Structure from function: screening structural models with functional data

Dissecting single-molecule signal transduction in carbon nanotube circuits with protein engineering

Single-molecule experimental methods have provided new insights into biomolecular function, dynamic disorder, and transient states that are all invisible to conventional measurements. A novel, nonfluorescent single-molecule technique involves attaching single molecules to single-walled carbon nanotube field-effective transistors (SWNT FETs). These ultrasensitive electronic devices provide long-duration, label-free monitoring of biomolecules and their dynamic motions. However, generalization of the SWNT FET technique first requires design rules that can predict the success and applicability of these devices. Here, we report on the transduction mechanism linking enzymatic processivity to electrical signal generation by a SWNT FET. The interaction between SWNT FETs and the enzyme lysozyme was systematically dissected using eight different lysozyme variants synthesized by protein engineering. The data prove that effective signal generation can be accomplished using a single charged amino acid, when appropriately located, providing a foundation to widely apply SWNT FET sensitivity to other biomolecular systems.

From words to literature in structural proteomics

Technical advances on several frontiers have expanded the applicability of existing methods in structural biology and helped close the resolution gaps between them. As a result, we are now poised to integrate structural information gathered at multiple levels of the biological hierarchy - from atoms to cells - into a common framework. The goal is a comprehensive description of the multitude of interactions between molecular entities, which in turn is a prerequisite for the discovery of general structural principles that underlie all cellular processes.

Differential Induction of Long-Term Synaptic Facilitation by Spaced and Massed Applications of Serotonin at Sensory Neuron Synapses of Aplysia californica

Serotonin (5HT)-induced facilitation of synaptic transmission from tail sensory neurons (SNs) to motor neurons (MNs) in the marine mollusc Aplysia provides a cellular model of short- and long-term memory for behavioral sensitization of the tail withdrawal reflex. Synaptic facilitation at these synapses occurs in three temporal phases: short-term (STF, lasting minutes), intermediate-term (ITF, lasting more than an hour), and long-term (LTF, lasting >24 hr). STF, ITF, and LTF differ in their induction requirements: A single brief exposure of 5HT induces STF, whereas five applications are required for ITF and LTF. Moreover, STF and LTF can be induced independently.

Different forms of memory often show differential sensitivity to the pattern of training trials. To begin to explore this effect at a cellular level, we examined ITF and LTF induced by one of two patterns of 5HT application: a spaced pattern (five 5-min exposures with an interval of 15 min) or a massed pattern (one continuous 25-min application). The spaced and massed patterns both induced ITF; however, spaced 5HT application was significantly more reliable at inducing LTF than was massed application. Thus, whereas induction of ITF and LTF require similar amounts of 5HT, the cellular mechanisms underlying the induction of LTF are more sensitive to the pattern of the induction trials. In the massed group, further analysis revealed a relationship between the expression of ITF and the subsequent expression of LTF, suggesting that these two processes may be mechanistically related.

The pore-lining region of shaker voltage-gated potassium channels: comparison of beta-barrel and alpha-helix bundle models

Although there is a large body of site-directed mutagenesis data that identify the pore-lining sequence of the voltage-gated potassium channel, the structure of this region remains unknown. We have interpreted the available biochemical data as a set of topological and orientational restraints and employed these restraints to produce molecular models of the potassium channel pore region, H5. The H5 sequence has been modeled either as a tetramer of membrane-spanning beta-hairpins, thus producing an eight-stranded beta-barrel, or as a tetramer of incompletely membrane-spanning alpha-helical hairpins, thus producing an eight-staved alpha-helix bundle. In total, restraints-directed modeling has produced 40 different configurations of the beta-barrel model, each configuration comprising an ensemble of 20 structures, and 24 different configurations of the alpha-helix bundle model, each comprising an ensemble of 24 structures. Thus, over 1300 model structures for H5 have been generated. Configurations have been ranked on the basis of their predicted pore properties and on the extent of their agreement with the biochemical data. This ranking is employed to identify particular configurations of H5 that may be explored further as models of the pore-lining region of the voltage-gated potassium channel pore.

Recognition of porcine growth hormone by a panel of monoclonal antibodies

A panel of murine monoclonal antibodies (MAbs) against porcine growth hormone (pGH) has been raised from BALB/c mice. MAbs were characterized for binding to growth hormones (GH), prolactins (PRL), and placental lactogen (PL) from different species and to the N-terminal peptides of GH. From their patterns of cross-reactivity MAbs were assigned into nine specificity groups. The sharing of pGH epitopes among hormones of different species was related to the sequence similarity to pGH, i.e., overlap was greatest for equine, ruminant, and rodent GHs and least for human GH, ovine, and porcine PRLs, and human PL. Partial epitope mapping was carried out by relating hormone cross-reactivity patterns with amino acid sequences. Two epitopes were localized to interhelical loops, around valine-73 and glycine-130, respectively. Direct mapping with synthetic peptides localized other epitopes (Groups 7, 8, and 9) to the N-terminal region of the GH molecule. Selected MAbs were studied for the enhancement of the somatogenic activity of pGH in the dwarf mouse bioassay, measuring weight gain and sulphate incorporation into costal cartilage. Only those antibodies with specificities for GHs and not PRL or PL showed significant enhancement in this assay.

Relationship between protein structure and geometrical constraints

We evaluate to what extent the structure of proteins can be deduced from incomplete knowledge of disulfide bridges, surface assignments, secondary structure assignments, and additional distance constraints. A cost function taking such constraints into account was used to obtain protein structures using a simple minimization algorithm. For small proteins, the approximate structure could be obtained using one additional distance constraint for each amino acid in the protein. We also studied the effect of using predicted secondary structure and surface assignments. The constraints used in this approach typically may be obtained from low-resolution experimental data. When using a cost function based on distances, half of the resulting structures will be mirrored, because the resulting structure and its mirror image will have the same cost. The secondary structure assignments were therefore divided into chirality constraints and distance constraints. Here we report that the problem of mirrored structures, in some cases, can be solved by using a chirality term in the cost function.

Prediction of the secondary structure of HIV-1 gp120

The secondary structure of HIV-1 gp120 was predicted using multiple alignment and a combination of two independent methods based on neural network and nearest-neighbor algorithms. The methods agreed on the secondary structure for 80% of the residues in BH10 gp120. Six helices were predicted in HIV strain BH10 gp120, as well as in 27 other HIV-1 strains examined. Two helical segments were predicted in regions displaying profound sequence variation, one in a region suggested to be critical for CD4 binding. The predicted content of helix, beta-strand, and coil was consistent with estimates from Fourier transform infrared spectroscopy. The predicted secondary structure of gp120 compared well with data from NMR analysis of synthetic peptides from the V3 loop and the C4 region. As a first step towards modeling the tertiary structure of gp120, the predicted secondary structure may guide the design of future HIV subunit vaccine candidates.

Molecular recognition of lysozyme by monoclonal antibodies

HEL was one of the first proteins to be mapped antigenically using mAb, and panels of mAb have been used as a measure of antigenicity in order to study regulation of the immune response and the apparent 'antigenic structure' of HEL. These studies have confirmed the multideterminant hypothesis derived from pAb. However, although the entire surface of HEL is potentially antigenic, the mature immune response appears to be dominated by three functionally nonoverlapping antigenic regions, defined operationally by antibody complementation assays. Recent structural studies have confirmed the existence of three distinct epitope clusters. Functional epitopes, defined by immunoassays, are generally only a subset of the structural epitope, the 14-17 amino acid residues which contact antibody in the X-ray structure of the complex. An even smaller subset of 'critical residues', the 'energetic' epitope, may predominate the interaction energetically. Antibody complex formation with HEL is enthalpically driven, and is accompanied by an unfavorable entropy change. Mutations of either antibody or antigen which lower affinity appear to do so primarily by increasing dissociation rates, and also appear to be accompanied by entropy/enthalpy compensation. The current availability of six structurally defined antibody-lysozyme complexes presents excellent opportunities for comparative studies in order to understand the structural bases of affinity, specificity, and thermodynamic properties, as well as the interrelationships of functional, structural, and energetic epitopes.

Evaluation of current techniques for ab initio protein structure prediction

The results of a protein structure prediction contest are reviewed. Twelve different groups entered predictions on 14 proteins of known sequence whose structures had been determined but not yet disseminated to the scientific community. Thus, these represent true tests of the current state of structure prediction methodologies. From this work, it is clear that accurate tertiary structure prediction is not yet possible. However, protein fold and motif prediction are possible when the motif is recognizable similar to another known structure. Internal symmetry and the information inherent in an aligned family of homologous sequences facilitate predictive efforts. Novel folds remain a major challenge for prediction efforts.