Areas of Interest
Bioinformatics and Axonal outgrowth.
Short functional peptide motifs
Developing protein-protein interaction theory is important for
our understanding of the cell, disease mechanisms, and to
facilitate drug design. The theory behind protein-protein
interactions is based on first principle theory of molecular
interactions and the identification of a rapidly growing number
of short peptide motifs (less than 15 amino acids) that can bind
to, or be acted upon by protein domains. Other than those
interactions mediated through short motifs we have virtually no
ability to predict protein-protein interactions. My lab is
continuing annotation of Minimotif Miner, the first
bioinformatics tool that is a comprehensive database of short
functional motifs currently containing ~1000 unique motifs (Balla
et al, 2006). Minimotif Miner can be used by any scientist to
generate new hypotheses about the function of any protein and
postulate mechanisms by which mutations cause any human disease
(Schiller, 2007). Current projects are aimed at completing this
database, enhancing the specificity of motif definitions and
using Minimotif miner to identify new drug targets in HIV.
Axonal Outgrowth
Another central focus of my laboratory is axonal outgrowth.
Understanding how neurons initiate axon outgrowth is important,
not just for our basic understanding of neuronal connectivity,
but also for treating neurodegenerative diseases, spinal cord
injury, and head trauma. Axonal outgrowth requires the
coordination of many cellular processes. As the axon navigates
the nervous system to find targets, it must make complicated
decisions that require a higher level of interpretation. Very
little is known how the axon is capable of interpreting the many
inputs it receives. to address this question, we are continuing
to study how a multidomain protein called Kalirin is involved in
coordination of axonal signal processing (May et al., 2001;
Penzes et al., 2003; Schiller et al., 2005, Schiller et al.,
2006, Chakrabarti et al., 2006, Schiller, 2007)
Lab Rotation Projects
Project A: Regulation of Kalirin’s GEF activity.
Understanding how neurons initiate neurite outgrowth is
important, not just for our basic understanding of development
of the nervous system and neuronal morphology, but also to aid
in the development of therapies for neurological disorders. The
Kalirin guanine nucleotide exchange factor (GEF) domain is
important for inducing neuronal outgrowth in large projection
neurons. We first plan to investigate the regulation of the GEF
domain in the full-length Kalirin protein, use these studies to
screen for drugs that disrupt the GEF regulation, and screen
drugs for their ability to induce neuronal regeneration in
rodent models. As a first step toward this goal we have
identified that the spectrin, repeats, pleckstrin homology (PH)
and Src homology 3 (SH3) domain(s) regulate Kalirins GEF
activity. We have identified that inter- and intramolecular
association of the SH3 domain is part of the mechanism that
controls GEF activity. The rotation project will begin to
investigate the mechanism by which the PH domain and
phosphoinositides control the GEF activity of Kalirin. The
project will involve, structural biology, cell biology and
enzyme kinetics.
Project B: The receptor for nerve growth factor TrkA is a
receptor tyrosine kinase involved in neuronal survival and
neurite outgrowth.
Our laboratory has identified that the
pleckstrin homology domain of Kalirin binds to the TrkA receptor
and that this interaction is critical for efficient activation
of and signaling from the TrkA receptor. With the long term goal
of making drugs that activate this receptor tyrosine kinase, our
lab has projects to solve the structure of the Kalirin-PH
domain/TrkA complex by NMR spectroscopy, map the motif in TrkA
that binds Kalirin-PH1, or explore the specificity of this
interaction.
Project C: Identification of novel short motifs in the
C-termini of proteins.
Homology analysis is one of the best approaches for identifying
domains and predicting gene function. In addition to domains,
many short minimotifs of less than 15 amino acids confer
functions to proteins such as posttranslation modification,
protein-protein interaction, and protein trafficking. While
comprehensive databases and search interfaces for analyzing
protein domains exist, resources to search proteins for
minimotifs are of narrow scope, with most minimotif databases
examining a small subset of the known minimotifs. We have
generated a Minimotif (MnM) database containing 312 minimotifs
and a web-based simple motif search (SMS) system for identifying
minimotifs in proteins. Statistical modeling of complete
proteomes and homology analysis are used to increase the
probability that the identified minimotifs are of biological
function. Using this approach we have also identified several
hundred novel motifs in the C-termini of proteins in the human
proteome, which are conserved in other proteomes. Many known
C-terminal motifs (e.g PDZ motif) are important for the
functions of neuronal proteins. The rotation project will
identify proteins that bind to several of these novel C-terminal
motifs.
Publications
Selected Publications
Machida K, Thompson CM, Dierck K, Jablonowski , K Karkkainen S,
Liu B, Zhang H, Nash PD, Newman DK, Nollau P, Pawson T, Renkema,
GH, Saksela K, Schiller MR, Shin DG, and Mayer BJ (2007)
"High-Throughput Phosphotyrosine Profiling Using SH2 Domains"
Mol. Cell 26:899-915. PMID: 17588523
Schiller MR (2007) "Minimotif Miner, a computational tool to
investigate protein function, disease, and genetic diversity"
Current Protocols in Protein Science, Eds. Coligan JE, Dunn BM,
Speicher DW, Winkler H., Unit 2.12.1 - 2.12.14 John Wiley &
Sons, Inc. PDF
Kaiser J (2006) News report about Minimotif miner website.
Science 311:925 PDF
Balla S, Thapar V, Verma S, Luong T, Faghri T, Huang C-H,
Rajasekaran S, del Campo JJ, Shinn JH, Mohler WA, Maciejewski
MW, Gryk MR, Piccirillo B, Schiller SR, and Schiller MR (2006)
Minimotif Miner, a tool for investigating protein function.
Nature Methods 3:175-177 PDF PMID: 16489333
Schiller MR (2006) Coupling Receptor Tyrosine Kinases to Rho
GTPases - GEFs what's the link. Cell. Signaling 18:1834-1843.
PDF PMID: 16725310
Schiller MR, Chakrabarti K, King GF, Schiller NI, Eipper BA,
and Maciejewski MW (2006) Regulation of RhoGEF activity by
intramolecular and intermolecular SH3 interactions J. Biol.
Chem. 281:17774-17786 PDF PMID: 16644733
Chakrabarti K, Lin R, Schiller NI, Wang Y, Fan Y-X, Koubi D,
Rudkin BB, Johnson GR, Schiller MR. (2005) A critical role for
Kalirin in NGF signaling through TrkA. Mol. Cell. Biol.
25:5106-5118. PDF PMID: 15923627
Penzes P, Beeser A, Chernoff J, Schiller MR, Eipper BA, Mains
RE, Huganir RL. (2003) Rapid induction of dendritic spine
morphogenesis by trans-synaptic ephrinB-EphB receptor activation
of the Rho-GEF kalirin. Neuron 37: 263-74. PDF PMID: 12546821
 View more publications, see
Pubmed listing. |
