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DENNIS L. MAEDER
Adjunct Assistant Professor,
UMBC
Assistant Professor, Center
of Marine Biotechnology (COMB)
Ph.D., Biochemistry, University
of Cape Town, 1981
dmaeder@umbc.edu
Fax 410-455-3875; Voice
410-455-8674 (UMBC); 410-234-8880 (COMB)
Research Interests
BIOINFORMATICS, PROTEIN ENGINEERING. Software for analysis and visualization of genomic data, molecular evolution, comparative genomics databases, architectural analysis of biomolecular structures with design of structural enhancement.
Analysis of genomic data
Comparative genomics databases
Visualization software for genomic data
Archaeal origins of replication
Molecular evolution
Structural analysis of biomacromolecules for functional enhancement
A major strand of my current work is the analysis of emerging genomic
sequences. I have been thoroughly involved in the P. furiosus genome
sequence project, principally in managing the annotation efforts of a
diffuse collaboration [Robb et al (2001), Weiss et al. - in prep.]. To
this end I built a web interface for collaborative annotation which allows
various modalities of editing, review and tracking [http://comb5-156.umbi.umd.edu/genemate/].
In support of our
investigations of the genome, I have developed a database of archaeal
and other completed microbial genome sequences together with their ORFs
that may be interrogated with BLAST queries of single genomes. In addition
to this, I have written CROSS, a PC program that offers an interactive
graphical view of BLAST output. Using CROSS I have discovered large scale
rearrangements of the genomes within the genus Pyrococcus, and have been
able to show many structural elements in the chromosome such as the origin
of replication (Robb et al 2000, prov. Pat.), transposon mediated rearrangements
and duplication of ancestral operons [http://comb5-156.umbi.umd.edu/poster/genetics/,
Maeder et al (1999)]
As genome sequencing projects mature from small genomes (about 2 million nt) to large ones (the human genome) with multiple chromosomes and very large sizes (>5000 million nt), the need to translate information into insight will grow. Tools such as those I am developing will become increasingly important to the process of digestion of vast data by scientists. I plan to consolidate and expand these tools and approaches to deal with the information challenges of the near future.
More exciting perhaps is the prospect of elucidating the mechanism by which organisms such as Pyrococcus replicate. We know that the archaea are bacterial in so far as they have circular chromosomes, and that many of their house keeping genes share much in common with the bacteria. However their mechanisms for replication are not clear. They contain proteins that are related to the life cycle functions (DNA replication and cell division) of eukaryotes epitomised by yeast. As such the archaea may well represent an excellent model for prototypic eukaryotic cell division, and for developing a detailed model of eukaryote-like cell division which could yield useful insights into the management of cell division in cancerous cells. Understanding the replicative process may well have consequences for the development of novel cell-free DNA amplification systems [Robb et al 2000, provisional patent application].
Thermostability
My foundations are in protein physical biochemistry, and I have become expert in the use of computers to model and (re)design biological macromolecules to customise their physical properties.
The most recent example of this is the case of glutamate dehydrogenase (GDH) an extremely thermostable homohexameric protein found in Pyrococcus furiosus and Thermococcus litoralis that melts at 112 and 105°C respectively.
Initial experimental attempts at elevating the melting temperature of
T. litoralis GDH using site directed mutagenesis (SDM) focused on
the internal packing of the subunits, but did not produce enhanced thermostability.
When I first became involved in this project I speculated that the hexamer
would have to dissociate before the protein monomers could unravel and
be denatured. If this were so then the quality of the association of the
subunits would be the primary determinant of thermostability. With this
in mind I did two things. I analysed the structure using molecular modelling
software and software that I have written for the purpose
(Contax) to determine the residues which are in intersubunit contact.
I also compared the sequences to determine the sites of natural divergence
between these homologs. By considering only those residues which were
both in contact and different, I was able to discount scores of potential
SDM targets and focus on just three candidates. Two of these (T138E and
D167T) were both physically close and complementary in the sense that
they contained a swap of a threonine and an acidic amino acid. In the
case of P. furiosus the charged amino acids were distant, whereas
in the case of T. litoralis they were half that distance apart and
clustered near the center of the hexamer. The "explosive force"
hypothesis was born, and subsequent SDM focused on this area. The single
mutant T138E introduces a second charge and is less stable than the GDH
of wild type T. litoralis, whereas removal of the buried charge (D167T)
abolished this repulsion and produced a GDH mutant of enhanced thermostability
[Vetriani et al (1998), Yip et al (1998), Robb & Maeder (1998) and
http://comb5-156.umbi.umd.edu/poster/gdh/]. This hybrid approach of structural
bioinformatics has yielded good results, and work in the lab continues
on the electrostatic effect, assaying the effect of ionic strength on
mutant thermostability.
Bioinformatics
My earliest efforts in bioinformatics [Maeder (1991)] related to the
analysis of the carboxy-terminal domain of histone H1. In eukaryotes,
the sequences of histones are generally highly conserved. However in the
case of H1 and H5, the lysine-rich "external" histones, there
is no good sequence homology determined by dot-plot analysis. I hypothesised
that sequence was not conserved, but that composition and structure were.
I wrote a module for my SAGA sequence analysis program that measured the
clustering of amino acids, and by sequence randomisation and sampling
I was able to draw statistical inferences about these
distributions. Furthermore, I used statistical mechanics to demonstrate
that this domain is likely to be unstructured in solution, but to adopt
an alpha helical conformation on binding to DNA.
MADIBA is my current multiple sequence comparison workbench which I have
developed as a graphical viewer for huge multiple sequence alignments,
as well as a tool for discovering either unique or common primer sequences
(for Taqman amplification and discrimination of environmental samples
using the ribosomal intergenic spacer region). In addition it determines
conserved sequence blocks, and produces formatted output for MS-Word
[http://comb5-156.umbi.umd.edu/poster/madiba/]. Tools such as MADIBA have
great value for diagnostic purposes, where polymorphisms in multiple sequences
are appreciated with ease.
Future Research
My future research plans may be summarised in the following broad objectives:
Build and consolidate computer tools for reducing genomic data to knowledge
using
Huge browsing
Smart data reduction
Whole genome comparison
Archaeal genetics - a systems approach
Analyse eukaryote-like systems
Analyse operon scale evolution
Develop collaborations with wet-bench experimentalists to test hypotheses developed from insights of genomic analysis.
In objective 1, I intend to collect all known genomic sequences (starting with microbial genome sequences), to compare each one with each other one (using Blast) and build a database of the resulting high scoring pairs (HSPs). This will allow whole multi-genome sequence comparisons to be done on the fly, and by analysing the overlaps of such HSPs reconstruct the order of divergence or rearrangement of these genomes. This approach becomes increasingly powerful as more genomic sequence becomes available. This will leverage the computational capacity of the SGI Origin 3200 which I am currently developing as a dedicated bioinformatics server. This approach has matured along with the prototyping of the CROSS desktop system which will be polished and adapted to interact with these HSP databases.
In objective 2 I will continue to analyze microbial genomes to understand
amongst others:
the structural basis of archaeal origins of replication (subject of a
provisional patent) which may impinge on our understanding of the fundamentals
of eukaryote replication, plasticity of genomes, in particular archaeal
model systems which may involve transposon-mediated together with other
forms of rearrangement, and thermostability of proteins from Pyrococcus
furiosus proteins and related systems.
Collaborations are essential to such bioinformatic studies because data generation cannot happen exclusively in silico, and ideas cannot exist in vacuo.
Relevant Links
My web site: http://comb5-156.umbi.umd.edu
GeneMate - my genomic workbench: http://comb5-156.umbi.umd.edu/genemate/
Thermostability studies: http://comb5-156.umbi.umd.edu/poster/gdh/
Genetic studies: http://comb5-156.umbi.umd.edu/poster/genetics/
CROSS introduction: http://comb5-156.umbi.umd.edu/poster/Cross/
CROSS genome comparison: http://comb5-156.umbi.umd.edu/poster/CrossGenomes/
CROSS 3-way Pyrococcus comparison: http://comb5-156.umbi.umd.edu/poster/3Dcross/
Selected Publications
Laksanalamai P, Maeder DL, and Robb FT: Protection of Escherichia coli
proteins and viable cells by the small heat shock protein from the hyperthermophilic
archaeon, Pyrococcus furiosus. J. Bacteriol (2001) 183 5198-202
Robb FT, Maeder DL, DiRuggiero J, Borges KM, and Tolliday N: Glutamate
Dehydrogenases from Hyperthermophiles. Methods in Enzymology (2001) 331
26-41
Robb FT, Maeder DL, Brown JR, DiRuggiero J, Stump MD, Yeh RK, Weiss RB,
Dunn DM: Genomic Sequence of Hyperthermophile Pyrococcus furiosus:
implications for Physiology and Enzymology. Methods in Enzymology (2001)
330 134-157
Robb FT, Maeder DL and DiRuggiero, J: Isothermal Amplification Of Megabase DNA Targets. (2000) Provisional US patent filing 09/243, 293
DiRuggiero J, Dunn JD, Maeder DL, Holley-Shanks R, Chatard J, Horlacher
R, Robb FT, Boos W, & Weiss RB: Evidence of recent lateral gene transfer
among hyperthermophilic Archaea Mol. Microbiol. (2000) 38, 684-693
Britton KL, Yip KS, Sedelnikova SE, Stillman TJ, Adams MW, Ma K, Maeder
DL, Robb FT, Tolliday N, Vetriani C, Rice DW, Baker PJ: Structure
Determination of the Glutamate Dehydrogenase from the Hyperthermophile
Thermococcus litoralis and its Comparison with that from Pyrococcus furiosus.
J.
Mol. Biol. (1999) 293(5) 1121-1132
Maeder DL, Weiss R, Dunn D, Cherry JL, González JM, DiRuggiero
J and Robb FT: Divergence of the hyperthermophilic Archaea, Pyrococcus
furiosus and
Pyrococcus horikoshii, inferred from complete genomic sequences Genetics
(1999) 152, 1299-1305
Vetriani C, Maeder, DL, Tolliday, N, Yip, K-S, Stillman, TJ, Britten,
KL, Rice, D, Klump, HH and Robb FT: Protein Thermostability Above 100°C:
A Key
Role For Ionic Interactions Proc. Nat. Acad. Sci. (USA) (1998), 95, 12300-12305.
González JM, Masuchi Y, Robb FT, Maeder DL, Ammerman JW, Yanagibayashi
M, Tamaoka J, and Kato C: Pyrococcus horikoshii sp. nov., a
hyperthermophilic archaeon isolated from a hydrothermal vent at the Okinawa
Trough. Extremophiles, (1998) 2, 123-130.
Yip KSP, Britton KL, Stillman TJ, Lebbink J, de Vos WM, Robb FT, Vetriani
C, Maeder DL and Rice DW: Insights into the molecular basis of thermal
stability from the analysis of ion-pair networks in the glutamate dehydrogenases.
Eur. J. Biochem. (1998) 255, 336-346.
Robb FT and Maeder DL: Novel evolutionary histories and adaptive features of proteins from hyperthermophiles. Curr. Opin. Biotech. (1998), 9, 288-291.
Vetriani C, Maeder DL, Tolliday N, Yip K-S, Stillman TJ, Britten KL,
Rice D, Klump HH and Robb FT: Improving Enzyme Thermostability: The
Thermococcus litoralis Glutamate Dehydrogenase model. In "New Developments
in Marine Biotechnology". Y. Le Gal and H.O. Halvorson (eds) Plenum
Publishing Corp NY pp. 231-235 (1998)
Maeder DL, Botes D, Sunde M, Matsebula, A., Roseman, A., and Tasker,
J: Design and Synthesis of Peptide Proteinase Inhibitors In: "Perspectives
in Protein
Engineering and Complementary Technologies" (Geisow, M. and Epton,
R., Eds.), Mayflower Worldwide Ltd., pp. 23-26 (1995)
Henderson HE, Ma Y, Liu M-S, Clark-Lewis I, Maeder DL, Kastelein JJP,
Brunzell JD and Hayden MR: Structure-function relationships of lipoprotein
lipase:
mutation analysis and mutagenesis of the loop region. J. Lipid Research
(1993) 34, 1593-1602
Caldwell JAR and Maeder DL: 3-D Visualization of the Intrinsic Shape
of the Small Magellanic Cloud In: "Variable Stars and Galaxies".
(Warner, B. ed.) ASP
Conference Series 30, 173-178 (1992)
Maeder DL, Sunde M and Botes DP: The Design and Inhibitory Properties
of Synthetic Bowman-Birk loops. Int. J. of Peptide & Protein Research
(1992) 40,
97-102
Blow DM, Shaw-Stewart PD, and Maeder DL: IMPAX Crystallisation method apparatus (1992) UK Patent GB 2 249 492
Klump HH, Völker J, Maeder DL, Niermann T, and Sobolewski C: Conformational
Changes in Nucleic Acids/Chromatin Structure Theoret. Chim. Acta
(1991) 193, 391-415
Klump HH and Maeder DL: The thermodynamic basis of the genetic code. Pure and Applied Chemistry (1991) 63, 1357-1366
Maeder DL, Sturrock ED and Kirsch RE: Subcellular Distribution of Asialoglycoprotein
Receptor in Liver Regeneration. S.A. Medical Journal (1991) 80,
195-197
Lindsey GG, Orgeig S, Thomson P, Davies N and Maeder DL: The C-terminal
extension of wheat histone H2A interacts with DNA of the "linker"
region. J.
Mol. Biol. (1991) 218, 805-813
Maeder DL and Böhm L: The C-domain in the H1 Histones is structurally conserved. Biophys. et Biochim. Acta (1991) 1076, 233-238
Chayen NE, Shaw Stewart PD, Maeder DL and Blow DM: An automated system
for micro-batch protein crystallisation and screening. J. Appl. Cryst.
(1990)
23, 297-302
Onesti S, Lloyd LF, Maeder DL, Mistry A, Brick P and Blow D: Crystallisation
and Preliminary Diffraction Studies of Erythrina Trypsin Inhibitor J.Mol.Biol.
(1989) 210, 241-242
Sturrock ED, Meissner PN, Maeder DL, and Kirsch RE: Uroporphyrinogen
decarboxylase and Protoporphyrinogen oxidase in dual porphyria. S.A.Medical
Journal (1989) 76, 405-408
Maeder DL: (1988-1991) XSTEP Automated Micro-batch Crystallisation Controller. Disoft, 25J Thames House, 140 Battersea Rd., London SW11 4NB
Maeder DL: (1988-1991) SAGA!! A Software package for Protein Sequence Analysis. Disoft, 25J Thames House, 140 Battersea Rd., London SW11 4NB
Böhm L, Sautiere P, Cary PD, and Maeder DL: (1988) Histone H1 structure
probed by Staphylococcus Aureus V8- proteinase. Biochim. et Biophys. Acta
(1988) 956, 224-231
Kruskal JB, Maeder DL, Purves LR, Franks JJ and Kirsch RE: A diazophenylthio-ether-IgG
probe for analysing fibrin- and fibrinogen- related antigens.
S.A.Medical Journal (1987) 71, 211-217
Ehlers MR, Maeder DL, and Kirsch RE: Rapid affinity chromatographic purification
of human lung and kidney angiotensin-converting enzyme with the novel
N-carboxyalkyl dipeptide inhibitor N-[1( S) -carboxy-5-aminopentyl]glycylglycine.
Biochim. et Biophys. Acta (1986) 883, 361-372
Maeder DL: Liver Regeneration In: "Liver Update 2 Proceedings of
an International Symposium on Recent Advances in Liver Physiology and
Disease"
R.E.Kirsch, J.B.Kruskal, G.Csomos and J.Terblanche (eds.) Bailliere Tindall
(London) p125 (1985)