, USA
| | | |
Collapse
|
18
|
|
19
|
|
20
|
Ricagno S, Pezzullo M, Barbiroli A, Manno M, Levantino M, Santangelo MG, Bonomi F, Bolognesi M. Two latent and two hyperstable polymeric forms of human neuroserpin. Biophys J 2010; 99:3402-11. [PMID: 21081089 PMCID: PMC2980742 DOI: 10.1016/j.bpj.2010.09.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 09/08/2010] [Accepted: 09/09/2010] [Indexed: 02/02/2023] Open
Abstract
Human neuroserpin (hNS) is a serine protease inhibitor that belongs to the serpin superfamily and is expressed in nervous tissues. The serpin fold is generally characterized by a long exposed loop, termed the reactive center loop, that acts as bait for the target protease. Intramolecular insertion of the reactive center loop into the main serpin β-sheet leads to the serpin latent form. As with other known serpins, hNS pathological mutants have been shown to accumulate as polymers composed of quasi-native protein molecules. Although hNS polymerization has been intensely studied, a general agreement about serpin polymer organization is still lacking. Here we report a biophysical characterization of native hNS that is shown to undergo two distinct conformational transitions, at 55°C and 85°C, both leading to distinct latent and polymeric species. The latent and polymer hNS forms obtained at 45°C and 85°C differ in their chemical and thermal stabilities; furthermore, the hNS polymers also differ in size and morphology. Finally, the 85°C polymer shows a higher content of intermolecular β-sheet interactions than the 45°C polymer. Together, these results suggest a more complex conformational scenario than was previously envisioned, and, in a general context, may help reconcile the current contrasting views on serpin polymerization.
Collapse
Affiliation(s)
- Stefano Ricagno
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Centro Interdisciplinare Materiali e Interfacce Nanostrutturati, Università di Milano, Milan, Italy
- Dipartimento di Biochimica, Università di Pavia, Pavia, Italy
- Laboratori di Biotecnologie, Istituto Di Ricovero e Cura a Carattere Scientifico Fondazione Policlinico San Matteo, Pavia, Italy
| | - Margherita Pezzullo
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Centro Interdisciplinare Materiali e Interfacce Nanostrutturati, Università di Milano, Milan, Italy
| | - Alberto Barbiroli
- Sezione di Biochimica, Dipartimento di Scienze Molecolari Agroalimentari, Università di Milano, Milan, Italy
| | - Mauro Manno
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, CNR, Palermo, Italy
| | - Matteo Levantino
- Dipartimento di Scienze Fisiche ed Astronomiche, Università of Palermo, Palermo, Italy
| | | | - Francesco Bonomi
- Sezione di Biochimica, Dipartimento di Scienze Molecolari Agroalimentari, Università di Milano, Milan, Italy
| | - Martino Bolognesi
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Centro Interdisciplinare Materiali e Interfacce Nanostrutturati, Università di Milano, Milan, Italy
| |
Collapse
|
21
|
Silverman GA, Whisstock JC, Bottomley SP, Huntington JA, Kaiserman D, Luke CJ, Pak SC, Reichhart JM, Bird PI. Serpins flex their muscle: I. Putting the clamps on proteolysis in diverse biological systems. J Biol Chem 2010; 285:24299-305. [PMID: 20498369 DOI: 10.1074/jbc.r110.112771] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Serpins compose the largest superfamily of peptidase inhibitors and are well known as regulators of hemostasis and thrombolysis. Studies using model organisms, from plants to vertebrates, now show that serpins and their unique inhibitory mechanism and conformational flexibility are exploited to control proteolysis in molecular pathways associated with cell survival, development, and host defense. In addition, an increasing number of non-inhibitory serpins are emerging as important elements within a diversity of biological systems by serving as chaperones, hormone transporters, or anti-angiogenic factors.
Collapse
Affiliation(s)
- Gary A Silverman
- Department of Pediatrics and Cell Biology and Physiology, Children's Hospital of Pittsburgh and Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Modulation of the proteolytic activity of the complement protease C1s by polyanions: implications for polyanion-mediated acceleration of interaction between C1s and SERPING1. Biochem J 2009; 422:295-303. [PMID: 19522701 DOI: 10.1042/bj20090198] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The complement system plays crucial roles in the immune system, but incorrect regulation causes inflammation and targeting of self-tissue, leading to diseases such as systemic lupus erythematosus, rheumatoid arthritis and age-related macular degeneration. In vivo, the initiating complexes of the classical complement and lectin pathways are controlled by SERPING1 [(C1 inhibitor) serpin peptidase inhibitor, clade G, member 1], which inactivates the components C1s and MASP-2 (mannan-binding lectin serine peptidase 2). GAGs (glycosaminoglycan) and DXS (dextran sulfate) are able to significantly accelerate SERPING1-mediated inactivation of C1s, the key effector enzyme of the classical C1 complex, although the mechanism is poorly understood. In the present study we have shown that C1s can bind to DXS and heparin and that these polyanions enhanced C1s proteolytic activity at low concentrations and inhibited it at higher concentrations. The recent determination of the crystal structure of SERPING1 has given rise to the hypothesis that both the serpin (serine protease inhibitor)-polyanion and protease-polyanion interactions might be required to accelerate the association rate of SERPING1 and C1s. To determine what proportion of the acceleration was due to protease-polyanion interactions, a chimaeric mutant of alpha1-antitrypsin containing the P4-P1 residues from the SERPING1 RCL (reactive-centre loop) was produced. Like SERPING1, this molecule is able to effectively inhibit C1s, but is unable to bind polyanions. DXS exerted a biphasic effect on the association rate of C1s which correlated strongly with the effect of DXS on C1s proteolytic activity. Thus, whereas polyanions are able to bind C1s and modulate its activity, polyanion interactions with SERPING1 must also play a vital role in the mechanism by which these cofactors accelerate the C1s-SERPING1 reaction.
Collapse
|
23
|
Gooptu B, Lomas DA. Conformational pathology of the serpins: themes, variations, and therapeutic strategies. Annu Rev Biochem 2009; 78:147-76. [PMID: 19245336 DOI: 10.1146/annurev.biochem.78.082107.133320] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Point mutations cause members of the serine protease inhibitor (serpin) superfamily to undergo a novel conformational transition, forming ordered polymers. These polymers characterize a group of diseases termed the serpinopathies. The formation of polymers underlies the retention of alpha(1)-antitrypsin within hepatocytes and of neuroserpin within neurons to cause cirrhosis and dementia, respectively. Point mutations of antithrombin, C1 inhibitor, alpha(1)-antichymotrypsin, and heparin cofactor II cause a similar conformational transition, resulting in a plasma deficiency that is associated with thrombosis, angioedema, and emphysema. Polymers of serpins can also form in extracellular tissues where they activate inflammatory cascades. This is best described for the Z variant of alpha(1)-antitrypsin in which the proinflammatory properties of polymers provide an explanation for both progressive emphysema and the selective advantage of this mutant allele. Therapeutic strategies are now being developed to block the aberrant conformational transitions and so treat the serpinopathies.
Collapse
Affiliation(s)
- Bibek Gooptu
- School of Crystallography, Birkbeck College, University of London, London, UK.
| | | |
Collapse
|
24
|
Gooptu B, Miranda E, Nobeli I, Mallya M, Purkiss A, Brown SCL, Summers C, Phillips RL, Lomas DA, Barrett TE. Crystallographic and cellular characterisation of two mechanisms stabilising the native fold of alpha1-antitrypsin: implications for disease and drug design. J Mol Biol 2009; 387:857-68. [PMID: 19232354 PMCID: PMC2723994 DOI: 10.1016/j.jmb.2009.01.069] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 01/31/2009] [Indexed: 11/28/2022]
Abstract
The common Z mutant (Glu342Lys) of alpha(1)-antitrypsin results in the formation of polymers that are retained within hepatocytes. This causes liver disease whilst the plasma deficiency of an important proteinase inhibitor predisposes to emphysema. The Thr114Phe and Gly117Phe mutations border a surface cavity identified as a target for rational drug design. These mutations preserve inhibitory activity but reduce the polymerisation of wild-type native alpha(1)-antitrypsin in vitro and increase secretion in a Xenopus oocyte model of disease. To understand these effects, we have crystallised both mutants and solved their structures. The 2.2 A structure of Thr114Phe alpha(1)-antitrypsin demonstrates that the effects of the mutation are mediated entirely by well-defined partial cavity blockade and allows in silico screening of fragments capable of mimicking the effects of the mutation. The Gly117Phe mutation operates differently, repacking aromatic side chains in the helix F-beta-sheet A interface to induce a half-turn downward shift of the adjacent F helix. We have further characterised the effects of these two mutations in combination with the Z mutation in a eukaryotic cell model of disease. Both mutations increase the secretion of Z alpha(1)-antitrypsin in the native conformation, but the double mutants remain more polymerogenic than the wild-type (M) protein. Taken together, these data support different mechanisms by which the Thr114Phe and Gly117Phe mutations stabilise the native fold of alpha(1)-antitrypsin and increase secretion of monomeric protein in cell models of disease.
Collapse
Affiliation(s)
- Bibek Gooptu
- School of Crystallography, Birkbeck College, University of London, London, UK.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Conformational change in the chromatin remodelling protein MENT. PLoS One 2009; 4:e4727. [PMID: 19266095 PMCID: PMC2648895 DOI: 10.1371/journal.pone.0004727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Accepted: 01/29/2009] [Indexed: 12/02/2022] Open
Abstract
Chromatin condensation to heterochromatin is a mechanism essential for widespread suppression of gene transcription, and the means by which a chromatin-associated protein, MENT, induces a terminally differentiated state in cells. MENT, a protease inhibitor of the serpin superfamily, is able to undergo conformational change in order to effect enzyme inhibition. Here, we sought to investigate whether conformational change in MENT is ‘fine-tuned’ in the presence of a bound ligand in an analogous manner to other serpins, such as antithrombin where such movements are reflected by a change in intrinsic tryptophan fluorescence. Using this technique, MENT was found to undergo structural shifts in the presence of DNA packaged into nucleosomes, but not naked DNA. The contribution of the four Trp residues of MENT to the fluorescence change was mapped using deconvolution analysis of variants containing single Trp to Phe mutations. The analysis indicated that the overall emission spectra is dominated by a helix-H tryptophan, but this residue did not dominate the conformational change in the presence of chromatin, suggesting that other Trp residues contained in the A-sheet and RCL regions contribute to the conformational change. Mutagenesis revealed that the conformational change requires the presence of the DNA-binding ‘M-loop’ and D-helix of MENT, but is independent of the protease specificity determining ‘reactive centre loop’. The D-helix mutant of MENT, which is unable to condense chromatin, does not undergo a conformational change, despite being able to bind chromatin, indicating that the conformational change may contribute to chromatin condensation by the serpin.
Collapse
|
26
|
Dewilde M, Strelkov SV, Rabijns A, Declerck PJ. High quality structure of cleaved PAI-1-stab. J Struct Biol 2008; 165:126-32. [PMID: 19059484 DOI: 10.1016/j.jsb.2008.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 09/30/2008] [Accepted: 11/06/2008] [Indexed: 11/16/2022]
Abstract
Here we report the crystal structure of a stablilized plasminogen activator inhibitor-1 variant (PAI-1-N150H-K154T-Q301P-Q319L-M354I (PAI-1-stab)) that shows a cleavage within the reactive centre loop. The new structure is of superior quality compared to the previously determined structure of the cleaved PAI-1-A335P mutant. We present a detailed comparison of the two structures and also compare them with the structure of the active PAI-1-stab. The structural data give important insights into the working mechanism of PAI-1 and also explain the role of various stabilizing mutations.
Collapse
Affiliation(s)
- M Dewilde
- Katholieke Universiteit Leuven, Belgium
| | | | | | | |
Collapse
|
27
|
Beinrohr L, Dobó J, Závodszky P, Gál P. C1, MBL-MASPs and C1-inhibitor: novel approaches for targeting complement-mediated inflammation. Trends Mol Med 2008; 14:511-21. [PMID: 18977695 DOI: 10.1016/j.molmed.2008.09.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2008] [Revised: 09/26/2008] [Accepted: 09/26/2008] [Indexed: 10/21/2022]
Abstract
Complement activation is initiated by the pattern-recognition molecules complement component C1q, mannose-binding lectin (MBL) and ficolins (H-, L-, M-ficolin), which typically recognize antibody-antigen complexes or foreign polysaccharides. The associated proteases (C1r, C1s, MASP-1 and MASP-2) then activate the complement system. The serpin C1-inhibitor (C1-inh) blocks activity of all these complexes and has been successfully used in models of disease. Many structures of these components became available recently, including that of C1-inh, facilitating the structure-guided design of drugs targeting complement activation. Here, we propose an approach in which therapeutic proteins are made up of natural protein domains and C1-inh to allow targeting to the site of inflammation and more specific inhibition of complement activation. In particular, engineering a fast-acting C1-inh or fusing it to an 'aiming module' has been shown to be feasible and economical using a humanized yeast expression system. Complement-mediated inflammation has been linked to ischemia-reperfusion injury, organ graft rejection and even neurodegeneration, so targeting this process has direct clinical implications.
Collapse
Affiliation(s)
- László Beinrohr
- Institute of Enzymology, Karolina út 29, H-1113 Budapest, Hungary.
| | | | | | | |
Collapse
|
28
|
Zlatanova J, Seebart C, Tomschik M. The linker-protein network: control of nucleosomal DNA accessibility. Trends Biochem Sci 2008; 33:247-53. [PMID: 18468442 DOI: 10.1016/j.tibs.2008.04.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Revised: 04/01/2008] [Accepted: 04/02/2008] [Indexed: 12/26/2022]
Abstract
Numerous studies have recently addressed the accessibility of nucleosomal DNA to protein factors. Two popular concepts - the histone code and chromatin remodeling - consider the nucleosome as a passive entity that 'waits' to be marked by histone modifications and is 'mobilized' by ATP-dependent remodelers. Here, we propose a holistic view of the nucleosome as an active, dynamic entity, the accessibility of which is controlled by binding of different linker proteins to the DNA entry/exit site. The linker proteins might directly compete for this binding site; alternatively, protein chaperones and/or chromatin remodelers might exchange one linker protein for another. Finally, according to our proposed model, the exchange factors are themselves controlled by post-translational modifications or binding of protein partners, to respond to the ever-changing intra- and extra-cellular environment.
Collapse
Affiliation(s)
- Jordanka Zlatanova
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
| | | | | |
Collapse
|
29
|
Li SH, Gorlatova NV, Lawrence DA, Schwartz BS. Structural differences between active forms of plasminogen activator inhibitor type 1 revealed by conformationally sensitive ligands. J Biol Chem 2008; 283:18147-57. [PMID: 18436534 DOI: 10.1074/jbc.m709455200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plasminogen activator inhibitor type 1 (PAI-1) is a serine protease inhibitor (serpin) in which the reactive center loop (RCL) spontaneously inserts into a central beta-sheet, beta-sheet A, resulting in inactive inhibitor. Available x-ray crystallographic studies of PAI-1 in an active conformation relied on the use of stabilizing mutations. Recently it has become evident that these structural models do not adequately explain the behavior of wild-type PAI-1 (wtPAI-1) in solution. To probe the structure of native wtPAI-1, we used three conformationally sensitive ligands: the physiologic cofactor, vitronectin; a monoclonal antibody, 33B8, that binds preferentially to RCL-inserted forms of PAI-1; and RCL-mimicking peptides that insert into beta-sheet A. From patterns of interaction with wtPAI-1 and the stable mutant, 14-1B, we propose a model of the native conformation of wtPAI-1 in which the bottom of the central sheet is closed, whereas the top of the beta-sheet A is open to allow partial insertion of the RCL. Because the incorporation of RCL-mimicking peptides into wtPAI-1 is accelerated by vitronectin, we further propose that vitronectin alters the conformation of the RCL to allow increased accessibility to beta-sheet A, yielding a structural hypothesis that is contradictory to the current structural model of PAI-1 in solution and its interaction with vitronectin.
Collapse
Affiliation(s)
- Shih-Hon Li
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
| | | | | | | |
Collapse
|
30
|
The silent information regulator 3 protein, SIR3p, binds to chromatin fibers and assembles a hypercondensed chromatin architecture in the presence of salt. Mol Cell Biol 2008; 28:3563-72. [PMID: 18362167 DOI: 10.1128/mcb.01389-07] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The telomeres and mating-type loci of budding yeast adopt a condensed, heterochromatin-like state through recruitment of the silent information regulator (SIR) proteins SIR2p, SIR3p, and SIR4p. In this study we characterize the chromatin binding determinants of recombinant SIR3p and identify how SIR3p mediates chromatin fiber condensation in vitro. Purified full-length SIR3p was incubated with naked DNA, nucleosome core particles, or defined nucleosomal arrays, and the resulting complexes were analyzed by electrophoretic shift assays, sedimentation velocity, and electron microscopy. SIR3p bound avidly to all three types of templates. SIR3p loading onto its nucleosomal sites in chromatin produced thickened condensed fibers that retained a beaded morphology. At higher SIR3p concentrations, individual nucleosomal arrays formed oligomeric suprastructures bridged by SIR3p oligomers. When condensed SIR3p-bound chromatin fibers were incubated in Mg(2+), they folded and oligomerized even further to produce hypercondensed higher-order chromatin structures. Collectively, these results define how SIR3p may function as a chromatin architectural protein and provide new insight into the interplay between endogenous and protein-mediated chromatin fiber condensation pathways.
Collapse
|
31
|
Abstract
The serpin α2-antiplasmin (SERPINF2) is the principal inhibitor of plasmin and inhibits fibrinolysis. Accordingly, α2-antiplasmin deficiency in humans results in uncontrolled fibrinolysis and a bleeding disorder. α2-antiplasmin is an unusual serpin, in that it contains extensive N- and C-terminal sequences flanking the serpin domain. The N-terminal sequence is crosslinked to fibrin by factor XIIIa, whereas the C-terminal region mediates the initial interaction with plasmin. To understand how this may happen, we have determined the 2.65Å X-ray crystal structure of an N-terminal truncated murine α2-antiplasmin. The structure reveals that part of the C-terminal sequence is tightly associated with the body of the serpin. This would be anticipated to position the flexible plasmin-binding portion of the C-terminus in close proximity to the serpin Reactive Center Loop where it may act as a template to accelerate serpin/protease interactions.
Collapse
|
32
|
Zhang Q, Law RHP, Bottomley SP, Whisstock JC, Buckle AM. A structural basis for loop C-sheet polymerization in serpins. J Mol Biol 2008; 376:1348-59. [PMID: 18234218 DOI: 10.1016/j.jmb.2007.12.050] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Revised: 12/17/2007] [Accepted: 12/20/2007] [Indexed: 10/22/2022]
Abstract
In this study, we report the X-ray crystal structure of an N-terminally truncated variant of the bacterial serpin, tengpin (tengpinDelta42). Our data reveal that tengpinDelta42 adopts a variation of the latent conformation in which the reactive center loop is hyperinserted into the A beta-sheet and removed from the vicinity of the C-sheet. This conformational change leaves the C beta-sheet completely exposed and permits antiparallel edge-strand interactions between the exposed portion of the reactive center loop of one molecule and strand s2C of the C beta-sheet of the neighboring molecule in the crystal lattice. Our structural data thus reveal that tengpinDelta42 forms a loop C-sheet polymer in the crystal lattice. In vivo serpins have a propensity to misfold and form long-chain polymers, a process that underlies serpinopathies such as emphysema, thrombosis and dementia. Native serpins are thought to polymerize via a loop A-sheet mechanism. However, studies on plasminogen activator inhibitor 1 and the S49P variant of human neuroserpin reveal that the latent form of these molecules can also polymerize. Polymerization of latent neuroserpin may be important for the development of familial encephalopathy with neuroserpin inclusion bodies. Our structural data provide a possible mechanism for polymerization by latent serpins.
Collapse
Affiliation(s)
- Qingwei Zhang
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | | | | | | | | |
Collapse
|
33
|
Ong PC, McGowan S, Pearce MC, Irving JA, Kan WT, Grigoryev SA, Turk B, Silverman GA, Brix K, Bottomley SP, Whisstock JC, Pike RN. DNA Accelerates the Inhibition of Human Cathepsin V by Serpins. J Biol Chem 2007; 282:36980-6. [DOI: 10.1074/jbc.m706991200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|
34
|
Serpins in plants and green algae. Funct Integr Genomics 2007; 8:1-27. [PMID: 18060440 DOI: 10.1007/s10142-007-0059-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 09/06/2007] [Accepted: 09/15/2007] [Indexed: 01/02/2023]
Abstract
Control of proteolysis is important for plant growth, development, responses to stress, and defence against insects and pathogens. Members of the serpin protein family are likely to play a critical role in this control through irreversible inhibition of endogenous and exogenous target proteinases. Serpins have been found in diverse species of the plant kingdom and represent a distinct clade among serpins in multicellular organisms. Serpins are also found in green algae, but the evolutionary relationship between these serpins and those of plants remains unknown. Plant serpins are potent inhibitors of mammalian serine proteinases of the chymotrypsin family in vitro but, intriguingly, plants and green algae lack endogenous members of this proteinase family, the most common targets for animal serpins. An Arabidopsis serpin with a conserved reactive centre is now known to be capable of inhibiting an endogenous cysteine proteinase. Here, knowledge of plant serpins in terms of sequence diversity, inhibitory specificity, gene expression and function is reviewed. This was advanced through a phylogenetic analysis of amino acid sequences of expressed plant serpins, delineation of plant serpin gene structures and prediction of inhibitory specificities based on identification of reactive centres. The review is intended to encourage elucidation of plant serpin functions.
Collapse
|
35
|
Guillebault D, Cotterill S. The Drosophila Df31 Protein Interacts with Histone H3 Tails and Promotes Chromatin Bridging In vitro. J Mol Biol 2007; 373:903-12. [PMID: 17889901 DOI: 10.1016/j.jmb.2007.07.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Revised: 07/11/2007] [Accepted: 07/24/2007] [Indexed: 10/23/2022]
Abstract
Df31 is a small hydrophilic protein from Drosophila melanogaster that can act as a histone chaperone in vitro. The protein is also detected as an integral component of chromatin, present at approximately the same level as histone H1. We have developed a simple assay to measure protein binding to oligonucleosomes and used it to characterise the DF31-oligonucleosome interaction. DF31 bound to chromatin in vitro at a level comparable to that observed in vivo. The DF31-chromatin interaction required the presence of core histone tails but binding was independent of the presence of H1 in the chromatin. Multiple regions of DF31 contributed to the interaction. Df31-chromatin binding still occurred on chromatin containing only H3/4, and cross-linking experiments showed that Df31 made intimate contact with H3, suggesting that this might be the primary contact site. Finally, using immobilised chromatin templates, we showed that DF31 promoted interstrand bridging between two independent oligonucleosome chains. These results provide strong evidence for a structural role of DF31 in chromatin folding and give an indication of the mechanism involved.
Collapse
Affiliation(s)
- Delphine Guillebault
- Department of Basic Medical Sciences, St. Georges University London, London SW17 0RE, UK
| | | |
Collapse
|
36
|
Nikitina T, Ghosh RP, Horowitz-Scherer RA, Hansen JC, Grigoryev SA, Woodcock CL. MeCP2-chromatin interactions include the formation of chromatosome-like structures and are altered in mutations causing Rett syndrome. J Biol Chem 2007; 282:28237-45. [PMID: 17660293 DOI: 10.1074/jbc.m704304200] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
hMeCP2 (human methylated DNA-binding protein 2), mutations of which cause most cases of Rett syndrome (RTT), is involved in the transmission of repressive epigenetic signals encoded by DNA methylation. The present work focuses on the modifications of chromatin architecture induced by MeCP2 and the effects of RTT-causing mutants. hMeCP2 binds to nucleosomes close to the linker DNA entry-exit site and protects approximately 11 bp of linker DNA from micrococcal nuclease. MeCP2 mutants differ in this property; the R106W mutant gives very little extra protection beyond the approximately 146-bp nucleosome core, whereas the large C-terminal truncation R294X reveals wild type behavior. Gel mobility assays show that linker DNA is essential for proper MeCP2 binding to nucleosomes, and electron microscopy visualization shows that the protein induces distinct conformational changes in the linker DNA. When bound to nucleosomes, MeCP2 is in close proximity to histone H3, which exits the nucleosome core close to the proposed MeCP2-binding site. These findings firmly establish nucleosomal linker DNA as a crucial binding partner of MeCP2 and show that different RTT-causing mutations of MeCP2 are correspondingly defective in different aspects of the interactions that alter chromatin architecture.
Collapse
Affiliation(s)
- Tatiana Nikitina
- Department of Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | | | | | | | | | | |
Collapse
|
37
|
Whisstock JC, Bottomley SP. Molecular gymnastics: serpin structure, folding and misfolding. Curr Opin Struct Biol 2006; 16:761-8. [PMID: 17079131 DOI: 10.1016/j.sbi.2006.10.005] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Revised: 09/10/2006] [Accepted: 10/19/2006] [Indexed: 11/25/2022]
Abstract
The native state of serpins represents a long-lived intermediate or metastable structure on the serpin folding pathway. Upon interaction with a protease, the serpin trap is sprung and the molecule continues to fold into a more stable conformation. However, thermodynamic stability can also be achieved through alternative, unproductive folding pathways that result in the formation of inactive conformations. Our increasing understanding of the mechanism of protease inhibition and the dynamics of native serpin structures has begun to reveal how evolution has harnessed the actual process of protein folding (rather than the final folded outcome) to elegantly achieve function. The cost of using metastability for function, however, is an increased propensity for misfolding.
Collapse
Affiliation(s)
- James C Whisstock
- Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, Clayton Campus, Melbourne 3800, Australia.
| | | |
Collapse
|