Jeffrey L. Mills

Creating nanocavities of tunable sizes: Hollow helices

A general strategy for creating nanocavities with tunable sizes based on the folding of unnatural oligomers is presented. The backbones of these oligomers are rigidified by localized, three-center intramolecular hydrogen bonds, which lead to well-defined hollow helical conformations. Changing the curvature of the oligomer backbone leads to the adjustment of the interior cavity size. Helices with interior cavities of 10 Å to >30 Å across, the largest thus far formed by the folding of unnatural foldamers, are generated. Cavities of these sizes are usually seen at the tertiary and quaternary structural levels of proteins. The ability to tune molecular dimensions without altering the underlying topology is seen in few natural and unnatural foldamer systems.

Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer.

Computationally designing protein-protein interactions with high affinity and desired orientation is a challenging task. Incorporating metal-binding sites at the target interface may be one approach for increasing affinity and specifying the binding mode, thereby improving robustness of designed interactions for use as tools in basic research as well as in applications from biotechnology to medicine. Here we describe a Rosetta-based approach for the rational design of a protein monomer to form a zinc-mediated, symmetric homodimer. Our metal interface design, named MID1 (NESG target ID OR37), forms a tight dimer in the presence of zinc (MID1-zinc) with a dissociation constant <30 nM. Without zinc the dissociation constant is 4 μM. The crystal structure of MID1-zinc shows good overall agreement with the computational model, but only three out of four designed histidines coordinate zinc. However, a histidine-to-glutamate point mutation resulted in four-coordination of zinc, and the resulting metal binding site and dimer orientation closely matches the computational model (Cα rmsd = 1.4 Å).

Protein dynamics in supercooled water: The search for slow motional modes

The impact of studying protein dynamics in supercooled water for identifying slow motional modes on the μs time scale is demonstrated. Backbone 15N spin relaxation parameters were measured at −13 °C for ubiquitin, which plays a central role for signaling proteolysis, cellular trafficking and kinase activation in eukaryotic organisms. A hitherto undetected motional mode involving Val 70 was found, which may well play an important role for ubiquitin recognition. The measurement of rotating frame 15N relaxation times as a function of the spin-lock field allowed determination of the correlation time of this motional mode, which would not have been feasible above 0 °C.

Accurate protein structure modeling using sparse NMR data and homologous structure information

While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining , 13C, and 15N backbone and 13Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2–1.9 Å relative to the conventional determined NMR ensembles and of 0.9–1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.

Combined NMR-observation of cold denaturation in supercooled water and heat denaturation enables accurate measurement of ΔCp of protein unfolding

Cold and heat denaturation of the double mutant Arg 3→Glu/Leu 66→Glu of cold shock protein Csp of Bacillus caldolyticus was monitored using 1D 1H NMR spectroscopy in the temperature range from −12°C in supercooled water up to +70°C. The fraction of unfolded protein, fu, was determined as a function of the temperature. The data characterizing the unfolding transitions could be consistently interpreted in the framework of two-state models: cold and heat denaturation temperatures were determined to be −11°C and 39°C, respectively. A joint fit to both cold and heat transition data enabled the accurate spectroscopic determination of the heat capacity difference between native and denatured state, ΔCp of unfolding. The approach described in this letter, or a variant thereof, is generally applicable and promises to be of value for routine studies of protein folding.

Adenovirus RIDα regulates endosome maturation by mimicking GTP-Rab7

The small guanosine triphosphatase Rab7 regulates late endocytic trafficking. Rab7-interacting lysosomal protein (RILP) and oxysterol-binding protein–related protein 1L (ORP1L) are guanosine triphosphate (GTP)–Rab7 effectors that instigate minus end–directed microtubule transport. We demonstrate that RILP and ORP1L both interact with the group C adenovirus protein known as receptor internalization and degradation α (RIDα), which was previously shown to clear the cell surface of several membrane proteins, including the epidermal growth factor receptor and Fas (Carlin, C.R., A.E. Tollefson, H.A. Brady, B.L. Hoffman, and W.S. Wold. 1989. Cell. 57:135–144; Shisler, J., C. Yang, B. Walter, C.F. Ware, and L.R. Gooding. 1997. J. Virol. 71:8299–8306). RIDα localizes to endocytic vesicles but is not homologous to Rab7 and is not catalytically active. We show that RIDα compensates for reduced Rab7 or dominant-negative (DN) Rab7(T22N) expression. In vitro, Cu2+ binding to RIDα residues His75 and His76 facilitates the RILP interaction. Site-directed mutagenesis of these His residues results in the loss of RIDα–RILP interaction and RIDα activity in cells. Additionally, expression of the RILP DN C-terminal region hinders RIDα activity during an acute adenovirus infection. We conclude that RIDα coordinates recruitment of these GTP-Rab7 effectors to compartments that would ordinarily be perceived as early endosomes, thereby promoting the degradation of selected cargo.

NMR-based structural biology of proteins in supercooled water

NMR-based structural biology of proteins can be pursued efficiently in supercooled water at temperatures well below the freezing point of water. This enables one to study protein structure, dynamics, hydration and cold denaturation in an unperturbed aqueous solution at very low temperatures. Furthermore, such studies enable one to accurately measure thermodynamic parameters associated with protein cold denaturation. Presently available approaches to acquire NMR data for supercooled aqueous protein solutions are surveyed, new insights obtained from such studies are summarized, and future perspectives are discussed.

Annotation of proteins of unknown function: initial enzyme results.

Working with a combination of ProMOL (a plugin for PyMOL that searches a library of enzymatic motifs for local structural homologs), BLAST and Pfam (servers that identify global sequence homologs), and Dali (a server that identifies global structural homologs), we have begun the process of assigning functional annotations to the approximately 3,500 structures in the Protein Data Bank that are currently classified as having “unknown function”. Using a limited template library of 388 motifs, over 500 promising in silico matches have been identified by ProMOL, among which 65 exceptionally good matches have been identified. The characteristics of the exceptionally good matches are discussed.

Resonance assignments for the hypothetical protein yggU from Escherichia coli.

James M. Araminia, Jeffrey L. Millsb, Rong Xiaoa, Thomas B. Actona, Maggie J. Wua, Thomas Szyperskib & Gaetano T. Montelionea,c,∗ aCenter for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, and Northeast Structural Genomics Consortium, U.S.A.; bDepartment of Chemistry and Structural Biology, The State University of New York, Buffalo, NY 14260, and Northeast Structural Genomics Consortium, U.S.A.; cDepartment of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway, NJ 08854, U.S.A.

A community resource of experimental data for NMR / X‐ray crystal structure pairs

We have developed an online NMR / X‐ray Structure Pair Data Repository. The NIGMS Protein Structure Initiative (PSI) has provided many valuable reagents, 3D structures, and technologies for structural biology. The Northeast Structural Genomics Consortium was one of several PSI centers. NESG used both X‐ray crystallography and NMR spectroscopy for protein structure determination. A key goal of the PSI was to provide experimental structures for at least one representative of each of hundreds of targeted protein domain families. In some cases, structures for identical (or nearly identical) constructs were determined by both NMR and X‐ray crystallography. NMR spectroscopy and X‐ray diffraction data for 41 of these “NMR / X‐ray” structure pairs determined using conventional triple‐resonance NMR methods with extensive sidechain resonance assignments have been organized in an online NMR / X‐ray Structure Pair Data Repository. In addition, several NMR data sets for perdeuterated, methyl‐protonated protein samples are included in this repository. As an example of the utility of this repository, these data were used to revisit questions about the precision and accuracy of protein NMR structures first outlined by Levy and coworkers several years ago (Andrec et al., Proteins 2007;69:449–465). These results demonstrate that the agreement between NMR and X‐ray crystal structures is improved using modern methods of protein NMR spectroscopy. The NMR / X‐ray Structure Pair Data Repository will provide a valuable resource for new computational NMR methods development.