James U. Bowie

The Database of Interacting Proteins: 2004 update

The Database of Interacting Proteins (http://dip.doe-mbi.ucla.edu) aims to integrate the diverse body of experimental evidence on protein-protein interactions into a single, easily accessible online database. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks.

VERIFY3D : ASSESSMENT OF PROTEIN MODELS WITH THREE-DIMENSIONAL PROFILES

Publisher Summary The three-dimensional (3D) profile of a protein structure is a table computed from the atomic coordinates of the structure that can be used to score the compatibility of the 3D structure model with any amino acid sequence. Three-dimensional profiles computed from correct protein structures match their own sequences with high scores. An incorrectly modeled segment in an otherwise correct structure can be identified by examining the profile score in a moving-window scan. Thus, the correctness of a protein model can be verified by its 3D profile, regardless of whether the model has been derived by X-ray, nuclear magnetic resonance (NMR), or computational procedures. For this reason, 3D profiles are useful in the evaluation of undetermined protein models, based on low-resolution electron-density maps, on NMR spectra with inadequate distance constraints, or on computational procedures. An advantage of using 3D profiles for testing models is that profiles have not themselves been used in the determination of the structure. Traditional R -factor tests in X-ray analysis depend on the comparison of observed properties—that is, the X-ray structure factor magnitudes with the same property calculated from the final protein model.

Solving the membrane protein folding problem

One of the great challenges for molecular biologists is to learn how a protein sequence defines its three-dimensional structure. For many years, the problem was even more difficult for membrane proteins because so little was known about what they looked like. The situation has improved markedly in recent years, and we now know over 90 unique structures. Our enhanced view of the structure universe, combined with an increasingly quantitative understanding of fold determination, engenders optimism that a solution to the folding problem for membrane proteins can be achieved.

Stabilizing membrane proteins.

Membrane proteins can be extremely stable in a bilayer environment, but are often unstable and rapidly lose activity after detergent solubilization. Poor stability can preclude the detailed characterization of many membrane proteins. One way to alleviate this problem is to find more stable mutants of a membrane protein of interest. This approach is made tractable by the finding that stability-enhancing mutations appear to be relatively common in membrane proteins.

The Many Faces of SAM

Protein-protein interactions are essential for the assembly, regulation, and localization of functional protein complexes in the cell. SAM domains are among the most abundant protein-protein interaction motifs in organisms from yeast to humans. Although SAM domains adopt similar folds, they are remarkably versatile in their binding properties. Some identical SAM domains can interact with each other to form homodimers or polymers. In other cases, SAM domains can bind to other related SAM domains, to non–SAM domain–containing proteins, and even to RNA. Such versatility earns them functional roles in myriad biological processes, from signal transduction to transcriptional and translational regulation. In this review, we describe the structural basis of SAM domain interactions and highlight their roles in the scaffolding of protein complexes in normal and pathological processes. Cells need to make appropriate responses to complex signals. One way in which they accomplish this task is by constructing large complexes of macromolecules, bringing together various sensors and effectors that facilitate the integration of input and output. Proteins are often brought into these macromolecular complexes by small modules that have specialized binding properties. The process of evolution can move these modules to different proteins, thereby conferring the distinctive binding properties of the module to new proteins. One particularly versatile protein module is called a SAM domain. SAM domains can associate into long strings containing many SAM domains or into small clusters of only a few SAM domains; they can bind to many different proteins, and they can also bind to RNA. It seems likely that some SAM domains could also provide functions that we do not yet know about. Efforts to learn about these additional functions continue. Ultimately, we would like to know how to predict the function of any SAM domain.

Polymerization of the SAM domain of TEL in leukemogenesis and transcriptional repression

TEL is a transcriptional repressor that is a frequent target of chromosomal translocations in a large number of hematalogical malignancies. These rearrangements fuse a potent oligomerization module, the SAM domain of TEL, to a variety of tyrosine kinases or transcriptional regulatory proteins. The self‐associating property of TEL–SAM is essential for cell transformation in many, if not all of these diseases. Here we show that the TEL–SAM domain forms a helical, head‐to‐tail polymeric structure held together by strong intermolecular contacts, providing the first clear demonstration that SAM domains can polymerize. Our results also suggest a mechanism by which SAM domains could mediate the spreading of transcriptional repression complexes along the chromosome.

Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins.

Understanding the energetics of molecular interactions is fundamental to all of the central quests of structural biology including structure prediction and design, mapping evolutionary pathways, learning how mutations cause disease, drug design, and relating structure to function. Hydrogen-bonding is widely regarded as an important force in a membrane environment because of the low dielectric constant of membranes and a lack of competition from water. Indeed, polar residue substitutions are the most common disease-causing mutations in membrane proteins. Because of limited structural information and technical challenges, however, there have been few quantitative tests of hydrogen-bond strength in the context of large membrane proteins. Here we show, by using a double-mutant cycle analysis, that the average contribution of eight interhelical side-chain hydrogen-bonding interactions throughout bacteriorhodopsin is only 0.6 kcal mol-1. In agreement with these experiments, we find that 4% of polar atoms in the non-polar core regions of membrane proteins have no hydrogen-bond partner and the lengths of buried hydrogen bonds in soluble proteins and membrane protein transmembrane regions are statistically identical. Our results indicate that most hydrogen-bond interactions in membrane proteins are only modestly stabilizing. Weak hydrogen-bonding should be reflected in considerations of membrane protein folding, dynamics, design, evolution and function.

THE SAM DOMAIN OF POLYHOMEOTIC FORMS A HELICAL POLYMER

The polycomb group (PcG) proteins are important in the maintenance of stable repression patterns during development. Several PcG members contain a protein–protein interaction module called a SAM domain (also known as SPM, PNT and HLH). Here we report the high-resolution structure of the SAM domain of polyhomeotic (Ph). Ph-SAM forms a helical polymer structure, providing a likely mechanism for the extension of PcG complexes. The structure of the polymer resembles that formed by the SAM domain of another transcriptional repressor, TEL. The formation of these polymer structures by SAM domains in two divergent repressors suggests a conserved mode of repression involving a higher order chromatin structure.

Transmembrane Domain Helix Packing Stabilizes Integrin αIIbβ3 in the Low Affinity State

Regulated changes in the affinity of integrin adhesion receptors (“activation”) play an important role in numerous biological functions including hemostasis, the immune response, and cell migration. Physiological integrin activation is the result of conformational changes in the extracellular domain initiated by the binding of cytoplasmic proteins to integrin cytoplasmic domains. The conformational changes in the extracellular domain are likely caused by disruption of intersubunit interactions between the α and β transmembrane (TM) and cytoplasmic domains. Here, we reasoned that mutation of residues contributing to α/β interactions that stabilize the low affinity state should lead to integrin activation. Thus, we subjected the entire intracellular domain of the β3 integrin subunit to unbiased random mutagenesis and selected it for activated mutants. 25 unique activating mutations were identified in the TM and membrane-proximal cytoplasmic domain. In contrast, no activating mutations were identified in the more distal cytoplasmic tail, suggesting that this region is dispensable for the maintenance of the inactive state. Among the 13 novel TM domain mutations that lead to integrin activation were several informative point mutations that, in combination with computational modeling, suggested the existence of a specific TM helix-helix packing interface that maintains the low affinity state. The interactions predicted by the model were used to identify additional activating mutations in both the α and β TM domains. Therefore, we propose that helical packing of the α and β TM domains forms a clasp that regulates integrin activation.

Building a Thermostable Membrane Protein

The poor stability of membrane proteins in detergent solution is one of the main technical barriers to their structural and functional characterization. Here we describe a solution to this problem for diacylglycerol kinase (DGK), an integral membrane protein from Escherichia coli. Twelve enhanced stability mutants of DGK were obtained using a simple screen. Four of the mutations were combined to create a quadruple mutant that had improved stability in a wide range of detergents. Inn-octylglucoside, the wild-type DGK had a thermal inactivation half-life of 6 min at 55 °C, while the quadruple mutant displayed a half-life of 35 min at 80 °C. In addition, the quadruple mutant had improved thermodynamic stability. Our approach should be applicable to other membrane proteins that can be conveniently assayed.