Does secondary structure determine tertiary structure in proteins?

Is highly approximate knowledge of a protein's backbone structure sufficient to successfully identify its family, superfamily, and tertiary fold? To explore this question, backbone dihedral angles were extracted from the known three‐dimensional structure of 2,439 proteins and mapped into 36 labeled, 60° × 60° bins, called mesostates. Using this coarse‐grained mapping, protein conformation can be approximated by a linear sequence of mesostates. These linear strings can then be aligned and assessed by conventional sequence‐comparison methods. We report that the mesostate sequence is sufficient to recognize a protein's family, superfamily, and fold with good fidelity. Proteins 2005. © 2005 Wiley‐Liss, Inc.     

Physical�Cchemical determinants of coil conformations in globular proteins

We present a method with the potential to generate a library of coil segments from first principles. Proteins are built from α‐helices and/or β‐strands interconnected by these coil segments. Here, we investigate the conformational determinants of short coil segments, with particular emphasis on chain turns. Toward this goal, we extracted a comprehensive set of two‐, three‐, and four‐residue turns from X‐ray–elucidated proteins and classified them by conformation. A remarkably small number of unique conformers account for most of this experimentally determined set, whereas remaining members span a large number of rare conformers, many occurring only once in the entire protein database. Factors determining conformation were identified via Metropolis Monte Carlo simulations devised to test the effectiveness of various energy terms. Simulated structures were validated by comparison to experimental counterparts. After filtering rare conformers, we found that 98% of the remaining experimentally determined turn population could be reproduced by applying a hydrogen bond energy term to an exhaustively generated ensemble of clash‐free conformers in which no backbone polar group lacks a hydrogen‐bond partner. Further, at least 90% of longer coil segments, ranging from 5‐ to 20 residues, were found to be structural composites of these shorter primitives. These results are pertinent to protein structure prediction, where approaches can be divided into either empirical or ab initio methods. Empirical methods use database‐derived information; ab initio methods rely on physical–chemical principles exclusively. Replacing the database‐derived coil library with one generated from first principles would transform any empirically based method into its corresponding ab initio homologue.     

CDR-H3 loop ensemble in solution – conformational selection upon antibody binding

ABSTRACT

We analyzed pairs of protein-binding, peptide-binding and hapten-binding antibodies crystallized as complex and in the absence of the antigen with and without conformational differences upon binding in the complementarity-determining region (CDR)-H3 loop. Here, we introduce a molecular dynamics-based approach to capture a diverse conformational ensemble of the CDR-H3 loop in solution. The results clearly indicate that the inherently flexible CDR-H3 loop indeed needs to be characterized as a conformational ensemble. The conformational changes of the CDR-H3 loop in all antibodies investigated follow the paradigm of conformation selection, because we observe the experimentally determined binding competent conformation without the presence of the antigen within the ensemble of pre-existing conformational states in solution before binding. We also demonstrate for several examples that the conformation observed in the antibody crystal structure without antigen present is actually selected to bind the carboxyterminal tail region of the antigen-binding fragment (Fab). Thus, special care must be taken when characterizing antibody CDR-H3 loops by Fab X-ray structures, and the possibility that pre-existing conformations are present should always be considered.     

Do plasma proteins distinguish between liposomes of varying charge density?

Cationic liposomes (CLs) are one of the most employed nonviral nanovector systems in gene therapy. However, their transfection efficiency is strongly affected by interactions with plasma components, that lead to the formation of a “protein corona” onto CL surface. The interactions between nanoparticles entering the body and biomolecules have an essential role for their biodistribution. Because the knowledge of proteins adsorbed onto vector surface could be useful in the screening of new, more efficient and more biocompatible liposomal formulations, the behavior of three CLs with different membrane charge densities was investigated. The proteins of the three coronas were identified by nano-liquid chromatography-tandem mass spectrometry, and quantified with label-free spectral counting strategy. Fibrinogen displayed higher association with CLs with high membrane charge density, while apolipoproteins and C4b-binding protein with CLs with low membrane charge density. These results are discussed in terms of the different lipid compositions of CLs and may have a deep biological impact for in vivo applications. Surface charge of nanoparticles is emerging as a relevant factor determining the corona composition after interaction with plasma proteins. Remarkably, it is also shown that the charge of the protein corona formed around CLs is strongly related to their membrane charge density.     

Organic free radicals and proteins in biochemical injury: electron- or hydrogen-transfer reactions?

The reactions of organic free radicals, acting as either reductants or oxidants, have been studied by pulse radiolysis in neutral aqueous solution at room temperature. Manyhydroxyl-substituted aliphatic carbon-centred radicals and one-electron adducts have been shown to be good one-electron reductants, while several oxygen-, sulphur- and nitrogen- (but not carbon-) centred free radicals have been shown to be good one-electron oxidants. Several carbon-centred radicals can be reduced rapidly by hydrogen transfer, from undissociated thiol compounds which can thus act as catalysts facilitating the overall reduction of a carbon-centred radical by an electron-donating molecule. Kinetic considerations influenced by the one-electron redox potentials of the radical-molecule couples involved, determine whether a particular reaction predominates. In this paper examples of such reactions, involving a water-soluble derivative of vitamin E (Trolox C) and the coenzyme NADH, are described, together with studies showing (a) that even in complex multi-solute systems some organic peroxy radicals can inactiviate alcohol dehydrogenase under conditions where the superoxide radical does not, and (b) the superoxide radical can be damaging if urate is also present, and this damage can be reduced by the presence of superoxide dismutase.     

Hydrophilic framework in proteins?

The spatial neighborhood composition of residues was determined in a 511-structure set by taking only side-chain atoms into account to generate a hydrophobicity scale. This scale is symmetrical and has been divided into seven functional groups. Hydrophobic (LIVFMCAWYG) and hydrophilic (PTHSQRNKED) residues obey an equipartition rule: not only are they found in equal proportions, but they play equivalent roles in many of their properties. The nearest neighbors of all residues are always hydrophilic. However, hydrophobic residues are mostly surrounded by other hydrophobic residues located at a peak at 3.9 Å, while hydrophilic residues show three peaks at 5.0, 6.5, and 8.0 Å, suggesting a hydrophilic structural framework. This leads us to question the importance of hydrophobic cores believed to be at the origin of protein folding.     

Actin-related proteins (Arps): conformational switches for chromatin-remodeling machines?

The actin superfamily of ATPases includes cytoskeletal actins, the stress 70 proteins (e.g. hsc70), sugar kinases, glycerol kinase, and several prokaryotic cell cycle proteins. Although these proteins share limited sequence identity, they all appear to maintain a similar tertiary structure, the "actin fold", which may serve to couple ATP hydrolysis to protein conformational changes. Recently, an actin-related protein (Arp) subfamily has been identified based on sequence homology to conventional actin. Although some Arps are clearly involved in cytoskeletal functions, both actin and/or Arps have been found as stoichiometric subunits of several nuclear chromatin-remodeling enzymes. Here we present two related models in which actin and/or Arps function as conformational switches that control either the activity or the assembly of chromatin-remodeling machines.     

Does high relatedness promote cheater‐free multicellularity in synthetic lifecycles?

The evolution of multicellularity is one of the key transitions in evolution and requires extreme levels of cooperation between cells. However, even when cells are genetically identical, noncooperative cheating mutants can arise that cause a breakdown in cooperation. How then, do multicellular organisms maintain cooperation between cells? A number of mechanisms that increase relatedness amongst cooperative cells have been implicated in the maintenance of cooperative multicellularity including single‐cell bottlenecks and kin recognition. In this study, we explore how relatively simple biological processes such as growth and dispersal can act to increase relatedness and promote multicellular cooperation. Using experimental populations of pseudo‐organisms, we found that manipulating growth and dispersal of clones of a social amoeba to create high levels of relatedness was sufficient to prevent the spread of cheating mutants. By contrast, cheaters were able to spread under low‐relatedness conditions. Most surprisingly, we saw the largest increase in cheating mutants under an experimental treatment that should create intermediate levels of relatedness. This is because one of the factors raising relatedness, structured growth, also causes high vulnerability to growth rate cheaters.     

What’s in a loop?

DNAs and proteins are major classes of biomolecules that differ in many aspects. However, a considerable number of their members also share a common architectural feature that enables the assembly of multi-protein complexes and thereby permits the effective processing of signals: loop structures of substantial sizes. Here we briefly review a few representative examples and suggest a functional classification of different types of loop structures. In proteins, these loops occur in protein regions classified as intrinsically disordered. Studying such loops, their binders and their interactions with other loops should reveal much about cellular information computation and signaling network architectures. It is also expected to provide critical information for synthetic biologists and bioengineers.     

Does energy availability predict gastropod reproductive strategies?

The diversity of reproductive strategies in nature is shaped by a plethora of factors including energy availability. For example, both low temperatures and limited food availability could increase larval exposure to predation by slowing development, selecting against pelagic and/or feeding larvae. The frequency of hermaphroditism could increase under low food availability as population density (and hence mate availability) decreases. We examine the relationship between reproductive/life-history traits and energy availability for 189 marine gastropod families. Only larval type was related to energy availability with the odds of having planktotrophic larvae versus direct development decreasing by 1% with every one-unit increase in the square root of carbon flux. Simultaneous hermaphroditism also potentially increases with carbon flux, but this effect disappears when accounting for evolutionary relationships among taxa. Our findings are in contrast to some theory and empirical work demonstrating that hermaphroditism should increase and planktotrophic development should decrease with decreasing productivity. Instead, they suggest that some reproductive strategies are too energetically expensive at low food availabilities, or arise only when energy is available, and others serve to capitalize on opportunities for aggregation or increased energy availability.     

Does ACE inhibition enhance endurance performance and muscle energy metabolism in rats?

The renin-angiotensin-aldosterone system plays an important role in the hydroelectrolytic balance, blood pressure regulation, and cell growth. In some studies, the insertion (I) allele of the angiotensin-converting enzyme (ACE) gene, associated with a lower ACE activity, has been found in excess frequency in elite endurance athletes, suggesting that decreased ACE activity could be involved in endurance performance (Myerson S, Hemingway H, Budget R, Martin J, Humphries S, and Montgomery H. J Appl Physiol 87: 1313-1316, 1999). To test this hypothesis, we evaluated whether ACE inhibition could be associated with improved endurance performance and muscle oxidative capacity in rats. Eight male Wistar rats were treated for 10-12 wk with an ACE inhibitor, perindopril (2 mg.kg-1.day-1), and compared with eight control rats. Endurance time was measured on a treadmill, and oxidative capacity and regulation of mitochondrial respiration by substrates were evaluated in saponin-permeabilized fibers of slow soleus and fast gastrocnemius muscles. Endurance time did not differ between groups (57 +/- 5 min for perindopril vs. 55 +/- 6 min for control). Absolute and relative (to body weight) left ventricular weight was 20% (P < 0.01) and 12% (P < 0.01) lower, respectively, in the treated group. No difference in oxidative capacity, mitochondrial enzyme activities, or mitochondrial regulation by ADP was observed in soleus or gastrocnemius. Mitochondrial respiration with glycerol 3-phosphate was 17% higher in gastrocnemius (P < 0.03) and with octanoylcarnitine 14% greater in soleus (P < 0.01) of treated rats. These results demonstrate that ACE inhibition was not associated with improved endurance time and maximal oxidative capacity of skeletal muscles. This suggests that ACE activity has no implication in endurance capacity and only minor effects on mitochondrial function in sedentary animals.     

Does inbreeding affect N-glycosylation of human plasma proteins?

Inbreeding depression and heterosis are the two ends of phenotypic changes defined by the genome-wide homozygosity. The aim of this study was to investigate the association of genetic marker-based homozygosity estimates with 46 N-glycan features measured in human plasma. The study was based on a total of 2,341 subjects, originating from three isolated island communities in Croatia (Vis and Korcula islands) and Scotland (Orkney Islands). Inbreeding estimates were associated with an increase in tetrantennary and tetrasialylated glycans, and a decrease in digalactosylated glycans (P?相似文献   

Does exogenous melatonin influence the free radicals metabolism and pain sensation in rat?

Melatonin has been shown to play a role in antioxidative defence. We therefore studied its effect on oxidative damage to the rat cerebral cortex evoked by painful stimulation and immobilization-induced stress. Moreover, the effect of melatonin on chronic pain perception was examined. Rats were injected with either a high dose of melatonin (100 mg/kg i.p.) or a vehicle for five days and were subjected to painful stimulation or immobilization stress 30 min after the treatment. To determine the degree of oxidative stress, the levels of free radicals, thiobarbituric acid reactive substances (TBARS) as indicators of lipid peroxidation and glutathione peroxidase (GSHPx) were estimated in somatosensory cortex. Pain perception was measured by the tail-flick and plantar test. Melatonin reduced the level of TBARS previously increased by painful stimulation. Melatonin also exhibited a slight analgesic effect in those animals exposed to painful stimulation but its role in free radical scavenging did not contribute to this effect.     

Closing loop base pairs in RNA loop–loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations

Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop–loop RNA duplexes neutralized by Mg²⁺ counterions in aqueous phases. Mismatches GA, CU and Watson–Crick GC base pairs have been considered for closing the loop of an RNA in complementary interaction with HIV-1 TAR. The simulations reveal that the mismatch GA base, mediated by a water molecule, leads to a complex that presents the best compromise between flexibility and energetic contributions. The mismatch CU base pair, in spite of the presence of an inserted water molecule, is too short to achieve a tight interaction at the closing-loop junction and seems to force TAR to reorganize upon binding. An energetic analysis has allowed us to quantify the strength of the interactions of the closing and the loop–loop pairs throughout the simulations. Although the water-mediated GA closing base pair presents an interaction energy similar to that found on fully geometry-optimized structure, the water-mediated CU closing base pair energy interaction reaches less than half the optimal value.     

Does water stress promote the proteome-wide adjustment of intrinsically disordered proteins in plants?

Plant response to water stress involves the activation of mechanisms expected to help them cope with water scarcity. Among these mechanisms, proteome-wide adjustment is well known. This includes actions to save energy, protect cellular and molecular components, and maintain vital functions of the cell. Intrinsically disordered proteins, which are proteins without a rigid three-dimensional structure, are seen as emerging multifunctional cellular components of proteomes. They are highly abundant in eukaryotic proteomes, and numerous functions for these proteins have been proposed. Here, we discuss several reasons why the collection of intrinsically disordered proteins in a proteome (disordome) could be subjected to an active regulation during conditions of water scarcity in plants. We also discuss the potential misinterpretations of disordome content estimations made so far due to bias-prone data and the need for reliable analysis based on experimental data in order to acknowledge the plasticity nature of the disordome.     

Does intrinsic fluorescence reflect conformational changes in the Ca2+-ATPase of sarcoplasmic reticulum?

We have investigated the kinetics of the intrinsic fluorescence drop observed when ATP is added to purified sarcoplasmic reticulum ATPase in a potassium-free medium containing magnesium and calcium, at pH 6 and 20°C. Under these conditions, analysis of the fluorescence drop is complex. Several events contributed to the rate of the fluorescence drop initiated by turnover, including phosphorylation, conformational transition of the phosphorylated complex, and dephosphorylation. On the other hand, when 75% of total fluorescence was quenched by energy transfer to the membrane-bound ionophore A23187, the observed turnoverdependent drop in residual fluorescence mainly reflected the conformational transition of the phosphorylated ATPase. Combination of fast kinetics with the quenching of selected tryptophan residues is suggested to be a promising tool for the study of proteins containing many of these residues.     

Does energy availability influence classical patterns of spatial variation in exotic species richness?

Aim At macroecological scales, exotic species richness is frequently positively correlated with human population density. Such patterns are typically thought to arise because high human densities are associated with increased introduction effort and/or habitat modification and disturbance. Exotic and native species richness are also frequently positively correlated, although the causal mechanisms remain unclear. Energy availability frequently explains much of the variation in species richness and we test whether such species–energy relationships may influence the relationships of exotic species richness with human population density and native species richness. Location Great Britain. Methods We first investigate how spatial variation in the distributions of the 10 exotic bird species is related to energy availability. We then model exotic species richness using native avian species richness, human population density and energy availability as predictors. Species richness is modelled using two sets of models: one assumes independent errors and the other takes spatial correlation into account. Results The probability of each exotic species occurring, in a 10‐km quadrat, increases with energy availability. Exotic species richness is positively correlated with energy availability, human population density and native species richness in univariate tests. When taking energy availability into account, exotic species richness is negligibly influenced by human population density, but remains positively associated with native species richness. Main conclusions We provide one of the few demonstrations that energy availability exerts a strong positive influence on exotic species richness. Within our data, the positive relationship between exotic species richness and human population density probably arises because both variables increase with energy availability, and may be independent of the influence of human density on the probability of establishment. Positive correlations between exotic and native species richness remain when controlling for the influence of energy on species richness. The relevance of such a finding to the debate on the relationship between diversity and invasibility is discussed.     

Transient conformational remodeling of folding proteins by GroES—individually and in concert with GroEL

The commonly accepted dogma of the bacterial GroE chaperonin system entails protein folding mediated by cycles of several ATP-dependent sequential steps where GroEL interacts with the folding client protein. In contrast, we herein report GroES-mediated dynamic remodeling (expansion and compression) of two different protein substrates during folding: the endogenous substrate MreB and carbonic anhydrase (HCAII), a well-characterized protein folding model. GroES was also found to influence GroEL binding induced unfolding and compression of the client protein underlining the synergistic activity of both chaperonins, even in the absence of ATP. This previously unidentified activity by GroES should have important implications for understanding the chaperonin mechanism and cellular stress response. Our findings necessitate a revision of the GroEL/ES mechanism.