Honors & Awards

  • Edwin Motel Award, San Francisco State University (2004)
  • Best Graduate Student Poster, UTSW, Molecular Biophysics Annual Symposium (2011)
  • Dean’s Discretionary Award & Molecular Biophysics Program Nominee for Nominata Award, UT Southwestern Medical Center at Dallas (2011)
  • Fellowship (Declined), Damon Runyon Cancer Research Foundation (2012)
  • Fellowship, Helen Hay Whitney Foundation (2013)
  • K01 Career Development Award, NCI (NIH) (2013-2018)

Professional Education

  • B.S., San Francisco State University, Biochemistry (2003)
  • Doctor of Philosophy, Univ of Texas Southwestern Medical Center (2011)

Stanford Advisors

All Publications

  • The Intergenic Recombinant HLA-B*46:01 Has a Distinctive Peptidome that Includes KIR2DL3 Ligands. Cell reports Hilton, H. G., McMurtrey, C. P., Han, A. S., Djaoud, Z., Guethlein, L. A., Blokhuis, J. H., Pugh, J. L., Goyos, A., Horowitz, A., Buchli, R., Jackson, K. W., Bardet, W., Bushnell, D. A., Robinson, P. J., Mendoza, J. L., Birnbaum, M. E., Nielsen, M., Garcia, K. C., Hildebrand, W. H., Parham, P. 2017; 19 (7): 1394-1405


    HLA-B(∗)46:01 was formed by an intergenic mini-conversion, between HLA-B(∗)15:01 and HLA-C(∗)01:02, in Southeast Asia during the last 50,000 years, and it has since become the most common HLA-B allele in the region. A functional effect of the mini-conversion was introduction of the C1 epitope into HLA-B(∗)46:01, making it an exceptional HLA-B allotype that is recognized by the C1-specific natural killer (NK) cell receptor KIR2DL3. High-resolution mass spectrometry showed that HLA-B(∗)46:01 has a low-diversity peptidome that is distinct from those of its parents. A minority (21%) of HLA-B(∗)46:01 peptides, with common C-terminal characteristics, form ligands for KIR2DL3. The HLA-B(∗)46:01 peptidome is predicted to be enriched for peptide antigens derived from Mycobacterium leprae. Overall, the results indicate that the distinctive peptidome and functions of HLA-B(∗)46:01 provide carriers with resistance to leprosy, which drove its rapid rise in frequency in Southeast Asia.

    View details for DOI 10.1016/j.celrep.2017.04.059

    View details for PubMedID 28514659

  • Synthekines are surrogate cytokine and growth factor agonists that compel signaling through non-natural receptor dimers ELIFE Moraga, I., Spangler, J. B., Mendoza, J. L., Gakovic, M., Wehrman, T. S., Krutzik, P., Garcia, K. C. 2017; 6


    Cytokine and growth-factor ligands typically signal through homo- or hetero-dimeric cell surface receptors via Janus Kinase (JAK/TYK), or Receptor Tyrosine Kinase (RTK)-mediated trans-phosphorylation. However, the number of receptor dimer pairings occurring in nature is limited to those driven by natural ligands encoded within our genome. We have engineered synthethic cytokines (synthekines) that drive formation of cytokine receptor dimer pairings that are not formed by endogenous cytokines and that are not found in nature, and which activate distinct signaling programs. We show that a wide range of non-natural cytokine receptor hetero-dimers are competent to elicit a signaling output. We engineered synthekine ligands that assembled IL-2Rβ/IL-4Rα or IL-4Rα/IFNAR2 receptor heterodimers, that do not occur naturally, triggering signaling and functional responses distinct from those activated by the endogenous cytokines IL-2, IL-4, and IFN. Furthermore, hybrid synthekine ligands that dimerized a JAK/STAT cytokine receptor with a receptor tyrosine kinase (RTK) also elicited a signaling response. Synthekines represent a new family of synthetic ligands with pre-defined receptors, but 'orphan' functions, that enable the full combinatorial scope of dimeric signaling receptors encoded within the human genome to be exploited for basic research and drug discovery.

    View details for DOI 10.7554/eLife.22882

    View details for Web of Science ID 000401062800001

    View details for PubMedID 28498099

  • The IFN-?-IFN-?R1-IL-10Rß Complex Reveals Structural Features Underlying Type III IFN Functional Plasticity. Immunity Mendoza, J. L., Schneider, W. M., Hoffmann, H., Vercauteren, K., Jude, K. M., Xiong, A., Moraga, I., Horton, T. M., Glenn, J. S., de Jong, Y. P., Rice, C. M., Garcia, K. C. 2017; 46 (3): 379-392


    Type III interferons (IFN-λs) signal through a heterodimeric receptor complex composed of the IFN-λR1 subunit, specific for IFN-λs, and interleukin-10Rβ (IL-10Rβ), which is shared by multiple cytokines in the IL-10 superfamily. Low affinity of IL-10Rβ for cytokines has impeded efforts aimed at crystallizing cytokine-receptor complexes. We used yeast surface display to engineer a higher-affinity IFN-λ variant, H11, which enabled crystallization of the ternary complex. The structure revealed that IL-10Rβ uses a network of tyrosine residues as hydrophobic anchor points to engage IL-10 family cytokines that present complementary hydrophobic binding patches, explaining its role as both a cross-reactive but cytokine-specific receptor. H11 elicited increased anti-proliferative and antiviral activities in vitro and in vivo. In contrast, engineered higher-affinity type I IFNs did not increase antiviral potency over wild-type type I IFNs. Our findings provide insight into cytokine recognition by the IL-10R family and highlight the plasticity of type III interferon signaling and its therapeutic potential.

    View details for DOI 10.1016/j.immuni.2017.02.017

    View details for PubMedID 28329704

  • Alpha and Beta Type 1 Interferon Signaling: Passage for Diverse Biologic Outcomes. Cell Ng, C. T., Mendoza, J. L., Garcia, K. C., Oldstone, M. B. 2016; 164 (3): 349-352


    Type I interferon (IFN-I) elicits a complex cascade of events in response to microbial infection. Here, we review recent developments illuminating the large number of IFN-I species and describing their unique biologic functions.

    View details for DOI 10.1016/j.cell.2015.12.027

    View details for PubMedID 26824652

  • Insights into Cytokine-Receptor Interactions from Cytokine Engineering ANNUAL REVIEW OF IMMUNOLOGY VOL 33 Spangler, J. B., Moraga, I., Mendoza, J. L., Garcia, K. C. 2015; 33: 139-?
  • Deconstructing the Peptide-MHC Specificity of T Cell Recognition. Cell Birnbaum, M. E., Mendoza, J. L., Sethi, D. K., Dong, S., Glanville, J., Dobbins, J., Ozkan, E., Davis, M. M., Wucherpfennig, K. W., Garcia, K. C. 2014; 157 (5): 1073-1087


    In order to survey a universe of major histocompatibility complex (MHC)-presented peptide antigens whose numbers greatly exceed the diversity of the T cell repertoire, T cell receptors (TCRs) are thought to be cross-reactive. However, the nature and extent of TCR cross-reactivity has not been conclusively measured experimentally. We developed a system to identify MHC-presented peptide ligands by combining TCR selection of highly diverse yeast-displayed peptide-MHC libraries with deep sequencing. Although we identified hundreds of peptides reactive with each of five different mouse and human TCRs, the selected peptides possessed TCR recognition motifs that bore a close resemblance to their known antigens. This structural conservation of the TCR interaction surface allowed us to exploit deep-sequencing information to computationally identify activating microbial and self-ligands for human autoimmune TCRs. The mechanistic basis of TCR cross-reactivity described here enables effective surveillance of diverse self and foreign antigens without necessitating degenerate recognition of nonhomologous peptides.

    View details for DOI 10.1016/j.cell.2014.03.047

    View details for PubMedID 24855945

    View details for PubMedCentralID PMC4071348

  • Multifarious determinants of cytokine receptor signaling specificity. Advances in immunology Moraga, I., Spangler, J., Mendoza, J. L., Garcia, K. C. 2014; 121: 1-39


    Cytokines play crucial roles in regulating immune homeostasis. Two important characteristics of most cytokines are pleiotropy, defined as the ability of one cytokine to exhibit diverse functionalities, and redundancy, defined as the ability of multiple cytokines to exert overlapping activities. Identifying the determinants for unique cellular responses to cytokines in the face of shared receptor usage, pleiotropy, and redundancy will be essential in order to harness the potential of cytokines as therapeutics. Here, we discuss the biophysical (ligand-receptor geometry and affinity) and cellular (receptor trafficking and intracellular abundance of signaling molecules) parameters that contribute to the specificity of cytokine bioactivities. Whereas the role of extracellular ternary complex geometry in cytokine-induced signaling is still not completely elucidated, cytokine-receptor affinity is known to impact signaling through modulation of the stability and kinetics of ternary complex formation. Receptor trafficking also plays an important and likely underappreciated role in the diversification of cytokine bioactivities but it has been challenging to experimentally probe trafficking effects. We also review recent efforts to quantify levels of intracellular signaling components, as second messenger abundance can affect cytokine-induced bioactivities both quantitatively and qualitatively. We conclude by discussing the application of protein engineering to develop therapeutically relevant cytokines with reduced pleiotropy and redirected biological functionalities.

    View details for DOI 10.1016/B978-0-12-800100-4.00001-5

    View details for PubMedID 24388212

  • Requirements for Efficient Correction of Delta F508 CFTR Revealed by Analyses of Evolved Sequences CELL Mendoza, J. L., Schmidt, A., Li, Q., Nuvaga, E., Barrett, T., Bridges, R. J., Feranchak, A. P., Brautigam, C. A., Thomas, P. J. 2012; 148 (1-2): 164-174


    Misfolding of ΔF508 cystic fibrosis (CF) transmembrane conductance regulator (CFTR) underlies pathology in most CF patients. F508 resides in the first nucleotide-binding domain (NBD1) of CFTR near a predicted interface with the fourth intracellular loop (ICL4). Efforts to identify small molecules that restore function by correcting the folding defect have revealed an apparent efficacy ceiling. To understand the mechanistic basis of this obstacle, positions statistically coupled to 508, in evolved sequences, were identified and assessed for their impact on both NBD1 and CFTR folding. The results indicate that both NBD1 folding and interaction with ICL4 are altered by the ΔF508 mutation and that correction of either individual process is only partially effective. By contrast, combination of mutations that counteract both defects restores ΔF508 maturation and function to wild-type levels. These results provide a mechanistic rationale for the limited efficacy of extant corrector compounds and suggest approaches for identifying compounds that correct both defective steps.

    View details for DOI 10.1016/j.cell.2011.11.023

    View details for Web of Science ID 000299540700022

    View details for PubMedID 22265409

  • Biochemical and biophysical approaches to probe CFTR structure. Methods in molecular biology (Clifton, N.J.) Schmidt, A., Mendoza, J. L., Thomas, P. J. 2011; 741: 365-376


    The cystic fibrosis transmembrane regulator (CFTR) is a multi-domain integral membrane protein central to epithelial fluid secretion (see Chapter 21). Its activity is defective in the recessive genetic disease cystic fibrosis (CF). The most common CF-causing mutation is F508del in the first nucleotide binding domain (NBD1) of CFTR. This mutation is found on at least one allele of more than 90% of all CF patients. It is known to interfere with the trafficking/maturation of CFTR through the secretory pathway, leading to a loss-of-function at the plasma membrane. Notably, correction of the trafficking defect by addition of intragenic second-site suppressor mutations, or the alteration of bulk solvent conditions, such as by reducing the temperature or adding osmolytes, leads to appearance of functional channels at the membrane--thus, the rescued F508del-CFTR retains measurable function. High-resolution structural models of NBD1 from X-ray crystallographic data indicate that F508 is exposed on the surface of the domain in a position predicted by homologous ABC transporter structures to lie at the interface with the intracellular loops (ICLs) connecting the transmembrane spans. Determining the relative impact of the F508del mutation directly on NBD1 folding or on steps of domain assembly or both domain folding and assembly requires methods for evaluating the structure and stability of the isolated domain.

    View details for DOI 10.1007/978-1-61779-117-8_24

    View details for PubMedID 21594797

  • Introduction to section IV: biophysical methods to approach CFTR structure. Methods in molecular biology (Clifton, N.J.) Mendoza, J. L., Schmidt, A., Thomas, P. J. 2011; 741: 321-327


    Inefficient folding of CFTR into a functional three-dimensional structure is the basic pathophysiologic mechanism leading to most cases of cystic fibrosis. Knowledge of the structure of CFTR and placement of these mutations into a structural context would provide information key for developing targeted therapeutic approaches for cystic fibrosis. As a large polytopic membrane protein containing disordered regions, intact CFTR has been refractory to efforts to solve a high-resolution structure using X-ray crystallography. The following chapters summarize current efforts to circumvent these obstacles by utilizing NMR, electron microscopy, and computational methodologies and by development of experimental models of the relevant domains of CFTR.

    View details for DOI 10.1007/978-1-61779-117-8_21

    View details for PubMedID 21594794

  • A Unique Redox-sensing Sensor II Motif in TorsinA Plays a Critical Role in Nucleotide and Partner Binding JOURNAL OF BIOLOGICAL CHEMISTRY Zhu, L., Millen, L., Mendoza, J. L., Thomas, P. J. 2010; 285 (48): 37271-37280


    Early onset dystonia is commonly associated with the deletion of one of a pair of glutamate residues (ΔE302/303) near the C terminus of torsinA, a member of the AAA+ protein family (ATPases associated with a variety of cellular activities) located in the endoplasmic reticulum lumen. The functional consequences of the disease-causing mutation, ΔE, are not currently understood. By contrast to other AAA+ proteins, torsin proteins contain two conserved cysteine residues in the C-terminal domain, one of which is located in the nucleotide sensor II motif. Depending on redox status, an ATP hydrolysis mutant of torsinA interacts with lamina-associated polypeptide 1 (LAP1) and lumenal domain like LAP1 (LULL1). Substitution of the cysteine in sensor II diminishes the redox-regulated interaction of torsinA with these substrates. Significantly, the dystonia-causing mutation, ΔE, alters the ability of torsinA to mediate the redox-regulated interactions with LAP1 and LULL1. Limited proteolysis experiments reveal redox- and mutation-dependent changes in the local conformation of torsinA as a function of nucleotide binding. These results indicate that the cysteine-containing sensor II plays a critical role in redox sensing and the nucleotide and partner binding functions of torsinA and suggest that loss of this function of torsinA contributes to the development of DYT1 dystonia.

    View details for DOI 10.1074/jbc.M110.123471

    View details for Web of Science ID 000284424000020

    View details for PubMedID 20861018

  • The Cystic Fibrosis-causing Mutation Delta F508 Affects Multiple Steps in Cystic Fibrosis Transmembrane Conductance Regulator Biogenesis JOURNAL OF BIOLOGICAL CHEMISTRY Thibodeau, P. H., Richardson, J. M., Wang, W., Millen, L., Watson, J., Mendoza, J. L., Du, K., Fischman, S., Senderowitz, H., Lukacs, G. L., Kirk, K., Thomas, P. J. 2010; 285 (46): 35825-35835


    The deletion of phenylalanine 508 in the first nucleotide binding domain of the cystic fibrosis transmembrane conductance regulator is directly associated with >90% of cystic fibrosis cases. This mutant protein fails to traffic out of the endoplasmic reticulum and is subsequently degraded by the proteasome. The effects of this mutation may be partially reversed by the application of exogenous osmolytes, expression at low temperature, and the introduction of second site suppressor mutations. However, the specific steps of folding and assembly of full-length cystic fibrosis transmembrane conductance regulator (CFTR) directly altered by the disease-causing mutation are unclear. To elucidate the effects of the ΔF508 mutation, on various steps in CFTR folding, a series of misfolding and suppressor mutations in the nucleotide binding and transmembrane domains were evaluated for effects on the folding and maturation of the protein. The results indicate that the isolated NBD1 responds to both the ΔF508 mutation and intradomain suppressors of this mutation. In addition, identification of a novel second site suppressor of the defect within the second transmembrane domain suggests that ΔF508 also effects interdomain interactions critical for later steps in the biosynthesis of CFTR.

    View details for DOI 10.1074/jbc.M110.131623

    View details for Web of Science ID 000283845300060

    View details for PubMedID 20667826

  • Optical Detection of Disordered Water within a Protein Cavity JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Goldbeck, R. A., Pillsbury, M. L., Jensen, R. A., Mendoza, J. L., Nguyen, R. L., Olson, J. S., Soman, J., Kliger, D. S., Esquerra, R. M. 2009; 131 (34): 12265-12272


    Internal water molecules are important to protein structure and function, but positional disorder and low occupancies can obscure their detection by X-ray crystallography. Here, we show that water can be detected within the distal cavities of myoglobin mutants by subtle changes in the absorbance spectrum of pentacoordinate heme, even when the presence of solvent is not readily observed in the corresponding crystal structures. A well-defined, noncoordinated water molecule hydrogen bonded to the distal histidine (His64) is seen within the distal heme pocket in the crystal structure of wild type (wt) deoxymyoglobin. Displacement of this water decreases the rate of ligand entry into wt Mb, and we have shown previously that the entry of this water is readily detected optically after laser photolysis of MbCO complexes. However, for L29F and V68L Mb no discrete positions for solvent molecules are seen in the electron density maps of the crystal structures even though His64 is still present and slow rates of ligand binding indicative of internal water are observed. In contrast, time-resolved perturbations of the visible absorption bands of L29F and V68L deoxyMb generated after laser photolysis detect the entry and significant occupancy of water within the distal pockets of these variants. Thus, the spectral perturbation of pentacoordinate heme offers a potentially robust system for measuring nonspecific hydration of the active sites of heme proteins.

    View details for DOI 10.1021/ja903409j

    View details for Web of Science ID 000269379600058

    View details for PubMedID 19655795

  • The pH dependence of heme pocket hydration and ligand rebinding kinetics in photodissociated carbonmonoxymyoglobin JOURNAL OF BIOLOGICAL CHEMISTRY Esquerra, R. M., Jensen, R. A., Bhaskaran, S., Pillsbury, M. L., Mendoza, J. L., Lintner, B. W., Kliger, D. S., Goldbeck, R. A. 2008; 283 (20): 14165-14175


    We monitored the occupancy of a functionally important non-coordinated water molecule in the distal heme pocket of sperm whale myoglobin over the pH range 4.3-9.4. Water occupancy was assessed by using time-resolved spectroscopy to detect the perturbation of the heme visible band absorption spectrum caused by water entry after CO photodissociation ( Goldbeck, R. A., Bhaskaran, S., Ortega, C., Mendoza, J. L., Olson, J. S., Soman, J., Kliger, D. S., and Esquerra, R. M. (2006) Proc. Natl. Acad. Sci. U. S. A. 103, 1254-1259 ). We found that the water occupancy observed during the time interval between ligand photolysis and diffusive recombination decreased by nearly 20% as the pH was lowered below 6. This decrease accounted for most of the concomitant increase in the observed CO bimolecular recombination rate constant, as the lower water occupancy presented a smaller kinetic barrier to CO entry into the pocket at lower pH. These results were consistent with a model in which the distal histidine, which stabilizes the water molecule within the distal pocket by accepting a hydrogen bond, tends to swing out of the pocket upon protonation and destabilize the water occupancy at low pH. Extrapolation of this model to lower pH suggests that the additional increase in ligand association rate constant observed previously in stopped-flow studies at pH 3 may also be due in part to reduced distal water occupancy concomitant with further His64 protonation and coupled protein conformational change.

    View details for DOI 10.1074/jbc.M709710200

    View details for Web of Science ID 000255728200070

    View details for PubMedID 18359768

  • Building an understanding of cystic fibrosis on the foundation of ABC transporter structures JOURNAL OF BIOENERGETICS AND BIOMEMBRANES Mendoza, J. L., Thomas, P. J. 2007; 39 (5-6): 499-505


    Cystic fibrosis (CF) is a fatal disease affecting the lungs and digestive system by impairment of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). While over 1000 mutations in CFTR have been associated with CF, the majority of cases are linked to the deletion of phenylalanine 508 (delta F508). F508 is located in the first nucleotide binding domain (NBD1) of CFTR. This mutation is sufficient to impair the trafficking of CFTR to the plasma membrane and, thus, its function. As an ABC transporter, recent structural data from the family provide a framework on which to consider the effect of the delta F508 mutation on CFTR. There are fifty-seven known structures of ABC transporters and domains thereof. Only six of these structures are of the intact transporters. In addition, modern bioinformatic tools provide a wealth of sequence and structural information on the family. We will review the structural information from the RCSB structure repository and sequence databases of the ABC transporters. The available structural information was used to construct a model for CFTR based on the ABC transporter homologue, Sav1866, and provide a context for understanding the molecular pathology of Cystic Fibrosis.

    View details for DOI 10.1007/s10863-007-9117-7

    View details for Web of Science ID 000252468500023

    View details for PubMedID 18080175

  • Water and ligand entry in myoglobin: Assessing the speed and extent of heme pocket hydration after CO photodissociation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Goldbeck, R. A., Bhaskaran, S., Ortega, C., Mendoza, J. L., Olson, J. S., Soman, J., Kliger, D. S., Esquerra, R. M. 2006; 103 (5): 1254-1259


    A previously undescribed spectrokinetic assay for the entry of water into the distal heme pocket of wild-type and mutant myoglobins is presented. Nanosecond photolysis difference spectra were measured in the visible bands of sperm whale myoglobin as a function of distal pocket mutation and temperature. A small blue shift in the 560-nm deoxy absorption peak marked water entry several hundred nanoseconds after CO photodissociation. The observed rate suggests that water entry is rate-limited by the escape of internal dissociated CO. The heme pocket hydration and geminate recombination yields were found to be the primary factors controlling the overall bimolecular association rate constants for CO binding to the mutants studied. The kinetic analysis provides estimates of 84%, 60%, 40%, 0%, and 99% for the steady-state hydrations of wild-type, H64Q, H64A, H64L, and V68F deoxymyoglobin, respectively. The second-order rate constants for CO and H(2)O entry into the empty distal pocket of myoglobin are markedly different, 8 x 10(7) and 2 x 10(5) M(-1).s(-1), respectively, suggesting that hydrophobic partitioning of the apolar gas from the aqueous phase into the relatively apolar protein interior lowers the free energy barrier for CO entry.

    View details for DOI 10.1073/pnas.0507840103

    View details for Web of Science ID 000235094300020

    View details for PubMedID 16432219