Biochemistry and Molecular Biology

Research Output 1993 2018

2010
5 Citations (Scopus)

Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design

Bordner, A. J., Apr 16 2010, In : BMC Bioinformatics. 11, 192.

Research output: Contribution to journalArticle

Backbone
Scoring
Proteins
Protein
Dependent
22 Citations (Scopus)

Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model

Bordner, A. J. & Mittelmann, H. D., Jan 20 2010, In : BMC Bioinformatics. 11, 41.

Research output: Contribution to journalArticle

Thermodynamics
Peptides
Affine transformation
Rapid thermal annealing
Prediction
3 Citations (Scopus)

Refinement of the pharmacophore of an agonist ligand of the secretin receptor using conformationally constrained cyclic hexapeptides

Dong, M., Narang, P., Pinon, D. I., Bordner, A. J. & Miller, L. J., Jun 2010, In : Peptides. 31, 6, p. 1094-1098 5 p.

Research output: Contribution to journalArticle

Ligands
Bioactivity
Cyclic Amino Acids
Peptides
Molecular modeling
5 Citations (Scopus)

Reprogrammed FoxP3+ T regulatory cells become IL-17+ antigen-specific autoimmune effectors in vitro and in vivo (The Journal of Immunology (2008) 181, (3137-3147))

Radhakrishnan, S., Cabrera, R., Schenk, E. L., Nava-Parada, P., Bell, M. P., Van Keulen, V. P., Marler, R. J., Felts, S. J. & Pease, L. R., Jun 1 2010, In : Journal of Immunology. 184, 11, p. 6556 1 p.

Research output: Contribution to journalArticle

Interleukin-17
Regulatory T-Lymphocytes
Allergy and Immunology
Antigens
In Vitro Techniques
2 Citations (Scopus)

Secretin Receptor Dimerization: A Possible Functionally Important Paradigm for Family B G Protein-Coupled Receptors

Harikumar, K. G., Dong, M. & Miller, L. J., Jul 15 2010, GPCR Molecular Pharmacology and Drug Targeting: Shifting Paradigms and New Directions. John Wiley and Sons, p. 138-164 27 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Dimerization
G-Protein-Coupled Receptors
secretin receptor
10 Citations (Scopus)

Structural conservation in band 4.1, ezrin, radixin, moesin (FERM) domains as a guide to identify inhibitors of the proline-rich tyrosine kinase 2

Meurice, N., Wang, L., Lipinski, C. A., Yang, Z., Hulme, C. & Loftus, J. C., 2010, In : Journal of Medicinal Chemistry. 53, 2, p. 669-677 9 p.

Research output: Contribution to journalArticle

Focal Adhesion Kinase 2
Focal Adhesion Protein-Tyrosine Kinases
Glioma
Site-Directed Mutagenesis
Protein-Tyrosine Kinases
17 Citations (Scopus)

Towards universal structure-based prediction of class II MHC epitopes for diverse allotypes

Bordner, A. J., 2010, In : PLoS One. 5, 12, e14383.

Research output: Contribution to journalArticle

epitopes
Epitopes
peptides
Peptides
prediction
41 Citations (Scopus)

TROY (TNFRSF19) is overexpressed in advanced glial tumors and promotes glioblastoma cell invasion via Pyk2-Rac1 signaling

Paulino, V. M., Yang, Z., Kloss, J., Ennis, M. J., Armstrong, B. A., Loftus, J. C. & Tran, N., Nov 2010, In : Molecular Cancer Research. 8, 11, p. 1558-1567 10 p.

Research output: Contribution to journalArticle

Glioblastoma
Glioma
Neuroglia
Neoplasms
Tumor Necrosis Factors
2009
131 Citations (Scopus)

A Novel Histologic Scoring System to Evaluate Mucosal Biopsies From Patients With Eosinophilic Esophagitis

Protheroe, C., Woodruff, S. A., de Petris, G., Mukkada, V., Ochkur, S. I., Janarthanan, S., Lewis, J. C., Pasha, S. F., Lunsford, T., Harris, L., Sharma, V. K., McGarry, M. P., Lee, N. A., Furuta, G. T. & Lee, J. J., Jul 2009, In : Clinical Gastroenterology and Hepatology. 7, 7

Research output: Contribution to journalArticle

Eosinophilic Esophagitis
Eosinophilia
Biopsy
Gastroesophageal Reflux
Eosinophil Peroxidase
2 Citations (Scopus)
Fluorescence Resonance Energy Transfer
Fluorescence
Ligands
Secretin
Energy Transfer
7 Citations (Scopus)

Differential effects of Pyk2 and FAK on the hypertrophic response of cardiac myocytes

Menashi, E. B. & Loftus, J. C., Aug 2009, In : Cell and Tissue Research. 337, 2, p. 243-255 13 p.

Research output: Contribution to journalArticle

Focal Adhesion Kinase 2
Focal Adhesion Protein-Tyrosine Kinases
Cardiac Myocytes
Atrial Natriuretic Factor
Phenylephrine
6 Citations (Scopus)

Effects of putative catalytic base mutation E211Q on ABCG2-mediated methotrexate transport

Hou, Y. X., Li, C. Z., Palaniyandi, K., Magtibay, P., Homolya, L., Sarkadi, B. & Chang, X-B. D., 2009, In : Biochemistry. 48, 38, p. 9122-9131 10 p.

Research output: Contribution to journalArticle

Methotrexate
Adenosine Triphosphate
Mutation
Membranes
Adenosine Triphosphatases
100 Citations (Scopus)

Eosinophil deficiency compromises parasite survival in chronic nematode infection

Fabre, V., Beiting, D. P., Bliss, S. K., Gebreselassie, N. G., Gagliardo, L. F., Lee, N. A., Lee, J. J. & Appleton, J. A., Feb 1 2009, In : Journal of Immunology. 182, 3, p. 1577-1583 7 p.

Research output: Contribution to journalArticle

Nematode Infections
Eosinophils
Parasites
Helminths
Trichinella spiralis
62 Citations (Scopus)

Eosinophils oxidize damage-associated molecular pattern molecules derived from stressed cells

Lotfi, R., Herzog, G. I., DeMarco, R. A., Beer-Stolz, D., Lee, J. J., Rubartelli, A., Schrezenmeier, H. & Lotze, M. T., Oct 15 2009, In : Journal of Immunology. 183, 8, p. 5023-5031 9 p.

Research output: Contribution to journalArticle

Eosinophils
Necrosis
Eosinophil Peroxidase
Alarmins
Respiratory Burst
23 Citations (Scopus)

Eosinophils utilize multiple chemokine receptors for chemotaxis to the parasitic nematode strongyloides stercoralis

Stein, L. H., Redding, K. M., Lee, J. J., Nolan, T. J., Schad, G. A., Lok, J. B. & Abraham, D., Oct 2009, In : Journal of Innate Immunity. 1, 6, p. 618-630 13 p.

Research output: Contribution to journalArticle

Strongyloides stercoralis
Chemokine Receptors
Chemotaxis
Eosinophils
Parasites
17 Citations (Scopus)

Expression of human MUC1 during early pregnancy in the human MUC1 transgenic mouse model

Dharmaraj, N., Gendler, S. J. & Carson, D. D., 2009, In : Biology of Reproduction. 81, 6, p. 1182-1188 7 p.

Research output: Contribution to journalArticle

Transgenic Mice
Pregnancy
Uterus
Epithelium
Genes
40 Citations (Scopus)

Functional importance of a structurally distinct homodimeric complex of the family B G protein-coupled secretin receptor

Gao, F., Harikumar, K. G., Dong, M., Lam, P. C. H., Sexton, P. M., Christopoulos, A., Bordner, A., Abagyan, R. & Miller, L. J., Aug 2009, In : Molecular Pharmacology. 76, 2, p. 264-274 11 p.

Research output: Contribution to journalArticle

Energy Transfer
G-Protein-Coupled Receptors
Cysteine
Guanine Nucleotides
Guanosine Triphosphate
44 Citations (Scopus)

Induced association of μ opioid (MOP) and type 2 cholecystokinin (CCK 2) receptors by novel bivalent ligands

Zheng, Y., Akgiin, E., Harikumar, K. G., Hopson, J., Powers, M. D., Lunzer, M. M., Miller, L. J. & Portoghese, P. S., Jan 22 2009, In : Journal of Medicinal Chemistry. 52, 2, p. 247-258 12 p.

Research output: Contribution to journalArticle

Cholecystokinin B Receptor
Cholecystokinin Receptors
Opioid Analgesics
Ligands
Energy Transfer
2 Citations (Scopus)

Intravitreal alemtuzumab penetrates full-thickness retina in rabbit eyes

Ekdawi, N. S., Pulido, J. S., Itty, S., Marler, R. J., Herman, D. C., Hardwig, P., Mohney, B. G., Valyi-Nagy, T. & Shukla, D., Nov 2009, In : Retina. 29, 10, p. 1532-1534 3 p.

Research output: Contribution to journalArticle

Retina
Rabbits
Coloring Agents
Staining and Labeling
Intravitreal Injections
24 Citations (Scopus)

Lack of muc1-regulated β-catenin stability results in aberrant expansion of cd11b +gr1 + Myeloid-derived suppressor cells from the bone marrow

Poh, T. W., Bradley, J. M., Mukherjee, P. & Gendler, S. J., Apr 15 2009, In : Cancer Research. 69, 8, p. 3554-3562 9 p.

Research output: Contribution to journalArticle

Catenins
Bone Marrow
Neoplasms
Knockout Mice
Carcinogenesis
35 Citations (Scopus)

Molecular basis of association of receptor activity-modifying protein 3 with the family B G protein-coupled secretin receptor

Harikumar, K. G., Simms, J., Christopoulos, G., Sexton, P. M. & Miller, L. J., Dec 15 2009, In : Biochemistry. 48, 49, p. 11773-11785 13 p.

Research output: Contribution to journalArticle

Receptor Activity-Modifying Protein 3
Receptor Activity-Modifying Proteins
G-Protein-Coupled Receptors
GTP-Binding Proteins
Association reactions
9 Citations (Scopus)

Molecular basis of metastasis [8]

Lee, J. J. & Lotze, M. T., Apr 16 2009, In : New England Journal of Medicine. 360, 16, p. 1679 1 p.

Research output: Contribution to journalArticle

Neoplasm Proteins
Circulating Neoplastic Cells
Neoplastic Stem Cells
Membrane Glycoproteins
Cadherins
51 Citations (Scopus)

Mouse eosinophils possess potent antibacterial properties in vivo

Linch, S. N., Kelly, A. M., Danielson, E. T., Pero, R., Lee, J. J. & Gold, J. A., Nov 2009, In : Infection and Immunity. 77, 11, p. 4976-4982 7 p.

Research output: Contribution to journalArticle

Eosinophils
Parasitic Diseases
Adoptive Transfer
Toll-Like Receptors
Interleukin-5
3 Citations (Scopus)

Pathology in practice

Gades, N. M. & Marler, R. J., Jun 15 2009, In : Journal of the American Veterinary Medical Association. 234, 12, p. 1535-1537 3 p.

Research output: Contribution to journalArticle

Monkey Diseases
Histoplasma
Pyogenic Granuloma
histoplasmosis
Histoplasmosis
21 Citations (Scopus)

Predicting protein-protein binding sites in membrane proteins

Bordner, A. J., Sep 24 2009, In : BMC Bioinformatics. 10, p. 312 1 p., 1471.

Research output: Contribution to journalArticle

Membrane Protein
Binding sites
Protein Binding
Membrane Proteins
Binding Sites
21 Citations (Scopus)

Synthesis and in vitro characterization of radioiodinatable benzodiazepines selective for type 1 and Type 2 cholecystokinin receptors

Akgün, E., Körner, M., Gao, F., Harikumar, K. G., Waser, B., Reubi, J. C., Portoghese, P. S. & Miller, L. J., Apr 9 2009, In : Journal of Medicinal Chemistry. 52, 7, p. 2138-2147 10 p.

Research output: Contribution to journalArticle

Cholecystokinin A Receptor
Cholecystokinin B Receptor
Benzodiazepines
Neoplasms
Binding Sites
16 Citations (Scopus)

Telomerase deficiency and telomere dysfunction inhibit mammary tumors induced by polyomavirus middle T oncogene

Jaskelioff, M., Song, W., Xia, J., Liu, C., Kramer, J., Koido, S., Gendler, S. J., Calderwood, S. K. & Gong, J., Dec 2009, In : Oncogene. 28, 48, p. 4225-4236 12 p.

Research output: Contribution to journalArticle

Polyomavirus
Telomerase
Telomere
Oncogenes
Breast Neoplasms
24 Citations (Scopus)

The Pyk2 FERM domain as a target to inhibit glioma migration

Loftus, J. C., Yang, Z., Tran, N., Kloss, J., Viso, C., Berens, M. E. & Lipinski, C. A., Jun 2009, In : Molecular Cancer Therapeutics. 8, 6, p. 1505-1514 10 p.

Research output: Contribution to journalArticle

Glioma
Phosphorylation
Epitopes
Cell Migration Inhibition
Immunoglobulin Variable Region
42 Citations (Scopus)

Tumor necrosis factor-like weak inducer of apoptosis stimulation of glioma cell survival is dependent on Akt2 function

Fortin, S. P., Ennis, M. J., Savitch, B. A., Carpentieri, D., McDonough, W. S., Winkles, J. A., Loftus, J. C., Kingsley, C., Hostetter, G. & Tran, N., Nov 2009, In : Molecular Cancer Research. 7, 11, p. 1871-1881 11 p.

Research output: Contribution to journalArticle

Glioma
Cell Survival
Tumor Necrosis Factor-alpha
Apoptosis
Small Interfering RNA
2 Citations (Scopus)

Use of fluorescence indicators in receptor ligands.

Harikumar, K. G. & Miller, L. J., 2009, In : Methods in molecular biology (Clifton, N.J.). 552, p. 279-291 13 p.

Research output: Contribution to journalArticle

Fluorescence
Ligands
Cholecystokinin A Receptor
Fluorescence Polarization
G-Protein-Coupled Receptors
2008
37 Citations (Scopus)

A3 adenosine receptor signaling influences pulmonary inflammation and fibrosis

Morschl, E., Molina, J. G., Volmer, J. B., Mohsenin, A., Pero, R. S., Hong, J. S., Kheradmand, F., Lee, J. J. & Blackburn, M. R., Dec 1 2008, In : American Journal of Respiratory Cell and Molecular Biology. 39, 6, p. 697-705 9 p.

Research output: Contribution to journalArticle

Adenosine A3 Receptors
Purinergic P1 Receptors
Pulmonary Fibrosis
Pneumonia
Bleomycin
42 Citations (Scopus)

Absence of histologic retinal toxicity of intravitreal nanogold in a rabbit model

Bakri, S. J., Pulido, J. S., Mukherjee, P., Marler, R. J. & Mukhopadhyay, D., Jan 2008, In : Retina. 28, 1, p. 147-149 3 p.

Research output: Contribution to journalArticle

Rabbits
Retinal Pigment Epithelium
Optic Nerve
Ganglia
Retina
172 Citations (Scopus)

Allergic pulmonary inflammation in mice is dependent on eosinophil-induced recruitment of effector T cells

Jacobsen, E., Ochkur, S. I., Pero, R. S., Taranova, A. G., Protheroe, C. A., Colbert, D. C., Lee, N. A. & Lee, J. J., Mar 17 2008, In : Journal of Experimental Medicine. 205, 3, p. 699-710 12 p.

Research output: Contribution to journalArticle

Eosinophils
Pneumonia
T-Lymphocytes
Ovalbumin
Lung
36 Citations (Scopus)

Allergic pulmonary inflammation promotes the recruitment of circulating tumor cells to the lung

Taranova, A. G., Maldonado, D., Vachon, C. M., Jacobsen, E., Abdala-Valencia, H., McGarry, M. P., Ochkur, S. I., Protheroe, C. A., Doyle, A., Grant, C. S., Cook-Mills, J., Birnbaumer, L., Lee, N. A. & Lee, J. J., Oct 15 2008, In : Cancer Research. 68, 20, p. 8582-8589 8 p.

Research output: Contribution to journalArticle

Circulating Neoplastic Cells
Pneumonia
Lung
Allergens
Neoplasm Metastasis
475 Citations (Scopus)

Catapult-like release of mitochondrial DNA by eosinophils contributes to antibacterial defense

Yousefi, S., Gold, J. A., Andina, N., Lee, J. J., Kelly, A. M., Kozlowski, E., Schmid, I., Straumann, A., Reichenbach, J., Gleich, G. J. & Simon, H. U., Sep 2008, In : Nature Medicine. 14, 9, p. 949-953 5 p.

Research output: Contribution to journalArticle

Mitochondrial DNA
Eosinophils
Bacteria
Immune system
DNA
24 Citations (Scopus)

Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces

Bordner, A. J. & Gorin, A. A., May 12 2008, In : BMC Bioinformatics. 9, 234.

Research output: Contribution to journalArticle

Databases
Proteins
Protein
Equipment and Supplies
Protein-protein Interaction

Corrigendum to "Multidrug resistance protein 1 is not associated to detergent-resistant membranes" [Biochem. Biophys. Res. Commun. 355 (2007) 1025-1030] (DOI: 10.1016/j.bbrc.2007.02.075)

Cerf, E., Gasper, R., Belani, J. D., Rychnovsky, S., Chang, X-B. D., Buyse, F. & Ruysschaert, J. M., Feb 8 2008, In : Biochemical and Biophysical Research Communications. 366, 2, p. 605 1 p.

Research output: Contribution to journalArticle

P-Glycoprotein
Detergents
Membranes
corrigendum
35 Citations (Scopus)

Dimerization in the absence of higher-order oligomerization of the G protein-coupled secretin receptor

Harikumar, K. G., Happs, R. M. & Miller, L. J., Nov 2008, In : Biochimica et Biophysica Acta - Biomembranes. 1778, 11, p. 2555-2563 9 p.

Research output: Contribution to journalArticle

Oligomerization
Dimerization
G-Protein-Coupled Receptors
GTP-Binding Proteins
Bioluminescence
134 Citations (Scopus)

Distinct binding modes specify the recognition of methylated histones H3K4 and H4K20 by JMJD2A-tudor

Lee, J., Thompson, J. R., Botuyan, M. V. & Mer, G., Jan 2008, In : Nature Structural and Molecular Biology. 15, 1, p. 109-111 3 p.

Research output: Contribution to journalArticle

Calorimetry
X Ray Crystallography
Point Mutation
Histones
Lysine
10 Citations (Scopus)

Effects of cholecystokinin-58 on type 1 cholecystokinin receptor function and regulation

Wu, S. V., Harikumar, K. G., Burgess, R. J., Reeve, J. R. & Miller, L. J., Sep 2008, In : American Journal of Physiology - Gastrointestinal and Liver Physiology. 295, 3

Research output: Contribution to journalArticle

Cholecystokinin Receptors
Sincalide
Peptides
Cholecystokinin A Receptor
Calcium
18 Citations (Scopus)

Extended survival of Pyk2 or FAK deficient orthotopic glioma xenografts

Lipinski, C. A., Tran, N., Viso, C., Kloss, J., Yang, Z., Berens, M. E. & Loftus, J. C., 2008, In : Journal of Neuro-Oncology. 90, 2, p. 181-189 9 p.

Research output: Contribution to journalArticle

Heterografts
Glioma
Disease Progression
Focal Adhesion Protein-Tyrosine Kinases
Tumor Microenvironment
44 Citations (Scopus)

Identification of kinetin riboside as a repressor of CCND1 and CCND2 with preclinical antimyeloma activity

Tiedemann, R. E., Mao, X., Shi, C. X., Yuan, X. Z., Palmer, S. E., Sebag, M., Marler, R. J., Chesi, M., Fonseca, R., Bergsagel, P. L., Schimmer, A. D. & Stewart, A. K., May 1 2008, In : Journal of Clinical Investigation. 118, 5, p. 1750-1764 15 p.

Research output: Contribution to journalArticle

Cyclin D
Cyclin D2
Neoplasms
bcl-1 Genes
Small Molecule Libraries
4 Citations (Scopus)
Multidrug Resistance-Associated Proteins
Leukotriene C4
Serine
Adenosine Triphosphate
Hydroxyl Radical
99 Citations (Scopus)

Intestinal macrophage/epithelial cell-derived CCL11/eotaxin-1 mediates eosinophil recruitment and function in pediatric ulcerative colitis

Ahrens, R., Waddell, A., Seidu, L., Blanchard, C., Carey, R., Forbes, E., Lampinen, M., Wilson, T., Cohen, E., Stringer, K., Ballard, E., Munitz, A., Xu, H., Lee, N. A., Lee, J. J., Rothenberg, M. E., Denson, L. & Hogan, S. P., Nov 15 2008, In : Journal of Immunology. 181, 10, p. 7390-7399 10 p.

Research output: Contribution to journalArticle

Chemokine CCL11
Eosinophils
Epithelial Cells
Macrophages
Chemokine CCL24
49 Citations (Scopus)

Major basic protein-1 promotes fibrosis of dystrophic muscle and attenuates the cellular immune response in muscular dystrophy

Wehling-henricks, M., Sokolow, S., Lee, J. J., Myung, K. H., Villalta, S. A. & Tidball, J. G., Aug 2008, In : Human Molecular Genetics. 17, 15, p. 2280-2292 13 p.

Research output: Contribution to journalArticle

Muscular Dystrophies
Cellular Immunity
Fibrosis
Inbred mdx Mouse
Eosinophil Major Basic Protein
2 Citations (Scopus)

Monitoring the state of cholecystokinin receptor oligomerization after ligand binding using decay of time-resolved fluorescence anisotropy

Harikumar, K. G. & Miller, L. J., Nov 2008, Annals of the New York Academy of Sciences. Vol. 1144. p. 21-27 7 p. (Annals of the New York Academy of Sciences; vol. 1144).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Cholecystokinin Receptors
Oligomerization
Fluorescence Polarization
Occupations
Anisotropy
106 Citations (Scopus)

MUC1 mucin is a negative regulator of toll-like receptor signaling

Ueno, K., Koga, T., Kato, K., Golenbock, D. T., Gendler, S. J., Kai, H. & Kim, K. C., Mar 1 2008, In : American Journal of Respiratory Cell and Molecular Biology. 38, 3, p. 263-268 6 p.

Research output: Contribution to journalArticle

Toll-Like Receptor 5
Flagellin
Toll-Like Receptors
Mucins
Pseudomonas aeruginosa
40 Citations (Scopus)

Pattern of intra-family hetero-oligomerization involving the G-protein-coupled secretin receptor

Harikumar, K. G., Morfis, M. M., Sexton, P. M. & Miller, L. J., Nov 2008, In : Journal of Molecular Neuroscience. 36, 1-3, p. 279-285 7 p.

Research output: Contribution to journalArticle

G-Protein-Coupled Receptors
Energy Transfer
Calcitonin Receptors
Ligands
secretin receptor
66 Citations (Scopus)

Phosphorylation of MUC1 by met modulates interaction with p53 and MMP1 expression

Singh, P. K., Behrens, M. E., Eggers, J. P., Cerny, R. L., Bailey, J. M., Shanmugam, K., Gendler, S. J., Bennett, E. P. & Hollingsworth, M. A., Oct 3 2008, In : Journal of Biological Chemistry. 283, 40, p. 26985-26995 11 p.

Research output: Contribution to journalArticle

Phosphorylation
Hepatocyte Growth Factor
Receptor Protein-Tyrosine Kinases
Mucins
Transcription
35 Citations (Scopus)

Post-translational tyrosine nitration of eosinophil granule toxins mediated by eosinophil peroxidase

Ulrich, M., Petre, A., Youhnovski, N., Prömm, F., Schirle, M., Schumm, M., Pero, R. S., Doyle, A., Checkel, J., Kita, H., Thiyagarajan, N., Acharya, K. R., Schmid-Grendelmeier, P., Simon, H. U., Schwarz, H., Tsutsui, M., Shimokawa, H., Bellon, G., Lee, J. J., Przybylski, M. & 1 others, Döring, G., Oct 17 2008, In : Journal of Biological Chemistry. 283, 42, p. 28629-28640 12 p.

Research output: Contribution to journalArticle

Eosinophil Peroxidase
Nitration
Eosinophils
Tyrosine
Eosinophil-Derived Neurotoxin