Kelly M. Elkins


Annual Report for EML and EMBL: Rebecca Wade's Group


2001 Publications


    1.K.M. Elkins, P.Z. Gatzeva-Topalova, and D.J. Nelson, Molecular Dynamics Study of Ca2+ Binding Loop Variants of Parvalbumin with Modifications at the 'Gateway' Position. Protein Engineering 14, 115-126 (2001).


    2.K.M. Elkins, K. Fahie, R. Pitts, S.P. Revett, and D.J. Nelson, Molecular Dynamics Simulations and Metal Binding Properties of Mutational Variants of a Functional Fragment of Silver Hake Parvalbumin (Isoform B). Journal of Biomolecular Structure and Dynamics 18, 938 (Abstract) (2001).


    3.K.M. Elkins and D.J. Nelson, Fluorescence and FT-IR Spectroscopic Studies of Suwannee River Fulvic Acid Complexation with Aluminum, Terbium and Calcium. Journal of Inorganic Biochemistry 87, 81-96 (2001).


    4.K. Fahie, R. Pitts, K.M. Elkins, and D.J. Nelson, Molecular Dynamics Study of Ca2+ Binding Loop Variants of Silver Hake Parvalbumin with Aspartic Acid at the Gateway Position. Journal of Biomolecular Structure and Dynamics, (2001), accepted.


    5.K.M. Elkins and D.J. Nelson, Spectroscopic Approaches to the Study of the Interaction of Aluminum with Humic Substances. Coordination Chemistry Reviews, (2001), submitted.



2001 Presentations


in BOLD were the group members present at the meetings


K.M. Elkins, S. Dunn, G. Rolle, and D.J. Nelson, Fulvic Acid Complexes with Aluminum, Lanthanum, and Terbium, platform presentation at The 4th Keele Meeting on Aluminium: The Biological Availability of Aluminium: Sources, Sinks and Symptoms (Stoke-on-Trent, England), February 25, 2001.


K.M. Elkins, K. Fahie, R. Pitts, S.P. Revett, and D.J. Nelson, Molecular Dynamics Simulations and Metal Binding Properties of a Wild-Type and Mutational Variants of Functional Fragments of Silver Hake Parvalbumin (Isoform B), poster presentation at Albany 2001 (Albany, NY): The 12th Conversation in Biomolecular Stereodynamics, June 20, 2001.



2001 Projects


  1. Computational study of the calcium-binding ability of computational site-directed mutants at the gateway position of a parvalbumin from the Silver Hake (SHPV-B) as evaluated using molecular mechanics calculations and molecular dynamics simulations

  2. Studies of metal-binding to Suwannee River Fulvic Acids (SRFA) using FT-IR, Fluorescence, and solid state NMR spectroscopy

  3. Computational study of the GTP-binding and association of the Escherichia coli signal recognition particle (Ffh*4.5S RNA) and its receptor (FtsY)



Applications


Computational Study of the Signal Recognition Particle


Signal recognition particle (SRP) proteins are GTP-binding proteins necessary for proper export/transport of secretory and plasma membrane proteins. Failure of this system results in diseases such as cystic fibrosis. Understanding the SRP is, therefore, the subject of intensive medical research as this transport system is a potential target for drug design. The structures of various GTP/Mg2+-binding (NG) domain SRP proteins have been solved by x-ray crystallography by the groups of Irmgard Sinning (EMBL-Heidelberg), Stephen Cusack (EMBL-Grenoble), Douglas Freymann (Northwestern University), Peter Walter (UCSF), and Jennifer Doudna (Yale). This project is a collaboration with the Sinning group. The available structures have all been solved without any nucleotide triphosphate or metal present or with only a GTP homologue, GDP, or GDP/Mg2+ present. No structures are available of SRP proteins in the presence of the activating GTP/Mg2+. Likewise, an interesting model of the association of the SRP and SRP receptor has been proposed by the Sinning group. However, this model fails to consider the conformational change that must occur upon binding Mg2+/GTP. It was also prepared without the M domain of Ffh entirely, without the M domain complexed with a signal peptide, without the 4.5S RNA, and without the acidic, membrane-associating, A domain of FtsY. The bacterial SRP found in Escherichia coli consists of a the Ffh protein and an 4.5 S RNA and a receptor protein, FtsY. This system is homologous, but simpler, than the one found in humans and, therefore, makes an excellent model for study and understanding the SRP mode of transport. Using the available crystal structure from the Sinning group of E. coli FtsY without nucleotide triphosphate (apo-form) and a model of the apo-Ffh for E. coli that we have made using crystal structures of the same protein from Thermus aquaticus (Walter group) and Acidianus ambivalens (Sinning group), we will dock GTP and Mg2+ to the two proteins using a docking program. The structures will then be sujected to energy minimization. This will enable us to study conformational changes in the two proteins upon nucleotide triphosphate binding. Preliminary examination of the apo-forms of Ffh and FtsY using UHBD to study the electrostatic surfaces suggests a potential surfaces in the two proteins where they may associate. It is known that the fully active forms of these proteins occur when the proteins form a complex and Ffh is bound also to a 4.5S RNA. Using these GTP/Mg2+-bound models, we will model an active complex between these two proteins and the required 4.5 S RNA by studying the electrostatics of the protein surfaces and using data available from experimental studies. This modeled active complex should prove useful in understanding how the components of the SRP interact to transport other proteins within and out of the cell.





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