Salt bridges in proteins are bonds between oppositely charged residues that are sufficiently close to each other to experience electrostatic attraction. They contribute to protein structure and to the specificity of interaction of proteins with other biomolecules, but in doing so they need not necessarily increase a protein's free energy of unfolding. The net electrostatic free energy of a salt bridge can be partitioned into three components: charge-charge interactions, interactions of charges with permanent dipoles, and desolvation of charges. Energetically favorable Coulombic charge-charge interaction is opposed by often unfavorable desolvation of interacting charges. As a consequence, salt bridges may destabilize the structure of the folded protein. There are two ways to estimate the free energy contribution of salt bridges by experiment: the pK(a) approach and the mutation approach. In the pK(a) approach, the contribution of charges to the free energy of unfolding of a protein is obtained from the change of pK(a) of ionizable groups caused by altered electrostatic interactions upon folding of the protein. The pK(a) approach provides the relative free energy gained or lost when ionizable groups are being charged. In the mutation approach, the coupling free energy between interacting charges is obtained from a double mutant cycle. The coupling free energy is an indirect and approximate measure of the free energy of charge-charge interaction. Neither the pK(a) approach nor the mutation approach can provide the net free energy of a salt bridge. Currently, this is obtained only by computational methods which, however, are often prone to large uncertainties due to simplifying assumptions and insufficient structural information on which calculations are based. This state of affairs makes the precise thermodynamic quantification of salt bridge energies very difficult. This review is focused on concepts and on the assessment of experimental methods and does not cover the vast literature.

Recently we have identified angiostatin, an endogenous angiogenesis inhibitor of 38 kDa which specifically blocks the growth of endothelial cells (O'Reilly, M. S., Holmgren, L., Shing, Y., Chen, C., Rosenthal, R. A., Moses, M., Lane, W. S., Cao, Y., Sage, E. H., and Folkman, J. (1994) Cell 79, 315-328; Folkman, J. (1995) Nat. Med. 1, 27-31). Angiostatin was shown to represent an internal fragment of plasminogen containing the first four kringle structures. We now report on the inhibitory effects of individual or combined kringle structures of angiostatin on capillary endothelial cell proliferation. Recombinant kringle 1 and kringle 3 exhibit potent inhibitory activity with half-maximal concentrations (ED 50 ) of 320 nM and 460 nM, respectively. Also, recombinant kringle 2 displays a significant inhibition, although decreased compared with both kringle 1 and kringle 3. In contrast, kringle 4 is an ineffective inhibitor of basic fibroblast growth factor-stimulated endothelial cell proliferation. Among the tandem kringle arrays, the recombinant kringle 2-3 fragment exerts inhibitory activity similar to kringle 2 alone. However, relative to kringle 2-3, a marked enhancement in inhibition is observed when individual kringle 2 and kringle 3 are added together to endothelial cells. This implies that it is necessary to open the cystine bridge between kringle 2 and kringle 3 to obtain the maximal inhibitory effect of kringle 2-3. An increased (<2-fold) inhibitory activity is observed for the kringle 1-3 fragment (ED 50 ‫؍‬ 70 nM) compared with kringle 1-4 (ED 50 ‫؍‬ 135 nM). These data indicate that the anti-proliferative activity of angiostatin on endothelial cells is shared by kringle 1, kringle 2, and kringle 3, but probably not by kringle 4 and that more potent inhibition results when kringle 4 is removed from angiostatin. Thus, in view of the variable lysine affinity of the homologous domains, it would appear that lysine binding capability does not correlate with the relative inhibitory effects of the kringle-containing constructs. However, as we also demonstrate, appropriate folding of kringle structures is essential for angiostatin to maintain its full anti-endothelial activity.

Networks of randomly connected neurons are among the most popular models in theoretical neuroscience. The connectivity between neurons in the cortex is however not fully random, the simplest and most prominent deviation from randomness found in experimental data being the overrepresentation of bidirectional connections among pyramidal cells. Using numerical and analytical methods, we investigate the effects of partially symmetric connectivity on the dynamics in networks of rate units. We consider the two dynamical regimes exhibited by random neural networks: the weak-coupling regime, where the firing activity decays to a single fixed point unless the network is stimulated, and the strong-coupling or chaotic regime, characterized by internally generated fluctuating firing rates. In the weak-coupling regime, we compute analytically, for an arbitrary degree of symmetry, the autocorrelation of network activity in the presence of external noise. In the chaotic regime, we perform simulations to determine the timescale of the intrinsic fluctuations. In both cases, symmetry increases the characteristic asymptotic decay time of the autocorrelation function and therefore slows down the dynamics in the network.

Angiogenesis is a complex process that involves endothelial cell proliferation, migration, basement membrane degradation, and neovessel organization. Angiostatin, consisting of four homologous triple-disulfide bridged kringle domains, has previously been shown to exhibit profound inhibition of endothelial cell proliferation in vitro and angiogenesis in vivo. It was also demonstrated that angiostatin could suppress the growth of a variety of tumors via the blocking of angiogenesis. The primary aim of our study was to characterize the kringle domains of angiostatin for their inhibitory activities of endothelial cell migration in order to elucidate their contributions to the anti-angiogenic function of angiostatin. In this report, we demonstrate for the first time that the kringles of angiostatin play different roles in inhibiting endothelial cell migration, a crucial process in angiogenesis. Kringle 4, which has only marginal anti-proliferative activity, is among the most potent fragments in inhibiting endothelial cell migration (IC50 of approximately 500 nM). In contrast, kringle 1-3, which is equivalent to angiostatin in inhibiting endothelial cell proliferation, manifests only a modest anti-migratory effect. The combination of kringle 1-3 and kringle 4 results in an anti-migratory activity comparable to that of angiostatin. When kringle 1 is removed from kringle 1-3, the resulting kringle 2-3 becomes more potent than kringle 1-3. This implies that kringle 1, although virtually ineffective in inhibiting endothelial cell migration, may influence the conformation of kringle 1-3 to alter its anti-migratory activity. We also show that disruption of the kringle structure by reducing/alkylating agents markedly attenuates the anti-migratory activity of angiostatin, demonstrating the significance of kringle conformation in maintaining the anti-angiogenic activity of angiostatin. Our data suggest that different kringle domains may contribute to the overall anti-angiogenic function of angiostatin by their distinct anti-migratory activities.

During coordinated eye– hand movements, saccade reaction times (SRTs) and reach reaction times (RRTs) are correlated in humans and monkeys. Reaction times (RTs) measure the degree of movement preparation and can correlate with movement speed and accuracy. However, RTs can also reflect effector nonspecific influences, such as motivation and arousal. We use a combination of behavioral psychophysics and computational modeling to identify plausible mechanisms for correlations in SRTs and RRTs. To disambiguate nonspecific mechanisms from mechanisms specific to movement coordination, we introduce a dual-task paradigm in which a reach and a saccade are cued with a stimulus onset asynchrony (SOA). We then develop several variants of integrate-to-threshold models of RT, which postulate that responses are initiated when the neural activity encoding effector-specific movement preparation reaches a threshold. The integrator models formalize hypotheses about RT correlations and make predictions for how each RT should vary with SOA. To test these hypotheses, we trained three monkeys to perform the eye– hand SOA task and analyzed their SRTs and RRTs. In all three subjects, RT correlations decreased with increasing SOA duration. Additionally, mean SRT decreased with decreasing SOA, revealing facilitation of saccades with simultaneous reaches, as predicted by the model. These results are not consistent with the predictions of the models with common modulation or common input but are compatible with the predictions of a model with mutual excitation between two effector-specific integrators. We propose that RT correlations are not simply attributable to motivation and arousal and are a signature of coordination.

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The kringle 2 (E161T/C162S/EEE[K2,,,/C169S]TT) and the kringle 3 (TYQ[K3,,]DS) domains of human plasminogen (HPg) were expressed in Eschericlzia coli in an expression vector with the phage T5 promotor/operator element N250PSN250P29 and the cDNA sequence for a hexahistidine tail to facilitate the isolation of the recombinant protein. A coagulation factor Xa (FXa)-sensitive cleavage site was introduced to remove the N-terminal histidine tag. In r-K2, mutations E161T and C162S were introduced to enhance the FXa cleavage yield and C169S to replace the cysteine residue, participating in the inter-kringle disulfide bridge between kringles 2 and 3. Recombinant proteins were isolated by affinity chromatography on Ni"-nitrilotriacetic acid/agarose and refolded under denaturing and reducing conditions followed by a non-denaturing and oxidising environment. The free thiol group in position 297 in r-K3 was selectively alkylated with iodoacetamide. The hexahistidine tail was successfully removed with FXa. The N-terminal sequence, the amino acid composition and the molecular mass analyses are in agreement with the expected data. The correct arrangement of the disulfide bonds was verified by sequence analysis of the corresponding thermolytic and subtilisin fragments. r-K2 exhibits weak binding to lysine-Bio-Gel. The weak binding affinity of r-K2 for o-aminocarboxylic acids is confirmed by intrinsic fluorescence titration with 6-aminohexanoic acid (NH,C,COOH) indicating a Kd of approximately 401 pM. In contrast, r-K3 seems to be devoid of a binding affinity for w-aminocarboxylic acids. Considering earlier determined Kd values of kringle 1, kringle 4 and kringle 5, the binding affinity of HPg kringle domains for NH,C,COOH is proposed to decrease in the following order, kringle 1 > kringle 4 > kringle 5 > kringle 2 > knngle 3.Plasminogen is the main component of the fibrinolytic system and its activated form, plasmin, is responsible for the proteolytic degradation of fibrin in blood clots. Human plasminogen (HPg) is a single-chain proenzyme of 791 amino acids. The sequence has been established by amino acid sequence analysis [l-31 and

Many cells express receptors for plasminogen (Pg), although the responsible molecules in most cases are poorly defined. In contrast, the group A streptococcal surface protein PAM contains a domain with two 13-amino acid residue long repeated sequences (a1 and a2) responsible for Pg binding. Here we identify the region in Pg that interacts with PAM. A radiolabeled proteolytic plasminogen fragment containing the first three kringles (K1-K3) interacted with streptococci expressing PAM or a chimeric surface protein harboring the a1a2 sequence. In contrast, plasminogen fragments containing kringle 4 or kringle 5 and the activable serine proteinase domain failed to bind to PAM-expressing group A streptococci. A synthetic and a recombinant polypeptide containing the a1a2 sequence both bound to immobilized recombinant K2 (rK2) but not to rK1 or rK3. The interaction between the a repeat region and rK2 was reversible, and rK2 completely blocked the binding of Pg to the a1a2 region. The binding of the a repeat containing polypeptide to K2 occurred with an equilibrium association constant of 4.5 ؋ 10 M ؊1, as determined by surface plasmon resonance, a value close to that (1.6 ؋ 10 7 M ؊1 ) calculated for the a1a2-Pg interaction. Inhibition experiments suggested involvement of the lysine-binding site of K2 in the interaction. These data demonstrate that K2 contains the major Pg-binding site for PAM, providing the first well defined example of an interaction between an internal Pg-binding region in a protein and a single kringle domain.The plasma glycoprotein plasminogen (Pg) 1 is a single-chain 92-kDa precursor for the broad spectrum serine proteinase plasmin (1, 2) (see Fig. 1A). In vivo, the tissue-type and urokinase-type plasminogen activators convert the zymogen into the two-chain proteinase by cleavage of a single peptide bond (Arg 561 -Val 562 ). Activation can also be achieved by some bacterial proteins, such as streptokinase from streptococci (1, 2). Plasmin plays a key role in fibrinolysis (1-3) but also participates in several other physiological and pathophysiological processes, including wound healing, tissue penetration of cancer cells, neuronal cell death, and bacterial dissemination (4 -8).The activable serine proteinase domain is located in the COOH-terminal third of Pg. The NH 2 -terminal two-thirds of Pg contains an 8-kDa preactivation peptide and five characteristic kringle domains (K1-K5), each ϳ9 kDa. The kringles mediate interactions with multiple ligands, including fibrin, the primary target of Pg, and ␣ 2 -plasmin inhibitor, its principal regulator (1, 2). The recognition events depend upon interactions between lysine-binding sites in the kringles and exposed COOH-terminal lysines in the ligands. Lysine analogues, such as 6-aminohexanoic acid (6-AHA), mimic COOH-terminal lysines in the interaction with kringles and the structural basis of the interactions between some kringles, particularly K1 and K4, and 6-AHA has been disclosed (9 -12). The affinity of the different kringles for lysine or 6-AHA is...