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Protein evolution and folding. computational de novo design of proteins and biomimeticsProject 1: Learning Tolerance From Proteins
The sequence of a natural protein is just one of a large subset of allowed
sequences that result in a functional molecule. While a sequence has been
optimized for function. it also must be an evolvable sequence - one that can
easily mutate in response to evolutionary pressures without radical perturbation
of structure or function. An optimal protein is one that not only is functional
but also is well connected to neighboring sequences. giving mutational pathways
for adaptation to traverse. Our lab will investigate the extent of these
limitations using novel computational protein design algorithms. bioinformatic
tools and protein library screening methods. Large scale mutagenesis studies of
proteins have demonstrated a remarkable malleability of a protein sequence to
change without disruption of structure. This begs the question - if proteins are
so accommodating to mutation. why is the de novo design of proteins challenging? Project 2: Design of Heterochiral ProteinsTremendous progress has been made in the rational and computational de novo design of proteins with novel structure and function. Many of the tools used in design are parameterized using the wealth of structural information in the Protein Data Bank (PDB). It would be useful to extend these methods to the design of synthetic folding polymers - foldamers. However. it is important to ask the question: How generally applicable is our accumulated structural and physical understanding of protein design?
We address this question by developing protein structure inspired computational methods towards the design of novel protein-like molecules where backbone stereochemistry is variable using a protocol that concurrently optimizes both structure and sequence. Nature occasionally makes use of short heterochiral peptides in the design of antimicrobials with novel secondary structures. Using chemical peptide synthesis. it is possible to build much larger molecules. extending the potential for heterochiral peptides to the design of new tertiary folds unprecedented in nature. We will design and characterize novel heterochiral polypeptide folds for stability and structure. The project consists of three major aims: One aim is to develop computational methods for designing heterochiral peptides using tools derived from de novo protein design. Goals include the development of backbone and sidechain energy potentials for rapid and accurate scoring of potential structures. These potentials will then be used to build a heterochiral peptide fragment library of secondary structure elements. Elements from the library can then be assembled into larger tertiary folds. Additionally. we plan to explore the rules of capping interactions in heterochiral peptides. In natural proteins. capping interactions stabilize helices and prevent fraying of the termini. A novel bent-helix structure predicted from simulations will be designed and synthesized. Based on modeling studies. a series of hinge capping residues that bridge the bent helix ends will be engineered and evaluated for stability and structural specificity. Finally. we will focus on the design of novel tertiary folds using our simulation methods. A heterochiral bundle consisting of alpha left and alpha right-helices will be designed and characterized. The design will be extended to the molecular recognition of the Lac-repressor tetramerization domain. with the intention of disrupting the protein-protein interface by competing heterochiral interactions. Selected PublicationsAnnavarapu S, Nanda V. (2009) Mirrors in the PDB: left-handed alpha-turns guide design with D-amino acids. BMC Struct Biol. 9:61. Kar K, Ibrar S, Nanda V, Getz TM, Kunapuli SP, Brodsky B. (2009) Aromatic interactions promote self-association of collagen triple-helical peptides to higher-order structures. Schmiedekamp A, Nanda V. (2009) Metal-activated histidine carbon donor hydrogen bonds contribute to metalloprotein folding and function. J Inorg Biochem. 103(7):1054-60. McAllister KA, Zou H, Cochran FV, Bender GM, Senes A, Fry HC, Nanda V, Keenan PA, Lear JD, Saven JG, Therien MJ, Blasie JK, DeGrado WF. (2008) Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays. J Am Chem Soc. 130(36):11921-7. Nanda V. (2008) Do-it-yourself enzymes. Nat Chem Biol. 4(5):273-5. Stouffer AL, Acharya R, Salom D, Levine AS, Di Costanzo L, Soto CS, Tereshko V, Nanda V, Stayrook S, DeGrado WF. (2008) Structural basis for the function and inhibition of an influenza virus proton channel. Nature. 451(7178):596-9. Erratum in: Nature. 2008 Mar Nanda V, Schmiedekamp A. (2008) Are aromatic carbon donor hydrogen bonds linear in proteins? Proteins. 70(2):489-97. Nanda V, Andrianarijaona A, Narayanan C. (2007) The role of protein homochirality in shaping the energy landscape of folding. Protein Sci. 16(8):1667-75. Senes A, Chadi DC, Law PB, Walters RF, Nanda V, Degrado WF. (2007) E(z), a depth-dependent potential for assessing the energies of insertion of amino acid side-chains into membranes: derivation and applications to determining the orientation of transmembrane and interfacial helices. J Mol Biol. 366(2):436-48. Tatko CD. Nanda V. Lear JD. Degrado WF. (2006) Polar networks control oligomeric assembly in membranes. J Am Chem Soc. 128(13):4170-1. Nanda V. DeGrado WF. (2006) Computational design of heterochiral peptides against a helical target. J Am Chem Soc. 128(3):809-16.
Nanda. V. Rosenblatt. MM. Osyczka. A. Kono. H. Getahun. Z. Dutton. PL. Saven. JG. DeGrado. WF. (2005) De novo design of a Redox-active minimal Rubredoxin mimic.
JACS. 127:5804-5. Cristian. L. Nanda. V. Lear. JD. DeGrado,WF. (2005) Synergistic interactions between aqueous and membrane domains of a designed protein determine its fold and stability. J. Mol. Biol. 348: 1225-33. http://dx.doi.org/10.1016/j.jmb.2005.03.053 Cochran. FV. Wu. S. Wang. W. Nanda. V. Saven. JG. Therien. MJ. DeGrado. WF. (2005) Computational de novo design and characterization of a four-helix bundle protein that selectively binds a non-biological cofactor. JACS. 127:1346-7.http://dx.doi.org/10.1021/ja044129a Nanda. V. DeGrado. WF. (2005) Automated use of mutagenesis data in structure prediction. Proteins. 59:454-66.http://dx.doi.org/10.1002/prot.20382 Nanda. V. DeGrado. WF. (2004) Simulated evolution of emergent chiral structures in Polyalanine. JACS. 126:14459-67. http://dx.doi.org/10.1021/ja0461825
Nanda. V. Brand. L. (2000) Aromatic interactions in homeodomains contribute to
the low quantum yield of a conserved. buried Tryptophan. Proteins. 40:112-25.
Nanda. V. Liang. S-M. Brand. L. (2000) Hydrophobic clustering in acid-denatured
IL-2 and fluorescence of a Trp NH-pi H-bond. Biochem. Biophys. Res. Comm.
279:770-8. Adamian. L. Nanda. V. DeGrado. WF. Liang. J. (2005) Empirical lipid propensities of amino acid residues in multispan helical membrane proteins. Proteins. 59:496-509.http://dx.doi.org/10.1002/prot.20456
Stouffer. A. Nanda. V. Lear. JD. DeGrado. WF (2005) Sequence determinants of a
membrane proton channel: An inverse relationship between stability and function.
J. Mol. Biol. 347:169-79. |
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