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1.  HBD-3 structure motifs important in CXCR4 antagonism 
The FEBS journal  2013;280(14):10.1111/febs.12328.
Previously, we reported that hBD-3 can both antagonize CXCR4 function on T cells, and promote receptor internalization in the absence of activation. In the present study, we explored the important structural elements of hBD-3 that are involved in blocking CXCR4 activation by its natural ligand, stromal derived factor 1α (SDF-1α; CXCL12). Results from site-directed mutagenesis studies suggest that the ability of hBD-3 to inhibit SDF-1α/CXCR4 interaction, as assayed either by blocking SDF-1 binding to CXCR4 or antagonizing SDF-1 induced Ca2+ mobilization, is correlated with the presence of hBD-3 cysteine residues, specific surface-distributed cationic residues, and the electrostatic properties and availability of both hBD-3 termini. Specifically, hBD-3 activity against CXCR4 is reduced by: 1) substituting all six cysteine residues; 2) substituting the cationic residues with acidic ones in the N- and C- termini; 3) removal of the first 10 N-terminal residues; and 4) substituting surface-exposed basic residues K8, K32 and R36 with neutral ones. The hBD-3/CXCR4 interaction has potentially wide ranging implications for HIV-related biology as well as for a host of CXCR4-dependent activities including hematopoiesis, neurogenesis, angiogenesis, carcinogenesis, and immune cell trafficking. CXCR4 is highly expressed on T cells, monocytes, and epithelial cells. Therefore, understanding the structure-function relationship between hBD-3 and CXCR4 that accounts for the antagonistic interaction between the two molecules may provide new insights into HIV/HAART-related pathology as well as novel insights into the interaction between innate and adaptive immunity at mucosal sites.
doi:10.1111/febs.12328
PMCID: PMC3831652  PMID: 23659571
Defensin; HBD-3; CXCR4; structure; antagonism
2.  Novel substrate-based inhibitors of human glutamate carboxypeptidase II with enhanced lipophilicity 
Journal of medicinal chemistry  2011;54(21):7535-7546.
Virtually all low molecular weight inhibitors of human glutamate carboxypeptidase II (GCPII) are highly polar compounds that have limited use in settings where more lipophilic molecules are desired. Here we report the identification and characterization of GCPII inhibitors with enhanced liphophilicity that are derived from a series of newly identified dipeptidic GCPII substrates featuring non-polar aliphatic side chains at the C-terminus. To analyze the interactions governing the substrate recognition by GCPII, we determined crystal structures of the inactive GCPII(E424A) mutant in complex with selected dipeptides and complemented the structural data with quantum mechanics/molecular mechanics calculations. Results reveal the importance of non-polar interactions governing GCPII affinity towards novel substrates as well as formerly unnoticed plasticity of the S1′ specificity pocket. Based on those data, we designed, synthesized and evaluated a series of novel GCPII inhibitors with enhanced lipophilicity, with the best candidates having low nanomolar inhibition constants and clogD > -0.3. Our findings offer new insights into the design of more lipophilic inhibitors targeting GCPII.
doi:10.1021/jm200807m
PMCID: PMC3222833  PMID: 21923190
PSMA; NAALADase; GCPII; zinc peptidase; folate hydrolase; inhibition; quantum mechanics/molecular mechanics (QM/MM)
3.  Structural Basis of Interaction between Urokinase-Type Plasminogen Activator and Its Receptor 
Journal of molecular biology  2006;363(2):482-495.
Summary
Recent studies indicate that binding of urokinase-type plasminogen activator (uPA) to its high affinity receptor (uPAR), orchestrates uPAR interactions with other cellular components that play a pivotal role in diverse (patho-)physiological processes including wound healing, angiogenesis, inflammation, and cancer metastasis. However, notwithstanding the wealth of biochemical data available describing the activities of uPAR, little is known as to the exact mode of uPAR-uPA interactions and the presumed conformational changes that accompanying uPA-uPAR engagement. Here we report the crystal structure of soluble urokinase plasminogen activator receptor (suPAR), which contains the three domains of the wild-type receptor but lacks the cell surface anchoring sequence, in complex with the amino terminal fragment of urokinase-type plasminogen activator (ATF), at the resolution of 2.8 Å. We also report the 1.9 Å crystal structure of the free ATF. Our results provide a structural basis, represented by conformational changes induced in uPAR, for several published biochemical observations describing the nature of uPAR-uPA interactions and provide insight into mechanisms that may be responsible for the cellular responses induced by uPA binding.
doi:10.1016/j.jmb.2006.08.063
PMCID: PMC3443620  PMID: 16979660
urokinase receptor; X-ray crystallography; protein-protein interactions; kringle domain; plasminogen
4.  A Remote Arene-Binding Site on Prostate Specific Membrane Antigen Revealed by Antibody-Recruiting Small Molecules 
Journal of the American Chemical Society  2010;132(36):12711-12716.
Prostate specific membrane antigen (PSMA) is a membrane-bound glutamate carboxypeptidase overexpressed in many forms of prostate cancer. Our laboratory has recently disclosed a class of small molecules, called ARM-Ps (antibody-recruiting molecule targeting prostate cancer) that are capable of enhancing antibody-mediated immune recognition of prostate cancer cells. Interestingly, during the course of these studies, we found ARM-Ps to exhibit extraordinarily high potencies toward PSMA, compared to previously reported inhibitors. Here, we report in-depth biochemical, crystallographic, and computational investigations which elucidate the origin of the observed affinity enhancement. These studies reveal a previously unreported arene-binding site on PSMA, which we believe participates in an aromatic stacking interaction with ARMs. Although this site is composed of only a few amino acid residues, it drastically enhances small molecule binding affinity. These results provide critical insights into the design of PSMA-targeted small molecules for prostate cancer diagnosis and treatment; more broadly, the presence of similar arene-binding sites throughout the proteome could prove widely enabling in the optimization of small-molecule–protein interactions.
doi:10.1021/ja104591m
PMCID: PMC2965167  PMID: 20726553
5.  Crystal structure of XMRV protease differs from the structures of other retropepsins 
Using energy and density guided Rosetta refinement to improve molecular replacement, we have determined the crystal structure of the protease (PR) encoded by xenotropic murine leukemia virus-related virus (XMRV). Despite overall similarity of XMRV PR to other retropepsins, the topology of its dimer interface more closely resembles the monomeric, pepsin-like enzymes. Thus, XMRV PR may represent a distinct evolutionary branch of the family of aspartic proteases.
doi:10.1038/nsmb.1964
PMCID: PMC3058223  PMID: 21258323
6.  Soluble TLT-1 modulates platelet-endothelial cell interactions and actin polymerization 
TREM like transcript-1 (TLT-1) is a membrane protein receptor found in α-granules of platelets and megakaryocytes. Upon platelet activation TLT-1 is rapidly brought to the surface of platelets. Recently, we demonstrated that activated platelets release a soluble form of TLT-1 (sTLT-1) that is found in serum but not in the plasma of healthy individuals and can enhance platelet aggregation in vitro. Furthermore, evaluation of patients diagnosed with inflammatory diseases, such as sepsis, show that these patients have significantly elevated levels of sTLT-1 in their blood. Accordingly, mice deficient in TLT-1 are predisposed to bleeding in response to an inflammatory challenge; however the mechanism of TLT-1 function remains unknown. In this investigation we demonstrate an increase in the amount of platelets that adhere to endothelial cell monolayers in the presence of recombinant sTLT-1 (rsTLT-1). Additionally we present evidence that rsTLT-1 increases platelet adherence to glass slides by stimulating actin polymerization in platelets as determined by increased staining of rodamine phalloidin. These results suggest that during inflammation, sTLT-1 may mediate hemostasis by enhancing actin polymerization, resulting in increased platelet aggregation and adherence to the endothelium.
doi:10.1097/MBC.0b013e3283358116
PMCID: PMC2886849  PMID: 20093931
7.  Resonance Assignment and Three-Dimensional Structure Determination of a Human Alpha-Defensin, HNP-1, by Solid-State NMR 
Journal of molecular biology  2010;397(2):408-422.
Human α-defensins (HNPs) are immune defense mini-proteins that act by disrupting microbial cell membranes. Elucidating the three-dimensional structures of HNPs in lipid membranes is important for understanding their mechanisms of action. Using solid-state NMR, we have determined the three-dimensional structure of HNP-1 in a microcrystalline state outside the lipid membrane, which provides benchmarks for structure determination and comparison with the membrane-bound state. From a suite of 2D and 3D magic-angle spinning experiments, 13C and 15N chemical shifts were obtained that yielded torsion angle constraints while inter-residue distances were obtained to restrain the three-dimensional fold. Together, these constraints led to the first high-resolution SSNMR structure of a human defensin. The SSNMR structure has close similarity to the crystal structures of the HNP family, with the exception of the loop region between the first and second β-strands. The difference, which is partially validated by direct torsion angle measurements of selected loop residues, suggests possible conformational variation and flexibility of this segment of the protein, which may regulate HNP interaction with the phospholipid membrane of microbial cells.
doi:10.1016/j.jmb.2010.01.030
PMCID: PMC2873975  PMID: 20097206
Human α-defensin; solid-state NMR; resonance assignment; structure determination; antimicrobial peptides
8.  Novel Peptides Based on HIV-1 gp120 Sequence with Homology to Chemokines Inhibit HIV Infection in Cell Culture 
PLoS ONE  2011;6(1):e14474.
The sequential interaction of the envelope glycoprotein of the human immunodeficiency virus type 1 (HIV-1) with CD4 and certain chemokine coreceptors initiates host cell entry of the virus. The appropriate chemokines have been shown to inhibit viral replication by blocking interaction of the gp120 envelope protein with the coreceptors. We considered the possibility that this interaction involves a motif of the gp120 that may be structurally homologous to the chemokines. In the amino acid sequences of most chemokines there is a Trp residue located at the beginning of the C-terminal α-helix, which is separated by six residues from the fourth Cys residue. The gp120 of all HIV-1 isolates have a similar motif, which includes the C-terminal part of a variable loop 3 (V3) and N-terminal part of a conserved region 3 (C3). Two synthetic peptides, derived from the relevant gp120 sequence inhibited HIV-1 replication in macrophages and T lymphocytes in sequence-dependent manner. The peptides also prevented binding of anti-CXCR4 antibodies to CXCR4, and inhibited the intracellular Ca2+ influx in response to CXCL12/SDF-1α. Thus these peptides can be used to dissect gp120 interactions with chemokine receptors and could serve as leads for the design of new inhibitors of HIV-1.
doi:10.1371/journal.pone.0014474
PMCID: PMC3019152  PMID: 21264298
9.  Bioisosterism of Urea-Based GCPII Inhibitors: Synthesis and Structure-Activity Relationships Studies 
We report a strategy based on bioisosterism to improve the physicochemical properties of existing hydrophilic, urea-based GCPII inhibitors. Comprehensive structure-activity relationship studies of the P1’ site of ZJ-43- and DCIBzL-based compounds identified several glutamate-free inhibitors with Ki values below 20 nM. Among them, compound 32d (Ki = 11 nM) exhibited selective uptake in GCPII-expressing tumors by SPECT-CT imaging in mice. A novel conformational change of amino acids in the S1’ pharmacophore pocket was observed in the X-ray crystal structure of GCPII complexed with 32d.
doi:10.1016/j.bmcl.2009.10.061
PMCID: PMC2818328  PMID: 19897367
PSMA; glutamate carboxypeptidase II; molecular imaging; radiopharmaceutical; SPECT
10.  Is too ‘creative’ language acceptable in crystallography? 
A brief comment is made on the need to use carefully selected, novel terms in crystallographic publications, especially publications addressing non-specialists.
While figures of speech are often useful and even educational, flashy titles combined with hyperbolae and imprecise language can mislead or deceive non-specialist readers and should therefore be avoided. The possibility of such confusion exists when poorly defined terms like ‘structure quality’ or ‘super-resolution’ are used to describe a protein structure.
doi:10.1107/S090744491002799X
PMCID: PMC2935284  PMID: 20823556
letters to the editor; crystallographic terminology
11.  Impact Of Pro Segments On The Folding And Function Of Human Neutrophil α-Defensins 
Journal of molecular biology  2007;368(2):537-549.
Summary
Human neutrophil α-defensins (HNPs) are synthesized in vivo as inactive precursor proteins, i.e., preproHNPs. A series of sequential proteolytic events excise the N-terminal inhibitory pro peptide, leading to defensin maturation and storage in azurophilic granules. The anionic pro peptide, required for correct sub-cellular trafficking and sorting of proHNPs, inhibits the antimicrobial activity of cationic defensins, either inter- or intra-molecularly, presumably through charge neutralization. To better understand the role of the pro peptide in the folding and functioning of α-defensins and/or pro α-defensins, we chemically attached the proHNP1 pro peptide or wtpro peptide and the following artificial pro segments to the N-terminus of HNP1: polyethylene glycol (PEG), Arg10 (polyR), Ser10 (polyS), and crpro peptide – a charge-reversing mutant of the pro peptide where Arg/Lys residues were changed to Asp, and Asp/Glu residues to Lys. Comparative in vitro folding suggested that while all artificial pro segments chaperoned defensin folding, with PEG being the most efficient, the pro peptide catalyzed the folding of proHNPs likely through two independent mechanisms: solubilization of and interaction with the C-terminal defensin domain. Further, the N-terminal artificial pro segments dramatically altered the bactericidal activity of HNP1 against both E. coli and S. aureus. Surprisingly, crpro peptide and wtpro peptide showed similar properties with respect to intra-molecular and inter-molecular catalysis of defensin folding as well as α-defensin binding, although their binding modes appeared different. Our findings identify a dual chaperone activity of the pro peptide and may shed light on the molecular mechanisms by which pro α-defensins fold in vivo.
doi:10.1016/j.jmb.2007.02.040
PMCID: PMC2754399  PMID: 17355880
defensin; HNP; pro peptide; native chemical ligation; chaperone
12.  Molecular determinants for the interaction of human neutrophil α defensin 1 with its pro peptide 
Journal of molecular biology  2008;381(5):1281-1291.
Summary
Human neutrophil α-defensins (HNPs) are cationic antimicrobial peptides that are synthesized in vivo as inactive precursors (proHNPs). Activation requires proteolytic excision of their anionic N-terminal inhibitory pro peptide. The pro peptide of proHNP1 also specifically interacts with and inhibits the antimicrobial activity of HNP1 intermolecularly. In the light of the opposite net charges segregated in proHNP1, functional inhibition of the C-terminal defensin domain by its pro peptide is generally thought to be of electrostatic nature. Using a battery of analogs of the pro peptide and of proHNP1, we identified residues in the pro peptide region important for HNP1 binding and inhibition. Only three anionic residues in the pro peptide, Glu15, Asp20 and Glu23, were modestly important for interactions with HNP1. By contrast, the hydrophobic residues in the central part of the pro peptide, and the conserved hydrophobic motif Val24Val25Val26Leu28 in particular, were critical for HNP1 binding and inhibition. Neutralization of all negative charges in the pro peptide only partially activated the bactericidal activity of proHNP1. Our data indicate that hydrophobic forces play a dominant role in mediating the interactions between HNP1 and its pro peptide – a finding largely contrasting the commonly held view that the interactions are of electrostatic nature.
doi:10.1016/j.jmb.2008.06.066
PMCID: PMC2754386  PMID: 18616948
defensin; HNP; antimicrobial peptide; pro peptide; electrostatic interaction; hydrophobic interaction
13.  Structural Basis of Interactions between Human Glutamate Carboxypeptidase II and Its Substrate Analogs 
Journal of molecular biology  2008;376(5):1438-1450.
Summary
Human glutamate carboxypeptidase II (GCPII) is involved in neuronal signal transduction and intestinal folate absorption by means of the hydrolysis of its two natural substrates, N-acetyl-aspartyl-glutamate (NAAG) and folyl-poly-γ-glutamates, respectively. During the past years, tremendous efforts have been made towards the structural analysis of GCPII. Crystal structures of GCPII in complex with various ligands have provided insight into the binding of these ligands, particularly to the S1′ site of the enzyme. In this paper, we have extended structural characterization of GCPII to its S1 site by using dipeptide-based inhibitors that interact with both S1 and S1′ sites of the enzyme. To this end, we have determined crystal structures of human GCPII in complex with phosphapeptide analogs of folyl-γ-glutamate, aspartyl-glutamate and γ-glutamyl-glutamate, reined at resolution of 1.50 Å, 1.60 Å and 1.67 Å, respectively. The S1 pocket of GCPII could be accurately defined and analyzed for the first time, and the data indicate the importance of Asn519, Arg463, Arg534, and Arg536 for recognition of the penultimate (i.e., P1) substrate residues. Direct interactions between the positively charged guanidinium groups of Arg534 and Arg536 and a P1 moiety of a substrate/inhibitor provide mechanistic explanation of GCPII preference for acidic dipeptides. Additionally, observed conformational flexibility of the Arg463 and Arg536 side chains likely regulates GCPII affinity towards different inhibitors and modulates GCPII substrate specificity. The biochemical experiments assessing the hydrolysis of several GCPII substrate derivatives modified at the P1 position, also included in this report, further complement and extend conclusions derived from the structural analysis. The data described here form an excellent foundation for the structurally aided design of novel low-molecular weight GCPII inhibitors and imaging agents.
doi:10.1016/j.jmb.2007.12.066
PMCID: PMC2753231  PMID: 18234225
prostate-specific membrane antigen; metallopeptidase; folate hydrolase; NAALADase; phosphapeptide
14.  TREM-like transcript-1 protects against inflammation-associated hemorrhage by facilitating platelet aggregation in mice and humans 
The Journal of Clinical Investigation  2009;119(6):1489-1501.
Triggering receptor expressed on myeloid cells–like (TREM-like) transcript-1 (TLT-1), a type 1 single Ig domain orphan receptor specific to platelet and megakaryocyte α-granules, relocates to the platelet surface upon platelet stimulation. We found here that patients diagnosed with sepsis, in contrast to healthy individuals, had substantial levels of soluble TLT-1 (sTLT-1) in their plasma that correlated with the presence of disseminated intravascular coagulation. sTLT-1 bound to fibrinogen and augmented platelet aggregation in vitro. Furthermore, the cytoplasmic domain of TLT-1 could also bind ezrin/radixin/moesin family proteins, suggesting its ability to link fibrinogen to the platelet cytoskeleton. Accordingly, platelets of Treml1–/– mice failed to aggregate efficiently, extending tail-bleeding times. Lipopolysaccharide-treated Treml1–/– mice developed higher plasma levels of TNF and D-dimers than wild-type mice and were more likely to succumb during challenge. Finally, Treml1–/– mice were predisposed to hemorrhage associated with localized inflammatory lesions. Taken together, our findings suggest that TLT-1 plays a protective role during inflammation by dampening the inflammatory response and facilitating platelet aggregation at sites of vascular injury. Therefore, therapeutic modulation of TLT-1–mediated effects may provide clinical benefit to patients with hypercoagulatory conditions, including those associated with inflammation.
doi:10.1172/JCI36175
PMCID: PMC2689104  PMID: 19436112
15.  A high-resolution structure of ligand-free human glutamate carboxypeptidase II 
A crystal structure of ligand-free human glutamate carboxypeptidase II refined to 1.65 Å resolution is reported. The structure provides insight into the active-site of the enzyme in its unliganded state.
Human glutamate carboxypeptidase II (GCPII; EC 3.4.17.21) is an established marker for prostate-cancer diagnosis as well as a candidate therapeutic target for the treatment of diverse pathologies that involve glutamatergic transmission. Structural data on GCPII are thus valuable for the design and optimization of GCPII-specific inhibitors and diagnostic probes. The currently available structure of ligand-free GCPII was refined to a resolution of 3.5 Å. This work reports the structure of the protein refined to 1.65 Å resolution, with crystallographic values of R = 0.207 and R free = 0.228. The new structure extends the resolution appreciably and the new model based on this data shows significant differences when compared with the previously published model.
doi:10.1107/S174430910700379X
PMCID: PMC2330195  PMID: 17329803
prostate-specific membrane antigens; metallopeptidase; folate hydrolases; NAALADase
16.  Antimicrobial Characterization of Human β-Defensin 3 Derivatives 
Human β-defensin 3 (hBD3) is a highly basic 45-amino-acid protein that acts both as an antimicrobial agent and as a chemoattractant molecule. Although the nature of its antimicrobial activity is largely electrostatic, the importance of the molecular structure on this activity is poorly understood. Two isoforms of hBD3 were synthesized: the first with native disulfide linkages and the second with nonnative linkages. In a third synthetic peptide, all cysteine residues were replaced with α-aminobutyric acid, creating a completely linear peptide. A series of six small, linear peptides corresponding to regions of hBD3 with net charges ranging from +4 to +8 (at pH 7) and lengths ranging from 9 to 20 amino acids were also synthesized. The linear full-length peptide showed the highest microbicidal activity against Escherichia coli and Staphylococcus aureus, while all three full-length forms showed equal activity against Candida albicans. The linear peptide also showed high activity against Enterococcus faecium and Pseudomonas aeruginosa. Peptides corresponding to the C terminus showed higher activities when tested against E. coli, with the most active peptides being the most basic. However, only the peptide corresponding to the N terminus of hBD3 showed any activity against S. aureus and C. albicans. Further, N-terminal deletion mutants of native hBD3 showed diminished activities against S. aureus. Thus, the antimicrobial properties of hBD3 derivatives are determined by both charge and structure.
doi:10.1128/AAC.47.9.2804-2809.2003
PMCID: PMC182640  PMID: 12936977
17.  DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis 
Nucleic Acids Research  2002;30(10):e43.
The availability of sequences of entire genomes has dramatically increased the number of protein targets, many of which will need to be overexpressed in cells other than the original source of DNA. Gene synthesis often provides a fast and economically efficient approach. The synthetic gene can be optimized for expression and constructed for easy mutational manipulation without regard to the parent genome. Yet design and construction of synthetic genes, especially those coding for large proteins, can be a slow, difficult and confusing process. We have written a computer program that automates the design of oligonucleotides for gene synthesis. Our program requires simple input information, i.e. amino acid sequence of the target protein and melting temperature (needed for the gene assembly) of synthetic oligonucleotides. The program outputs a series of oligonucleotide sequences with codons optimized for expression in an organism of choice. Those oligonucleotides are characterized by highly homogeneous melting temperatures and a minimized tendency for hairpin formation. With the help of this program and a two-step PCR method, we have successfully constructed numerous synthetic genes, ranging from 139 to 1042 bp. The approach presented here simplifies the production of proteins from a wide variety of organisms for genomics-based studies.
PMCID: PMC115297  PMID: 12000848

Results 1-17 (17)