Handel Lab Publications 


HANDEL LAB, UCSD, SKAGGS SCHOOL OF PHARMACY AND PHARMACEUTICAL SCIENCES

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Computational Redesign of the SHV-1 b-lactamase/b-lactamase Inhibitor Protein Interface.  K.A. Reynolds, M.S. Hanes, J.M. Thomson, A.J. Antczak, J.M. Berger, R.A. Bonomo, J.F. Kirsch, and T.M. Handel (2008) Accepted to J. Mol Biol. 

An engineered monomer of CCL2 has anti-inflammatory properties emphasizing the importance of oligomerization for chemokine activity in vivo.   T.M. Handel, Z. Johnson, M. Mack, R. Cirillo, V. Muzio, M. Teixiera, M. Déruaz, F. Borlat, T.N.C. Wells, and A.E.I. Proudfoot (2008) Accepted to J. Leukocyte Biology.

Chemokines and cancer: migration, intracellular signaling, and intercellular communication in the microenvironment. M. O'Hayre, C.L. Salanga,T.M. Handel, and S.J. Allen. (2008) Biochemical J. 409:635-49. PDF

Quantum mechanical design of enzyme active sites. X. Zhang; J, DeChancie, H. Gunaydin, A.  Chowdry, F. Clemente, A. Smith S. T.M. Handel, and K. Houk, (2008) J Org Chem. 73:889-99. 

Inhibition of MCP-1 ameliorates rat adjuvant induced arthritis. S. Shahrara, AE.I. Proudfoot, C.C. Park, M.V. Volin, G.K. Haines, J.M. Woods, C.H. Aikens, T.M. Handel, R.M. Pope. (2008) Journal of Immunology, 180: 3447-3456.  PDF

NMR Assignment of Human Chemerin, a Novel Chemoattractant. S.J. Allen, B. A. Zabel, J. Kirkpatrick, E.J. Butcher, D. Nietlispach, and T.M. Handel (2007). Biomol. NMR Assignments. 1:171-173.

Staphylococcus Aureus-derived Staphopain B, a Potent Cysteine Protease Activator of Plasma Chemerin. P. Kulig, B.A. Zabel, G. Dubin, S.J. Allen, T. Ohyama, J. Potempa, T.M. Handel, E.C. Butcher and J. Cichy (2007) J. Immunology, 178:3713-20.

Structure of M11L: A Myxoma Virus Structural Homolog of the Apoptosis Inhibitor, Bcl-2. A.E. Douglas, K.D. Corbett, J.M. Berger, G. McFadden, and T.M. Handel (2007)  Protein Science. 6:695-703.

An Object-Oriented Library for Computational Protein Design. A.B. Chowdry, K. A. Reynolds, M. S.  Hanes, M. Voorhies, N.  Pokala, T.M. Handel. (2007) J. Computational Chem. 28:2378-88. Click here to download software

Chemokine:Receptor Structure, Interactions and Antagonism. S.J. Allen, S.E. Crown and T.M. Handel. (2007) Annu Rev Immunology, 25:787-820.

Potential inhibitors of chemokine function: Analysis of noncovalent complexes of CC chemokines and small polyanionic molecules by ESI FT-ICR Mass Spectrometry. Y. Yu, M.D. Sweeney, O.M. Saad, S.E. Crown, T.M. Handel and J.A Leary. (2006) J Am Soc Mass Spectrom 4:524-35.

Chemoattractants, extracellular proteases, and the integrated host defense response.  B.A. Zabel, S.J. Allen, P. Kulig, J.A. Allen, J. Cichy, T.M. Handel, E.C. Butcher. (2006) Exp Hemat 34:1021-32. 

Chemokine-like Receptor 1 expression by macrophages:  Chemerin-responsiveness and opposing regulation by TGF-beta and TLR Ligands. B.A. Zabel, T. Ohyama, L. Zuniga, J.Y. Kim, B. Johnston, S.J. Allen, D.G. Guido, T.M. Handel, E.C. Butcher. (2006) J Expt Hemat 34:1106-14.

Heterodimerization of CCR2 chemokines and regulation by glycosaminoglycan binding. S.E. Crown, Y. Yu, M.D. Sweeney, S.E. Crown, J.A Leary and T.M. Handel. (2006) J Biol Chem 281(35):25438-46.

Structural and computational characterization of the SHV-1 b-lactamase/b-lactamase inhibitor protein (BLIP) interface. K. A. Reynolds, J. M. Thomson, K.D. Corbett, C. R. Bethel, J.M. Berger, J.F. Kirsch, R.A. Bonomo, and T.M. Handel.  (2006) J Biol Chem 28:26745-26753.

Chemokine-glycosaminoglycan binding: specificity for CCR2 ligand binding to highly sulfated oligosaccharides using FTICR mass spectrometry. Y. Yu, M.D. Sweeney, O.M. Saad, A. Hsu, S.E. Crown, T.M. Handel and J.A Leary. (2005)  J Biol Chem 280:32200-8. 

Interaction of Chemokines and Glycosaminoglycans: A New Twist in the Regulation of Chemokine Function with Opportunities for Therapeutic Intervention. Z. Johnson, A.E.I. Proudfoot and T.M. Handel. (2005) Cytokine Growth Factor Rev 16:625-36. 

Chemerin Activation by Serine Proteases by Fibrinolytic and Inflammatory Cascades. B.A. Zabel, S.J. Allen, P. Kulig, J. Cichy, T.M. Handel, E.C. Butcher. (2005) J Biol Chem 280:34661-6. 

Regulation of Chemokine Function by Glycosaminoglycans - As Exemplified by Chemokines. T.M. Handel, Z. Johnson, S.E. Crown, M. Sweeney, A.E. Proudfoot. (2005). Annu Rev Biochem 74:385-410. 

 

Chemokines Bind to Sulfatides as Revealed by Surface Plasmon Resonance. Sandhoff, H. Grieshaber; R. Djafarzadeh, T.P. Sijmonsma, A.E.I. Proudfoot, T.M.  Handel, H. Wiegandt, H. Wiegandt, P.J.  Nelson. (2005)  Biochim Biophys Acta, 1687:52-63. 

Chronic Expression of Monocyte Chemoattractant Protein-1 in the Central Nervous System Causes Delayed Encephalopathy and Impaired Migroglial Function in Mice. D. Huang, J. Wujek, G. Kidd, T. He, A. Cardona, M. Sasse, E. Stein, J. Kish, M. Tani, A.E. Proudfoot, B.J. Rollins, T.M. Handel, R.M. Ransohoff. (2005)  The Faseb Journal, 19:761-72. 

Energy Functions for Protein Design II: Adjustment with Protein Complex Affinities, Reference States, and Properties of Designed Sequences N. Pokala and T.M. Handel. (2005) . J Mol Biol 347:203-27.  

Energy Functions for Protein Design I: Efficient and Accurate Continuum Electrostatics and Solvation. N. Pokala and T.M. Handel.  (2004)  Protein Science 13:925-36. 

Chemokine-Receptor Interactions: GPCRs, Glycosaminoglycans and Viral Chemokine Binding Proteins. E.K. Lau, A. Hsu, S. Allens and T.M. Handel (2004).  Adv Protein Chem 68:351-91.

Examination of of MCP-1 (CCL2) Partitioning During Transendothelial Migration. L.A. Hardy, T.A. Booth, E.K. Lau, S. Ali, T.M. Handel and J.A. Kirby. (2004) Lab Invest 84:81-90.
 

Identification of the Glycosaminoglycan Binding Site of the CC Chemokine, MCP-1; Implications for Structure and Function In Vivo. E.K. Lau, A. Kungl, C. Paavola, Z. Johnson, F. Borlat, A.E.I. Proudfoot, T.M. Handel. (2004) J Biol Chem, 279:22294-305.

Chemokine Structure and Receptor Interactions. T.M. Handel and E.K. Lau. (2003) Ernst Shering Research Foundation Workshop Series (45), 101-124. 

Analysis of an orf virus chemokine-binding protein: Shifting ligand specificities among a family of poxvirus viroceptors. B.T. Seet, C.A. McCaughan, T.M. Handel, G. McFadden and S. B. Fleming. (2003) PNAS 100:15137-42. 

Glycosaminoglycan Binding and Oligomerization are Essential for the In Vivo Activity of Certain Chemokines. A.E.I. Proudfoot, T.M. Handel, Z. Johnson, E.K. Lau, P. Liwang, I. Clark-Lewis, F. Borlat, T.N.C. Wells and M. Kosco-Vilbois. (2003)  PNAS 100:1885-1890. 

Structural Basis of Chemokine Sequestration by a Herpesvirus Decoy Receptor. J.M. Alexander, C.A. Nelson, V. van Berkel Fezzie, E.K. Lau, J.M. Studts, T.J. Brett, S.H. Speck, T.M. Handel, H.W. Virgin and D.H. Fremont. (2002)  Cell, 111:343-56. 

Solution Structure and Dynamics of the Melanoma Inhibitory Activity Protein (MIA). J.C. Lougheed, P.J. Domaille  and T.M. Handel. (2002)  J. Biomolecular NMR, 22:211-23. 

Molecular Determinants for CC Chemokine Recognition by a Poxvirus CC-Chemokine Inhibitor. B.T. Seet, R. Singh, C. Paavola, E.K. Lau, T.M. Handel and G. McFadden. (2001)  PNAS,98:9008-13. 

Protein Design: Where We Were, Where We Are, Where We're Going.  N. Pokala  and T.M. Handel  (2001) Journal of Structural Biology, 134:269-281. 

Structure Of Melanoma Inhibitory Activity Protein (MIA), A Member Of A New Family Of Secreted Proteins.  J.C. Lougheed, J.M. Holton, T. Alber, J.F. Bazan, and T.M. Handel. (2001) PNAS: 98:5515-20.  

Recognition Of The CX3C Chemokine, Fractalkine, By Its Cognate Receptor And The Viral Receptor US28. L.S. Mizoue, T.N.  Kledal, K.B. Bacon, T.M. Handel. (2001) J. Biological Chemistry, 276: 33906-14. 

Chemical Synthesis of Lymphotactin, a Glycosylated Chemokine with a C-Terminal Mucin-like Domain.  L.A. Marcaurelle, J. Wilken, L.S. Mizoue, L. Oldham, T.M. Handel and C.R. Bertozzi. (2001)  Chemistry: A European Journal 7:1129-1132. 

The Crystal Structure Of The Chemokine Domain Of Fractalkine Shows A Novel Quaternary Arrangement.   D.A. Hoover, L. Mizoue, T.M. Handel and J. Lubkowski. (2000) J. Biological Chemistry 275:23187-23193. 

Folding of an Isolated Ribonuclease H Core Fragment.  A.K. Chamberlain, K.M. Fisher, D. Reardon, T.M. Handel and S. Marqusee. (1999) Protein Science.8:2251-2257.

Rotamer Strain as a Determinant of Protein Specificity. G.A. Lazar, E.C. Johnson, J.R. Desjarlais and T.M. Handel. (1999)  Protein Science. 8:2598-2610. 

The Effect of Hydrophobic Core Packing on Side Chain Dynamics. E.C. Johnson and T.M. Handel. (1999) J. BIOMOLECULAR NMR. 15:135-143.

Identification of Residues in the Monocyte Chemotactic Protein-1 that Contact the MCP-1 Receptor, CCR2b. S. Hemmerich, C. Paavola, A. Bloom, S. Bhakta, R. Freedman, D. Grunberger, J. Krstenansky, S. Lee, D. McCarley, M. Mulkins, B. Wong, J. Pease, L. Mizoue, I. Polsky, K. Thompson, T.M. Handel, K. Jarnagin. (1999) BIOCHEMISTRY 38:13013-13025. 

Identification of Surface Residues of the Monocyte Chemotactic Protein-1 that Affect Signaling through the MCP-1 Receptor, CCR2b. K. Jarnagin, D. Grunberger, M. Mulkins, B.Wong, S. Hemmerich, C. Paavola, A.Bloom, S. Bhakta, R. Freedman, D. McCarley, I. Polsky, A. Ping-Tsou, A. Kosaka, T.M. Handel. (1999)  BIOCHEMISTRY 38:16167-16177. 

Solution Structure and Dynamics of a Designed Hydrophobic Core Variant of Ubiquitin. E.C. Johnson, G.A. Lazar, J.R. Desjarlais and T.M. Handel. (1999) STRUCTURE WITH FOLDING & DESIGN 7:967-76.  

Hydrophobic Core Design and Structure Prediction with Backbone Flexibility. J.R. Desjarlais and T.M. Handel. (1999) J. MOLECULAR BIOLOGY 289:3 05-318. 

The Putative Low Barrier Hydrogen Bond in Pyridoxal Phosphate Dependent Enzymes. Kirsch, J. F., Apicella, C. and Handel T. (1999) In "ENZYMATIC MECHANISMS" Steenbock Symposium. IOS Press, Amsterdam. pp.198-203.  

Solution Structure and Dynamics of the CX3C Chemokine Domain of Fractalkine and its Interaction with an N-terminal Fragment of CX3CR1. L. Mizoue, J.F. Bazan, E.C. Johnson and T.M. Handel. (1999) BIOCHEMISTRY 38:1402-1414. 

From Coiled Coils To Small Globular Proteins: Design of a Native-Like Three-Helix Bundle. J.W. Bryson, J.R. Desjarlais, T.M. Handel, TM and W.F. DeGrado. (1998) PROTEIN SCIENCE, 7:1404-1414. 

Hydrophobic Core Packing and Protein Design.  G.A. Lazar and T.M. Handel. (1998) CURRENT OPINION  IN CHEMICAL BIOLOGY 2:675-679. 

Monomeric Monocyte Chemoattractant Protein-1 (MCP-1) Binds and Activates the MCP-1 Receptor CCR2b.  C. Paavola, S. Hemmerich, D. Grunberger, I. Polsky, A. Bloom, R. Freedman, M. Mulkins, S. Bhakta, D. McCarley, L. Wiesent, B. Wong, K. Jarnagin, T.M. Handel. (1998) J. OF BIOLOGICAL CHEMISTRY 273:33157-33165. 

Characterization of a Folding Intermediate from HIV-1 RNase H.  G. Kern, T.M. Handel and S. Marqusee. (1998) PROTEIN SCIENCE 7:2164-2174. 

Lymphotactin is Produced by NK Cells and Attracts both NK and T Cells in vitro. J. Hedrick, V. Saylor, D. Figueroa, L. Mizoue, Y. Xu, S. Menon, J. Abrams, T.M. Handel, and A. Zlotnick. (1997) J. OF IMMUNOLOGY. 158:1533-1540. 

Alterations in Chemical Shifts and Exchange Broadening Upon Peptide Boronic Acid Inhibitor Binding to a-lytic Protease. J. Davis, D. Agard, T.M. Handel and V. Basus. (1997) J. BIOMOLECULAR NMR 10:21-27.  

De Novo Design of the Hydrophobic Core of Ubiquitin. G. Lazar, JR Desjarlais, T.M. Handel. (1997) PROTEIN SCIENCE 6:1167-1178.

Detection of Protein Unfolding and Native State Fluctuations by Hydrogen Exchange. A.K. Chamberlain, T.M. Handel, and S. Marqusee. (1997) TECHNIQUES IN PROTEIN CHEMISTRY VIII. 727-734. 

Structure of MCP-1 in Two Crystal Forms: A Rare Example of Variable Quaternary Interactions. J. Lubkowski, G. Bujacz, L. Boque, P.J. Domaille, T.M. Handel and A. Wlodawer. (1997) NATURE STRUCTURAL BIOLOGY 4:64-9. 

Heteronuclear (1H, 13C, 15N) NMR Assignments and Secondary Structure of the Basic Region-Helix-Loop-Helix Domain of E47. R. Fairman, R. Steed and T.M. Handel. (1997) PROTEIN SCIENCE 6:175-85.  

Detection of Rare Partially Folded Molecules in Equilibrium with the Native Conformation of RNASE H. A.K. Chamberlain, T.M. Handel, and S. Marqusee. (1996)  NATURE STRUCTURAL BIOLOGY 3:782-7.  

Heteronuclear (1H, 13C, 15N) NMR Assignments and Solution Structure of the Monocyte Chemotactic Protein-1 (MCP-1) Dimer. T.M. Handel and P.J. Domaille. (1996) BIOCHEMISTRY 35:6569-6584.

De novo Design of the Hydrophobic Cores of Proteins.  J.R. Desjarlais and T.M. Handel. (1995) PROTEIN SCIENCE 4:2006-2018.

Principles of Protein Design. J.R. Desjarlais and T.M. Handel. (1995) CURRENT OPINIONS IN
BIOTECHNOLOGY 6:460-466.  

Metal-Ion Dependent Modulation of the Dynamics of a Designed Protein. T.M. Handel, S.A. Williams, and W.F. DeGrado (1993) SCIENCE 261:879-885. 

Introduction of a Trp Resdiue into a4 as a Probe of Dynamics. T.M. Handel, and W.F. DeGrado (1993) J. AMER. CHEM. SOC. 115:4457-4460.

Identification of a Peptide which Binds to the Carbohydrate Specific Monoclonal Antibody B3. R. Hoess, U. Brinkmann, T.M. Handel and I. Pastian. (1993)  GENE. 128:43-49.  

Protein Design. T.M.Handel.  In: "First Forsight Conference on Nanotechnology" (Crandall, B.C. and Lewis,
 J., Eds.) MIT Press, 1992, pg 37-45.  

Characterization of the Structural Properties of Alpha-1b, a Peptide Designed to Form a 4-Helix Bundle. J. Osterhout, T.M. Handel, A. Toumadje,W.C. Johnson, W.C. J. Hoch,  D. Live, and W.F. DeGrado. (1992) J. AMER. CHEM. SOC. 114:331-337.

Protein Design, What are We Learning? W.F.DeGrado, D.P. Raleigh and T.M. Handel. (1991) CURRENT OPINIONS IN STRUCTURAL BIOLOGY 1:984-993.

De Novo Design of  Zn+2-Binding Proteins. T.M. Handel and W.F. DeGrado (1990) J. AMER. CHEM, SOC. 112:6710-6711.

De Novo Design of a/b Barrel Proteins. T.M. Handel. (1990) PROTEIN ENGINEERING 3:233-234.

Effect of Cholesterol on the Uptake and Intracellular Degradation of Liposomes by Liver and Spleen: A Combined Biochemical and g-ray Perturbed Angular Correlation Study. F.H. Roerdink, J. Regts, T.M. Handel, S.M. Sullivan, J.D. Baldeschwieler and G.L. Scherphof. (1989) BIOCHIMICA ET BIOPHYSICA ACTA 980:234-240.

Stereochemical Assignment of Neocarzinostatin Chromophore: Structures of Neocarzinostatin Chromophore-Methyl Thioglycolate Adducts. A.G. Myers, P.J. Proteau and T.M. Handel. (1988) J. AMER. CHEM.  SOC. 110:7212-7214.

Modification of Lipid Phase Behavior with Membrane-Bound Cryoprotectants. R.P. Goodrich, T.M. Handel and J.D. Baldeschwieler. (1988) BIOCHIMICA ET BIOPHYSICA ACTA 938:143-54. 

Effects of Side-Chain Structure on Polymer Conformation: Synthesis and Dilute Solution Properties. T.M. Handel, I.S. Ponticello and J.S. Tan. (1987) MACROMOLECULES 20:264-7.  

Cooperative Interactions of Anionic Dyes with Imidazole-Containing Polymers. J.S. Tan and T.M. Handel. (1985)  MICRODOMAINS IN POLYMER SOLUTIONS 417-427.  

Dye Binding Characteristics of Imidazole-Containing Polymers.  T.M. Handel. and J.S. Tan. (1985) MACROMOLECULES 18:1200-1206.  

Trans-[(en)2Co(Cl)(S2O3)], Na[trans-[(en)2Co(C2O4)(S2O3)]], trans-[(en2Co(NCO)(S203)], and the Nature of [(en)2Co(OH2)(S2O3)]+ in Aqeous Solution. J.N. Cooper, J.G. Bentsen, T.M. Handel, K.M. Strohmaier, W.A. Porter, B.C. Johnson, A.M. Carr, D.A.  Farnath and S.L. Appleton. (1983) INORGANIC CHEM.  22:3060-3065.  

Cooperative Interactions of Anionic Dyes with Imidazole- Containing Polymers. J.S. Tan and T.M. Handel. (1982) POLYMER PREPRINTS. 23:48-49.

Interaction of Polymers with Dyes and Ions. J.S. Tan and T.M. Handel. (1982) Proc IUPAC, I.U.P.A.C. MACROMOLECULAR SYMPOSIUM, 28th, 885.