Vanderbilt University School of
5140 BIOSCI/MRBIII Vanderbilt University Center for Structural Biology 37232-8725
DNA replication, DNA recombination, DNA repair, DNA damage response, cancer, cardiac arrhythmia, innate immunity, calcium signal transduction, ubiquitination, structural biology, cell biology, protein structure, protein dynamics, proteomics, NMR, biochemistry,Bacteria,Biochemistry,Cancer,Cardiac function,DNA repair,DNA synthesis,NMR,Post-transcriptional modification,Protein Structure,Spectroscopy,Structural Biology,Toxicology
Structural Cell Biology: DNA replication, damage response and repair; ubiquitination; calcium signal transduction.
Research in my laboratory uses a multi-disciplinary, collaborative and structurally-oriented approach to address key problems in biology and medicine. At the molecular level, we study the structure and dynamics of proteins and their complexes with other proteins, nucleic acids and small molecule ligands. My independent career began as a biomolecular NMR spectroscopist, but has evolved to a point where I could be categorized as a structural biochemist. At the technical level, we now make use of many structural and biophysical techniques, including calorimetry, fluorescence spectroscopy, X-ray crystallography, X-ray/neutron scattering, cryo electron microscopy and computation. These studies are integrated with in vitro and cell-based biochemistry, in our own lab and by numerous collaborators at our institution, around the country and across the world. The following sections outline our three research programs.
I. The Structural Basis for Function of DNA Processing Machinery
One of the great scientific challenges today is to understand how proteins act together to perform the major processes in a cell such as DNA replication, all of which involve a sequence of multiple biochemical steps. Much of our work has revolved around human Replication Protein A (RPA), the major eukaryotic single-strand DNA (ssDNA) binding protein, which is essential for most DNA transactions in all cells. RPA is structurally very complex with three subunits containing eight different domains. It functions by constantly adjusting its binding of ssDNA and other proteins through structural changes within its domains as well as by altering the organization of its domains.
Our work has helped delineate the way in which RPA helps to orchestrate the intricate dance of proteins that is required to replicate DNA, respond when DNA is damaged, and repair the damage. Important insights have been obtained by identifying, and structurally characterizing, the interactions of RPA with specific proteins required for each of these processes. Recently, we have focused on the rearrangements in the global architecture of RPA, the mechanisms of binding and unbinding DNA, and how the binding of protein partners alter the landscape. As we have progressed, there has been an increasing need to determine structures of RPA binding partners. Current efforts center on human DNA primase, XPA and XPC. Together, these studies are laying the foundation to determine how mutations in the DNA processing proteins cause defects that lead to cancer and other diseases. Moreover, we are well invested into exploring translation of this knowledge into potential therapeutics by using fragment-based inhibitor discovery targeted to suppressing RPA-mediated recruitment of proteins to sites of DNA damage.
II. Structure and Function of U-box E3 Ubiquitin Ligases.
Covalent attachment of ubiquitin to a target protein serves as a cellular signal. For example, poly-ubiquitination of a target typically signals for degradation in the proteasome. Defects in this process are associated with cancer, for example a target can become overabundant if it is not degraded at a sufficient rate. The process of attaching ubquitin to a substrate protein involves a dynamic multi-protein machine comprised of E1, E2 and E3 enzymes. Our laboratory was the first to experimentally determine the structure of the U-box class of E3 ligases. Our studies of U-box proteins have focused on the mechanism of activation of the E2~ubiquitin conjugates, understanding how target proteins are recognized, and what factors control the type of ubiquitin chain attached. We are also investigating how the U-box E3 CHIP differentially regulates targets in the cell stress response.
III. Ca2+ Signal Transduction by EF-hand Proteins
Change in levels of calcium inside a cell is a common means for regulating biochemical signaling cascades and stimulating biomechanical actions. EF-hand calcium binding proteins play a central role in virtually every aspect of calcium signaling. Consequently, studies of their response to the binding of calcium and activation of targets are keys to understanding how this ion influences so many aspects of health and disease. I have worked in this field for nearly 30 years, starting as a postdoctoral fellow. Currently we have two active research programs.
The first program investigates the structural basis for how changes in intracellular calcium levels control inactivation gating of the human cardiac sodium channel NaV1.5. We found a complex mechanism involving both an EF-hand domain in NaV1.5 that directly binds calcium, and the ubiquitous EF-hand protein calmodulin. These two calcium sensors act in concert to re-position a flap at the edge of the channel pore that controls movement of sodium from outside to inside the cell. Mutations in the corresponding regions of NaV1.5 lead to cardiac arrhythmia syndromes and we are determining if new therapeutic strategies for these diseases can be developed based on our structural insights. We have also been working in concert with deep sequencing of patients suffering from cardiac arrhythmia syndromes to discern the physical basis of the defects caused by mutations in calmodulin genes, which came as a complete surprise because this protein is almost completely conserved in organisms from plants to man.
We also study the unique S100 EF-hand proteins, the first structures of which were determined in our laboratory. These proteins are distinguished by their ability to exert activity both inside and outside cells. We currently focus on calprotectin (CP), a dimer of S100A8 and S100A9 that plays a role in mediating inflammation and serves as an integral part of the innate immune response to invading microorganisms. We have shown that CP exhibits a remarkable ability to suppress infections by S. aureus and other bacteria by using a mechanism known as nutritional immunity, i.e. starving the pathogen of essential metals needed for survival. Our ultimate goal is to develop new approaches for antimicrobial agents that are based on the mechanism of action of CP. A second project involves determining the structural basis of CP activity in inflammatory processes, which results from its activation of the cell surface receptor RAGE. We have determined the structure of the RAGE ligand-binding domain and are analyzing the structural basis for RAGE activation by CP. These studies will provide critical insights for understanding chronic inflammation and atherosclerosis in diabetics and have the potential to reveal new avenues for treating these and other chronic inflammatory disorders. To this end, we have initiated a CP-RAGE fragment-based inhibitor discovery program.
Chazin, Ede L, Reis, Rda R, Junior, WT, Moor, LF, Vasconcelos, TR. An overview on the development of new potentially active camptothecin analogs against cancer. Mini Rev Med Chem, 14(12), 953-62, 2014.
Feldkamp, MD, Mason, AC, Eichman, BF, Chazin, WJ. Structural analysis of replication protein A recruitment of the DNA damage response protein SMARCAL1. Biochemistry, 53(18), 3052-61, 2014.
Frank, AO, Vangamudi, B, Feldkamp, MD, Souza-Fagundes, EM, Luzwick, JW, Cortez, D, Olejniczak, ET, Waterson, AG, Rossanese, OW, Chazin, WJ, Fesik, SW. Discovery of a potent stapled helix peptide that binds to the 70N domain of replication protein A. J Med Chem, 57(6), 2455-61, 2014.
Gaddy, JA, Radin, JN, Loh, JT, Piazuelo, MB, Kehl-Fie, TE, Delgado, AG, Ilca, FT, Peek, RM, Cover, TL, Chazin, WJ, Skaar, EP, Scott Algood, HM. The host protein calprotectin modulates the Helicobacter pylori cag type IV secretion system via zinc sequestration. PLoS Pathog, 10(10), e1004450, 2014.
Hwang, HS, Nitu, FR, Yang, Y, Walweel, K, Pereira, L, Johnson, CN, Faggioni, M, Chazin, WJ, Laver, D, George, AL, Cornea, RL, Bers, DM, Knollmann, BC. Divergent regulation of ryanodine receptor 2 calcium release channels by arrhythmogenic human calmodulin missense mutants. Circ Res, 114(7), 1114-24, 2014.
Makita, N, Yagihara, N, Crotti, L, Johnson, CN, Beckmann, BM, Roh, MS, Shigemizu, D, Lichtner, P, Ishikawa, T, Aiba, T, Homfray, T, Behr, ER, Klug, D, Denjoy, I, Mastantuono, E, Theisen, D, Tsunoda, T, Satake, W, Toda, T, Nakagawa, H, Tsuji, Y, Tsuchiya, T, Yamamoto, H, Miyamoto, Y, Endo, N, Kimura, A, Ozaki, K, Motomura, H, Suda, K, Tanaka, T, Schwartz, PJ, Meitinger, T, K????b, S, Guicheney, P, Shimizu, W, Bhuiyan, ZA, Watanabe, H, Chazin, WJ, George, AL. Novel calmodulin mutations associated with congenital arrhythmia susceptibility. Circ Cardiovasc Genet, 7(4), 466-74, 2014.
Mortensen, BL, Rathi, S, Chazin, WJ, Skaar, EP. Acinetobacter baumannii response to host-mediated zinc limitation requires the transcriptional regulator Zur. J Bacteriol, 196(14), 2616-26, 2014.
Shuck, SC, Wauchope, OR, Rose, KL, Kingsley, PJ, Rouzer, CA, Shell, SM, Sugitani, N, Chazin, WJ, Zagol-Ikapitte, I, Boutaud, O, Oates, JA, Galligan, JJ, Beavers, WN, Marnett, LJ. Protein modification by adenine propenal. Chem Res Toxicol, 27(10), 1732-42, 2014.
Sugitani, N, Shell, SM, Soss, SE, Chazin, WJ. Redefining the DNA-binding domain of human XPA. J Am Chem Soc, 136(31), 10830-3, 2014.
Vaithiyalingam, S, Arnett, DR, Aggarwal, A, Eichman, BF, Fanning, E, Chazin, WJ. Insights into eukaryotic primer synthesis from structures of the p48 subunit of human DNA primase. J Mol Biol, 426(3), 558-69, 2014.
Brosey, CA, Yan, C, Tsutakawa, SE, Heller, WT, Rambo, RP, Tainer, JA, Ivanov, I, Chazin, WJ. A new structural framework for integrating replication protein A into DNA processing machinery. Nucleic Acids Res, 41(4), 2313-27, 2013.
Crotti, L, Johnson, CN, Graf, E, De Ferrari, GM, Cuneo, BF, Ovadia, M, Papagiannis, J, Feldkamp, MD, Rathi, SG, Kunic, JD, Pedrazzini, M, Wieland, T, Lichtner, P, Beckmann, BM, Clark, T, Shaffer, C, Benson, DW, K????b, S, Meitinger, T, Strom, TM, Chazin, WJ, Schwartz, PJ, George, AL. Calmodulin mutations associated with recurrent cardiac arrest in infants. Circulation, 127(9), 1009-17, 2013.
Damo, SM, Feldkamp, MD, Chagot, B, Chazin, WJ. NMR studies of the interaction of calmodulin with IQ motif peptides. Methods Mol Biol, 963, 173-86, 2013.
Damo, SM, Kehl-Fie, TE, Sugitani, N, Holt, ME, Rathi, S, Murphy, WJ, Zhang, Y, Betz, C, Hench, L, Fritz, G, Skaar, EP, Chazin, WJ. Molecular basis for manganese sequestration by calprotectin and roles in the innate immune response to invading bacterial pathogens. Proc Natl Acad Sci U S A, 110(10), 3841-6, 2013.
Feldkamp, MD, Frank, AO, Kennedy, JP, Patrone, JD, Vangamudi, B, Waterson, AG, Fesik, SW, Chazin, WJ. Surface reengineering of RPA70N enables cocrystallization with an inhibitor of the replication protein A interaction motif of ATR interacting protein. Biochemistry, 52(37), 6515-24, 2013.
Frank, AO, Feldkamp, MD, Kennedy, JP, Waterson, AG, Pelz, NF, Patrone, JD, Vangamudi, B, Camper, DV, Rossanese, OW, Chazin, WJ, Fesik, SW. Discovery of a potent inhibitor of replication protein a protein-protein interactions using a fragment-linking approach. J Med Chem, 56(22), 9242-50, 2013.
Kehl-Fie, TE, Zhang, Y, Moore, JL, Farrand, AJ, Hood, MI, Rathi, S, Chazin, WJ, Caprioli, RM, Skaar, EP. MntABC and MntH contribute to systemic Staphylococcus aureus infection by competing with calprotectin for nutrient manganese. Infect Immun, 81(9), 3395-405, 2013.
Patrone, JD, Kennedy, JP, Frank, AO, Feldkamp, MD, Vangamudi, B, Pelz, NF, Rossanese, OW, Waterson, AG, Chazin, WJ, Fesik, SW. Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A. ACS Med Chem Lett, 4(7), 601-605, 2013.
Shell, SM, Hawkins, EK, Tsai, MS, Hlaing, AS, Rizzo, CJ, Chazin, WJ. Xeroderma pigmentosum complementation group C protein (XPC) serves as a general sensor of damaged DNA. DNA Repair (Amst), 12(11), 947-53, 2013.
Soss, SE, Klevit, RE, Chazin, WJ. Activation of UbcH5c~Ub is the result of a shift in interdomain motions of the conjugate bound to U-box E3 ligase E4B. Biochemistry, 52(17), 2991-9, 2013.
Stork, M, Grijpstra, J, Bos, MP, Ma??as Torres, C, Devos, N, Poolman, JT, Chazin, WJ, Tommassen, J. Zinc piracy as a mechanism of Neisseria meningitidis for evasion of nutritional immunity. PLoS Pathog, 9(10), e1003733, 2013.
Wells, CE, Bhaskara, S, Stengel, KR, Zhao, Y, Sirbu, B, Chagot, B, Cortez, D, Khabele, D, Chazin, WJ, Cooper, A, Jacques, V, Rusche, J, Eischen, CM, McGirt, LY, Hiebert, SW. Inhibition of histone deacetylase 3 causes replication stress in cutaneous T cell lymphoma. PLoS One, 8(7), e68915, 2013.
Xu, D, Young, JH, Krahn, JM, Song, D, Corbett, KD, Chazin, WJ, Pedersen, LC, Esko, JD. Stable RAGE-heparan sulfate complexes are essential for signal transduction. ACS Chem Biol, 8(7), 1611-20, 2013.
Brosey, CA, Tsutakawa, SE, Chazin, WJ. Sample preparation methods to analyze DNA-induced structural changes in replication protein A. Methods Mol Biol, 922, 101-22, 2012.
Hood, MI, Mortensen, BL, Moore, JL, Zhang, Y, Kehl-Fie, TE, Sugitani, N, Chazin, WJ, Caprioli, RM, Skaar, EP. Identification of an Acinetobacter baumannii zinc acquisition system that facilitates resistance to calprotectin-mediated zinc sequestration. PLoS Pathog, 8(12), e1003068, 2012.
Chazin, WJ. Evolution of the NIGMS Protein Structure Initiative. Structure, 16(1), 12-4, 2008.
Corbin, BD, Seeley, EH, Raab, A, Feldmann, J, Miller, MR, Torres, VJ, Anderson, KL, Dattilo, BM, Dunman, PM, Gerads, R, Caprioli, RM, Nacken, W, Chazin, WJ, Skaar, EP. Metal chelation and inhibition of bacterial growth in tissue abscesses. Science, 319(5865), 962-5, 2008.
Ball, HL, Ehrhardt, MR, Mordes, DA, Glick, GG, Chazin, WJ, Cortez, D. Function of a Conserved Checkpoint Recruitment Domain in ATRIP Proteins. Mol Cell Biol, , , 2007. PMCID:1899971
Chazin, WJ. The impact of X-ray crystallography and NMR on intracellular calcium signal transduction by EF-hand proteins: crossing the threshold from structure to biology and medicine. Sci STKE, 2007(388), pe27, 2007.
Dattilo, BM, Fritz, G, Leclerc, E, Kooi, CW, Heizmann, CW, Chazin, WJ. The extracellular region of the receptor for advanced glycation end products is composed of two independent structural units. Biochemistry, 46(23), 6957-70, 2007. PMCID:2527459
Weiner, BE, Huang, H, Dattilo, BM, Nilges, MJ, Fanning, E, Chazin, WJ. An Iron-Sulfur Cluster in the C-terminal Domain of the p58 Subunit of Human DNA Primase. J Biol Chem, 282(46), 33444-51, 2007.
Bunick, CG, Miller, MR, Fuller, BE, Fanning, E, Chazin, WJ. Biochemical and structural domain analysis of xeroderma pigmentosum complementation
group C protein. Biochemistry, 45(50), 14965-79, 2006. PMCID:2579963
Jiang, X, Klimovich, V, Arunkumar, AI, Hysinger, EB, Wang, Y, Ott, RD, Guler, GD, Weiner, B, Chazin, WJ, Fanning, E. Structural mechanism of RPA loading on DNA during activation of a simple pre-replication
complex. EMBO J, 25(23), 5516-26, 2006. PMCID:1679769
Johnson, E, Chazin, WJ, Rance, M. Effects of calcium binding on the side-chain methyl dynamics of calbindin D9k:
a 2H NMR relaxation study. J Mol Biol, 357(4), 1237-52, 2006.
Meyn, SM, Seda, C, Campbell, M, Weiss, KL, Hu, H, Pastrana-Rios, B, Chazin, WJ. The biochemical effect of Ser167 phosphorylation on Chlamydomonas reinhardtii
centrin. Biochem Biophys Res Commun, 342(1), 342-8, 2006.
Shah, VN, Wingo, TL, Weiss, KL, Williams, CK, Balser, JR, Chazin, WJ. Calcium-dependent regulation of the voltage-gated sodium channel hH1: Intrinsic
and extrinsic sensors use a common molecular switch. Proc Natl Acad Sci U S A, , , 2006. PMCID:1450128
Sheehan, JH, Bunick, CG, Hu, H, Fagan, PA, Meyn, SM, Chazin, WJ. Structure of the N-terminal calcium sensor domain of centrin reveals the biochemical
basis for domain-specific function. J Biol Chem, 281(5), 2876-81, 2006.
Sunahori, K, Yamamura, M, Yamana, J, Takasugi, K, Kawashima, M, Yamamoto, H, Chazin, WJ, Nakatani, Y, Yui, S, Makino, H. The S100A8/A9 heterodimer amplifies proinflammatory cytokine production by
macrophages via activation of nuclear factor kappa B and p38 mitogen-activated protein kinase in rheumatoid
arthritis. Arthritis Res Ther, 8(3), R69, 2006. PMCID:1526633
Vander Kooi, CW, Ohi, MD, Rosenberg, JA, Oldham, ML, Newcomer, ME, Gould, KL, Chazin, WJ. The Prp19 U-box crystal structure suggests a common dimeric architecture for
a class of oligomeric E3 ubiquitin ligases. Biochemistry, 45(1), 121-30, 2006. PMCID:2570371
Arunkumar, AI, Klimovich, V, Jiang, X, Ott, RD, Mizoue, L, Fanning, E, Chazin, WJ. Insights into hRPA32 C-terminal domain-mediated assembly of the simian virus
40 replisome. Nat Struct Mol Biol, 12(4), 332-9, 2005. PMCID:2600586
Bhattacharya, S, Lee, YT, Michowski, W, Jastrzebska, B, Filipek, A, Kuznicki, J, Chazin, WJ. The modular structure of SIP facilitates its role in stabilizing multiprotein
assemblies. Biochemistry, 44(27), 9462-71, 2005.
Malmendal, A, Vander Kooi, CW, Nielsen, NC, Chazin, WJ. Calcium-Modulated S100 Protein-Phospholipid Interactions. An NMR Study of Calbindin
D(9k) and DPC. Biochemistry, 44(17), 6502-6512, 2005.
Nakatani, Y, Yamazaki, M, Chazin, WJ, Yui, S. Regulation of S100A8/A9 (calprotectin) binding to tumor cells by zinc ion and
its implication for apoptosis-inducing activity. Mediators Inflamm, 2005(5), 280-92, 2005. PMCID:1279038
Bhattacharya, Shibani, Bunick, Christopher G, Chazin, Walter J. Target selectivity in EF-hand calcium binding proteins. Biochim Biophys Acta, 1742(1-3), 69-79, 2004.
Bunick, Christopher G, Nelson, Melanie R, Mangahas, Sheryll, Hunter, Michael J, Sheehan, Jonathan H, Mizoue, Laura S, Bunick, Gerard J, Chazin, Walter J. Designing sequence to control protein function in an EF-hand protein. J Am Chem Soc, 126(19), 5990-8, 2004.
Christodoulou, John, Malmendal, Anders, Harper, Jeffrey F, Chazin, Walter J. Evidence for differing roles for each lobe of the calmodulin-like domain in a calcium-dependent protein kinase. J Biol Chem, 279(28), 29092-100, 2004.
Hu, Haitao, Sheehan, Jonathan H, Chazin, Walter J. The mode of action of centrin. Binding of Ca2+ and a peptide fragment of Kar1p
to the C-terminal domain. J Biol Chem, 279(49), 50895-903, 2004.
Lee, Young-Tae, Jacob, Jaison, Michowski, Wojciech, Nowotny, Marcin, Kuznicki, Jacek, Chazin, Walter J. Human Sgt1 binds HSP90 through the CHORD-Sgt1 domain and not the tetratricopeptide repeat domain. J Biol Chem, 279(16), 16511-7, 2004.
Stauffer, Melissa E, Chazin, Walter J. Structural mechanisms of DNA replication, repair, and recombination. J Biol Chem, 279(30), 30915-8, 2004.
Stauffer, Melissa E, Chazin, Walter J. Physical interaction between replication protein A and Rad51 promotes exchange on single-stranded DNA. J Biol Chem, 279(24), 25638-45, 2004.
Wingo, Tammy L, Shah, Vikas N, Anderson, Mark E, Lybrand, Terry P, Chazin, Walter J, Balser, Jeffrey R. An EF-hand in the sodium channel couples intracellular calcium to cardiac excitability. Nat Struct Mol Biol, 11(3), 219-25, 2004.
Arunkumar, AI, Stauffer, ME, Bochkareva, E, Bochkarev, A, Chazin, WJ. Independent and coordinated functions of replication protein A tandem high
affinity single-stranded DNA binding domains. J Biol Chem, 278(42), 41077-82, 2003.
Bhattacharya, S, Large, E, Heizmann, CW, Hemmings, B, Chazin, WJ. Structure of the Ca2+/S100B/NDR kinase peptide complex: insights into S100
target specificity and activation of the kinase. Biochemistry, 42(49), 14416-26, 2003.
Hu, H, Chazin, WJ. Unique features in the C-terminal domain provide caltractin with target specificity. J Mol Biol, 330(3), 473-84, 2003.
Ohi, Melanie D, Vander Kooi, Craig W, Rosenberg, Joshua A, Chazin, Walter J, Gould, Kathleen L. Structural insights into the U-box, a domain associated with multi-ubiquitination. Nat Struct Biol, 10, 250-5, 2003.
Mer, G, Bochkarev, A, Gupta, R, Bochkareva, E, Frappier, L, Ingles, C J, Edwards, A M, Chazin, W J. Structural basis for the recognition of DNA repair proteins UNG2, XPA, and RAD52 by replication factor RPA. Cell, 103(3), 449-56, 2000.
M??ler, L, Blankenship, J, Rance, M, Chazin, W J. Site-site communication in the EF-hand Ca2+-binding protein calbindin D9k. Nat Struct Biol, 7(3), 245-50, 2000.
Smith, JA, Bifulco, G, Case, DA, Boger, DL, Gomez-Paloma, L, Chazin, WJ. The structural basis for in situ activation of DNA alkylation by duocarmycin
SA. J Mol Biol, 300(5), 1195-204, 2000.
Botuyan, M V, Koth, C M, Mer, G, Chakrabartty, A, Conaway, J W, Conaway, R C, Edwards, A M, Arrowsmith, C H, Chazin, W J. Binding of elongin A or a von Hippel-Lindau peptide stabilizes the structure of yeast elongin C. Proc Natl Acad Sci U S A, 96(16), 9033-8, 1999. PMCID:17727
Miick, S M, Fee, R S, Millar, D P, Chazin, W J. Crossover isomer bias is the primary sequence-dependent property of immobilized Holliday junctions. Proc Natl Acad Sci U S A, 94(17), 9080-4, 1997. PMCID:23039
Linse, S, J??nsson, B, Chazin, W J. The effect of protein concentration on ion binding. Proc Natl Acad Sci U S A, 92(11), 4748-52, 1995. PMCID:41784
Potts, B C, Smith, J, Akke, M, Macke, T J, Okazaki, K, Hidaka, H, Case, D A, Chazin, W J. The structure of calcyclin reveals a novel homodimeric fold for S100 Ca(2+)-binding proteins. Nat Struct Biol, 2(9), 790-6, 1995.
Skelton, N J, K??rdel, J, Akke, M, Fors??n, S, Chazin, W J. Signal transduction versus buffering activity in Ca(2+)-binding proteins. Nat Struct Biol, 1(4), 239-45, 1994.
One is for accomplished structural biologist to work on the assembly and function of multi-protein E3 ubiquitin ligases. A second position is for US citizen or green card holder for work on DNA replication and repair proteins. Please apply by e-mail to email@example.com sending CV and names of three references.
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