We propose a method of quantifying the degree of frustration manifested by spatially local interactions in protein biomolecules. This method of localization smoothly generalizes the global criterion for an energy landscape to be funneled to the native state, which is in keeping with the principle of minimal frustration. A survey of the structural database shows that natural proteins are multiply connected by a web of local interactions that are individually minimally frustrated. In contrast, highly frustrated interactions are found clustered on the surface, often near binding sites. These binding sites become less frustrated upon complex formation.protein folding ͉ protein function ͉ energy landscape

Several complementary physical techniques have been used to characterize the aggregate structures formed in solutions containing dimyristoylphosphatidylcholine (DMPC)/dihexanoylphosphatidylcholine (DHPC) at ratios of < or =0.5 and to establish their morphology and lipid organization as that of bicelles. (31)P NMR studies showed that the DMPC and DHPC components were highly segregated over a wide range of DMPC/DHPC ratios (q = 0.05-0.5) and temperatures (15 degrees C and 37 degrees C). Only at phospholipid concentrations below 130 mM did the bicelles appear to undergo a change in morphology. These results were corroborated by fluorescence data, which demonstrated the inverse dependence of bicelle size on phospholipid concentration as well as a distinctive change in phospholipid arrangement at low concentrations. In addition, dynamic light scattering and electron microscopy studies supported the hypothesis that the bicellar phospholipid aggregates are disk-shaped. The radius of the planar domain of the disk was found to be directly proportional to the ratio of DMPC/DHPC and inversely proportional to the total phospholipid concentration when the DMPC/DHPC ratio was held constant at 0.5. Taken together, these results suggest that bicelles with low q retain the morphology and bilayer organization typical of their liquid-crystalline counterparts, making them useful membrane mimetics.

Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their own structures and dynamics using as input seemingly random character strings of their sequence, following which they coalesce and perform integrated cellular functions. In large computational systems with a finite interaction-codes, the appearance of conflicting goals is inevitable. Simple conflicting forces can lead to quite complex structures and behaviors, leading to the concept of frustration in condensed matter. We present here some basic ideas about frustration in biomolecules and how the frustration concept leads to a better appreciation of many aspects of the architecture of biomolecules, and how biomolecular structure connects to function. These ideas are simultaneously both seductively simple and perilously subtle to grasp completely. The energy landscape theory of protein folding provides a framework for quantifying frustration in large systems and has been implemented at many levels of description. We first review the notion of frustration from the areas of abstract logic and its uses in simple condensed matter systems. We discuss then how the frustration concept applies specifically to heteropolymers, testing folding landscape theory in computer simulations of protein models and in experimentally accessible systems. Studying the aspects of frustration averaged over many proteins provides ways to infer energy functions useful for reliable structure prediction. We discuss how frustration affects folding mechanisms. We review here how a large part of the biological functions of proteins are related to subtle local physical frustration effects and how frustration influences the appearance of metastable states, the nature of binding processes, catalysis and allosteric transitions. We hope to illustrate how Frustration is a fundamental concept in relating function to structural biology.

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) was used to determine amide proton/deuteron (H/D) exchange rates. The method has broad application to the study of protein conformation and folding and to the study of protein-ligand interactions and requires no modifications of the instrument. Amide protons were allowed to exchange with deuterons in buffered D2O at room temperature, pD 7.25. Exchanged deuterons were "frozen" in the exchanged state by quenching at pH 2.5, 0 degree C and analyzed by MALDI-TOF MS. The matrix mixture consisted of 5 mg/mL alpha-cyano-4-hydroxycinnamic acid, acetonitrile, ethanol, and 0.1% TFA. The matrix was adjusted to pH 2.5, and the chilled MALDI target was rapidly dried. Deuteration of amide protons on cyclic AMP-dependent protein kinase was measured after short times of incubation in deuterium by pepsin protein digestion and MALDI-TOF MS analysis. The unseparated peptic digest was analyzed in a single spectrum of the mixture. From five spectra, H/D exchange rates were determined for some 40 peptides covering 65% of the protein sequence.

Matrix-assisted laser desorption ionizationtime-of-f light mass spectrometry was used to identify peptic fragments from protein complexes that retained deuterium under hydrogen exchange conditions due to decreased solvent accessibility at the interface of the complex. Short deuteration times allowed preferential labeling of rapidly exchanging surface amides so that primarily solvent accessibility changes and not conformational changes were detected. A single mass spectrum of the peptic digest mixture was analyzed to determine the deuterium content of all proteolytic fragments of the protein. Amide hydrogens provide individualized probes along the entire protein sequence and measurements of amide proton [hydrogen͞deuterium (H͞D)] exchange rates have been used to analyze protein conformational changes, protein folding, and protein-protein interactions (1-3). NMR has been the method most used to study protein-protein interactions by amide H͞D exchange since the first report in 1990 by Paterson et al. (4). NMR studies of other protein-protein complexes have not yielded unambiguous identification of the interface because amide H͞D exchange rate variations also resulted from conformational changes (5-11). We propose that the key to separating conformational changes from interface information is to consider only those amides with rapid exchange rates in the uncomplexed state because these amides should be near the protein surface. An observed decrease in the exchange rate of a surface amide should primarily result from solvent accessibility changes, not from conformational changes. Information on the rapidly exchanging surface amides is nearly inaccessible by NMR because the surface amides exchange faster than the time required for measurement. In contrast, mass spectrometry is an ideal method to acquire information about decreased solvent accessibility of rapidly exchanging amides (12).Two protein-protein complexes were analyzed. The first was a complex of known structure, the catalytic subunit of murine cAMP-dependent protein kinase (PKA) complexed to the kinase inhibitor, PKI(5-24) (13). A complex of unknown structure was also analyzed, human ␣-thrombin bound to an 83-aa fragment of human thrombomodulin ]. The surfaces of PKA that interact with PKI(5-24) are consistent with the crystal structure of the complex. The results of the thrombin-TMEGF(4-5) complex are consistent with the structure of the complex between thrombin and a 19-aa peptide from TM (14) and provide new information about where this important anticoagulant protein directly contacts thrombin.