bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surface salt bridges stabilize the GCN4 leucine zipper
Authors: Spek Erik J. , Bui Au H. , Lu Min , Kallenbach Neville R. 
Published: February 2009

AbstractWe present a study of the role of salt bridges in stabilizing a simplified tertiary structural motif, the coiled‐coil. Changes in GCN4 sequence have been engineered that introduce trial patterns of single and multiple salt bridges at solvent exposed sites. At the same sites, a set of alanine mutants was generated to provide a reference for thermodynamic analysis of the salt bridges. Introduction of three alanines stabilizes the dimer by 1. 1 kcal/mol relative to the wild‐type. An arrangement corresponding to a complex type of salt bridge involving three groups stabilizes the dimer by 1. 7 kcal/mol, an apparent elevation of the melting temperature relative to wild type of about 22°C. While identifying local from nonlocal contributions to protein stability is difficult, stabilizing interactions can be identified by use of cycles. Introduction of alanines for side chains of lower helix propensity and complex salt bridges both stabilize the coiled‐coil, so that combining the two should yield melting temperatures substantially higher than the starting species, approaching those of thermophilic sequences.
Proteolysis as a measure of the free energy difference between cytochrome c and its derivatives
Authors: Wang L. , Kallenbach N. R. 
Published: February 2009

AbstractLimited cleavage of oxidized and reduced horse heart cytochrome c (Cyt c) and the azide complex of Cyt c by proteinase K at room temperature yields a single cut within the central loop (36–60 in the sequence). Using an assay that allows spectroscopic evaluation of the fraction of intact protein as a function of time, together with a simple kinetic model for proteolysis, fluctuation opening of the loop can be related to the free energy of the corresponding protein. This allows us to estimate quantitatively the free energy difference between the oxidized form of Cyt c and other states using proteolysis as a probe. The results we obtain indicate that oxidized Cyt c is 2. 0 kcal mol−1 less stable than the reduced form, and 0. 07 kcal mol−1 is more stable than the Cyt c: azide complex at 25°C. These values agree in magnitude with results from hydrogen exchange and unfolding studies, suggesting that the stability of a protein can be directly related to its structural dynamics.
Evidence that peroxiredoxins are novel members of the thioredoxin fold superfamily
Authors: Schröder Ewald , Ponting Chris P. 
Published: February 2009

AbstractPeroxiredoxins catalyze reduction of hydrogen peroxide or alkyl peroxide, to water or the corresponding alcohol. Detailed analysis of their sequences indicates that these enzymes possess a thioredoxin (Trx)‐like fold and consequently are homologues of both thioredoxin and glutathione peroxidase (GPx). Sequence‐ and structure‐based multiple sequence alignments indicate that the peroxiredoxin active site cysteine and GPx active site selenocysteine are structurally equivalent. Homologous peroxiredoxin and GPx enzymes are predicted to catalyze equivalent reactions via similar reaction intermediates.
HOMSTRAD: A database of protein structure alignments for homologous families
Authors: Mizuguchi Kenji , Deane Charlotte M. , Blundell Tom L. , Overington John P. 
Published: February 2009

AbstractWe describe a database of protein structure alignments for homologous families. The database HOMSTRAD presently contains 130 protein families and 590 aligned structures, which have been selected on the basis of quality of the X‐ray analysis and accuracy of the structure. For each family, the database provides a structure‐based alignment derived using COMPARER and annotated with JOY in a special format that represents the local structural environment of each amino acid residue. HOMSTRAD also provides a set of superposed atomic coordinates obtained using MNYFIT, which can be viewed with a graphical user interface or used for comparative modeling studies. The database is freely available on the World Wide Web at: http://www‐cryst. bioc. cam. ac. uk/homstrad/, with search facilities and links to other databases.
A homology identification method that combines protein sequence and structure information
Authors: Yu Lihua , White James V. , Smith Temple F. 
Published: February 2009

AbstractA new method is presented for identifying distantly related homologous proteins that are unrecognizable by conventional sequence comparison methods. The method combines information about functionally conserved sequence patterns with information about structure context. This information is encoded in stochastic discrete state‐space models (DSMs) that comprise a new family of hidden Markov models. The new models are called sequence‐pattern‐embedded DSMs (pDSMs). This method can identify distantly related protein family members with a high sensitivity and specificity. The method is illustrated with trypsin‐like serine proteases and globins. The strategy for building pDSMs is presented. The method has been validated using carefully constructed positive and negative control sets. In addition to the ability to recognize remote homologs, pDSM sequence analysis predicts secondary structures with higher sensitivity, specificity, and Q3 accuracy than DSM analysis, which omits information about conserved sequence patterns. The identification of trypsin‐like serine proteases in new genomes is discussed.
Pulmonary surfactant‐associated polypeptide C in a mixed organic solvent transforms from a monomeric α‐helical state into insoluble β‐sheet aggregates
Authors: Szyperski Thomas , Wüthrich Kurt , Vandenbussche Guy , Ruysschaert Jean‐Marie , Curstedt Tore , Johansson Jan 
Published: February 2009

AbstractIn the 35‐residue pulmonary surfactant‐associated lipopolypeptide C (SP‐C), the stability of the valyl‐rich α‐helix comprising residues 9–34 has been monitored by circular dichroism, nuclear magnetic resonance, and Fourier transform infrared spectroscopy in both a mixed organic solvent and in phospholipid micelles. The α‐helical form of SP‐C observed in freshly prepared solutions in a mixed solvent of CHCl3/CH3OH/0.1 M HCl 32:64:5 (v/v/v) at 10°C undergoes within a few days an irreversible transformation to an insoluble aggregate that contains β‐sheet secondary structure. Hydrogen exchange experiments revealed that this conformational transition proceeds through a transition state with an Eyring free activation enthalpy of about 100 kJ mol–1, in which the polypeptide segment 9–27 largely retains a helical conformation. In dodecylphosphocholine micelles, the helical form of SP‐C was maintained after seven weeks at 50 °C. The α‐helical form of SP‐C thus seems to be the thermodynamically most stable state in this micellar environment, whereas its presence in freshly prepared samples in the aforementioned mixed solvent is due to a high kinetic barrier for unfolding. These observations support a previously proposed pathway for in vivo synthesis of SP‐C through proteolytic processing from a 21‐kDa precursor protein.
Recognition of partially‐folded mitochondrial malate dehydrogenase by GroEL. Steady and time‐dependent emission anisotropy measurements
Authors: Churchich Jorge E. 
Published: February 2009

AbstractThe binding of partially‐folded mitochondrial malate dehydrogenase (mMDH) to GroEL was assessed by steady and nanosecond emission spectroscopy. Partially‐folded intermediates of mMDH show significant residual secondary structure when examined by CD spectroscopy in the far UV. They bind the extrinsic fluorescent probe ANS and the protein‐ANS complexes display a rotational correlation time of 19 ns. Similar rotational correlation time (ø = 18.6 ns) was determined for partially‐folded species tagged with anthraniloyl. GroEL recognizes partially‐folded species with a KD ⋍ 60 nM. The rotational correlation time of the complex, i.e., GroEL‐mMDH‐ANT, approaches a value of 280 ns in the absence of ATP. Reactivation of mMDH‐ANT by addition of GroEL and ATP brings about a significant decrease in the observed rotational correlation time. The results indicate that partially‐folded malate dehydrogenase is rigidly trapped by GroEL in the absence of ATP, whereas addition of ATP facilitates reactivation and release of folded conformations endowed with catalytic activity.
Cupryphans, metal‐binding, redox‐active, redesigned conopeptides
Authors: Barba Marco , Sobolev Anatoli P. , Romeo Cristina , Schininà M. Eugenia , Pietraforte Donatella , Mannina Luisa , Musci Giovanni , Polticelli Fabio 
Published: February 2009

AbstractContryphans are bioactive peptides, isolated from the venom of marine snails of the genus Conus, which are characterized by the short length of the polypeptide chain and the high degree of unusual post‐translational modifications. The cyclization of the polypeptide chain through a single disulphide bond, the presence of two conserved Pro residues, and the epimerization of a Trp/Leu residue confer to Contryphans a stable and well‐defined structure in solution, conserved in all members of the family, and tolerant to multiple substitutions. The potential of Contryphans as scaffolds for the design of redox‐active (macro)molecules was tested by engineering a copper‐binding site on two different variants of the natural peptide Contryphan‐Vn. The binding site was designed by computational modeling, and the redesigned peptides were synthesized and characterized by optical, fluorescence, electron spin resonance, and nuclear magnetic resonance spectroscopy. The novel peptides, named Cupryphan and Arg–Cupryphan, bind Cu2+ ions with a 1:1 stoichiometry and a Kd in the 100 nM range. Other divalent metals (e.g., Zn2+ and Mg2+) are bound with much lower affinity. In addition, Cupryphans catalyze the dismutation of superoxide anions with an activity comparable to other nonpeptidic superoxide dismutase mimics. We conclude that the Contryphan motif represents a natural robust scaffold which can be engineered to perform different functions, providing additional means for the design of catalytically active mini metalloproteins.
Triad of polar residues implicated in pH specificity of acidic mammalian chitinase
Authors: Olland Andrea M. , Strand James , Presman Eleonora , Czerwinski Robert , Joseph‐McCarthy Diane , Krykbaev Rustem , Schlingmann Gerhard , Chopra Rajiv , Lin Laura , Fleming Margaret , Kriz Ron , Stahl Mark , Somers William , Fitz Lori , Mosyak Lidia 
Published: February 2009

AbstractAcidic mammalian chitinase (AMCase) is a mammalian chitinase that has been implicated in allergic asthma. One of only two active mammalian chinases, AMCase, is distinguished from other chitinases by several unique features. Here, we present the novel structure of the AMCase catalytic domain, both in the apo form and in complex with the inhibitor methylallosamidin, determined to high resolution by X‐ray crystallography. These results provide a structural basis for understanding some of the unique characteristics of this enzyme, including the low pH optimum and the preference for the β‐anomer of the substrate. A triad of polar residues in the second‐shell is found to modulate the highly conserved chitinase active site. As a novel target for asthma therapy, structural details of AMCase activity will help guide the future design of specific and potent AMCase inhibitors.
Lone pair ··· π interactions between water oxygens and aromatic residues: Quantum chemical studies based on high‐resolution protein structures and model compounds
Authors: Jain Alok , Ramanathan Venkatnarayan , Sankararamakrishnan Ramasubbu 
Published: February 2009

AbstractThe π electron cloud of aromatic centers is known to be involved in several noncovalent interactions such as CH···π, OH···π, and π···π interactions in biomolecules. Lone‐pair (lp) ··· π interactions have gained attention recently and their role in biomolecular structures is being recognized. In this article, we have carried out systematic analysis of high‐resolution protein structures and identified more than 400 examples in which water oxygen atoms are in close contact (distance < 3.5 Å) with the aromatic centers of aromatic residues. Three different methods were used to build hydrogen atoms and we used a consensus approach to find out potential candidates for lp···π interactions between water oxygen and aromatic residues. Quantum mechanical calculations at MP2/6‐311++G(d,p) level on model systems based on protein structures indicate that majority of the identified examples have energetically favorable interactions. The influence of water hydrogen atoms was investigated by sampling water orientations as a function of two parameters: distance from the aromatic center and the angle between the aromatic plane and the plane formed by the three water atoms. Intermolecular potential surfaces were constructed using six model compounds representing the four aromatic amino acids and 510 different water orientations for each model compound. Ab initio molecular orbital calculations at MP2/6‐311++G(d,p) level show that the interaction energy is favorable even when hydrogen atoms are farthest from the aromatic plane while water oxygen is pointing toward the aromatic center. The strength of such interaction depends upon the distance of water hydrogen atoms from the aromatic substituents. Our calculations clearly show that the lp···π interactions due to the close approach of water oxygen and aromatic center are influenced by the positions of water hydrogen atoms and the aromatic substituents.
C‐terminal domain of SARS‐CoV main protease can form a 3D domain‐swapped dimer
Authors: Zhong Nan , Zhang Shengnan , Xue Fei , Kang Xue , Zou Peng , Chen Jiaxuan , Liang Chao , Rao Zihe , Jin Changwen , Lou Zhiyong , Xia Bin 
Published: February 2009

AbstractSARS coronavirus main protease (Mpro) plays an essential role in the extensive proteolytic processing of the viral polyproteins (pp1a and pp1ab), and it is an important target for anti‐SARS drug development. We have reported that both the Mpro C‐terminal domain alone (Mpro‐C) and the N‐finger deletion mutant of Mpro (Mpro‐Δ7) exist as a stable dimer and a stable monomer (Zhong et al., J Virol 2008; 82:4227‐4234). Here, we report structures of both Mpro‐C monomer and dimer. The structure of the Mpro‐C monomer is almost identical to that of the C‐terminal domain in the crystal structure of Mpro. Interestingly, the Mpro‐C dimer structure is characterized by 3D domain‐swapping, in which the first helices of the two protomers are interchanged and each is enwrapped by four other helices from the other protomer. Each folding subunit of the Mpro‐C domain‐swapped dimer still has the same general fold as that of the Mpro‐C monomer. This special dimerization elucidates the structural basis for the observation that there is no exchange between monomeric and dimeric forms of Mpro‐C and Mpro‐Δ7.
CPDadh: A new peptidase family homologous to the cysteine protease domain in bacterial MARTX toxins
Authors: Pei Jimin , Lupardus Patrick J. , Garcia K. Christopher , Grishin Nick V. 
Published: February 2009

AbstractA cysteine protease domain (CPD) has been recently discovered in a group of multifunctional, autoprocessing RTX toxins (MARTX) and Clostridium difficile toxins A and B. These CPDs (referred to as CPDmartx) autocleave the toxins to release domains with toxic effects inside host cells. We report identification and computational analysis of CPDadh, a new cysteine peptidase family homologous to CPDmartx. CPDadh and CPDmartx share a Rossmann‐like structural core and conserved catalytic residues. In bacteria, domains of the CPDadh family are present at the N‐termini of a diverse group of putative cell‐cell interaction proteins and at the C‐termini of some RHS (recombination hot spot) proteins. In eukaryotes, catalytically inactive members of the CPDadh family are found in cell surface protein NELF (nasal embryonic LHRH factor) and some putative signaling proteins.
Structure of dystrophia myotonica protein kinase
Authors: Elkins Jonathan M. , Amos Ann , Niesen Frank H. , Pike Ashley C.W. , Fedorov Oleg , Knapp Stefan 
Published: February 2009

AbstractDystrophia myotonica protein kinase (DMPK) is a serine/threonine kinase composed of a kinase domain and a coiled‐coil domain involved in the multimerization. The crystal structure of the kinase domain of DMPK bound to the inhibitor bisindolylmaleimide VIII (BIM‐8) revealed a dimeric enzyme associated by a conserved dimerization domain. The affinity of dimerisation suggested that the kinase domain alone is insufficient for dimerisation in vivo and that the coiled‐coil domains are required for stable dimer formation. The kinase domain is in an active conformation, with a fully‐ordered and correctly positioned αC helix, and catalytic residues in a conformation competent for catalysis. The conserved hydrophobic motif at the C‐terminal extension of the kinase domain is bound to the N‐terminal lobe of the kinase domain, despite being unphosphorylated. Differences in the arrangement of the C‐terminal extension compared to the closely related Rho‐associated kinases include an altered PXXP motif, a different conformation and binding arrangement for the turn motif, and a different location for the conserved NFD motif. The BIM‐8 inhibitor occupies the ATP site and has similar binding mode as observed in PDK1.
Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small‐angle X‐ray scattering
Authors: Bernadó Pau , Pérez Yolanda , Blobel Jascha , Fernández‐Recio Juan , Svergun Dmitri I. , Pons Miquel 
Published: February 2009

AbstractSignal transducer and activator of transcription (STAT) proteins play a crucial role in the activation of gene transcription in response to extracellular stimuli. The regulation and activity of these proteins require a complex rearrangement of the domains. According to the established models, based on crystallographic data, STATs convert from a basal antiparallel inactive dimer into a parallel active one following phosphorylation. The simultaneous analysis of small‐angle X‐ray scattering data measured at different concentrations of unphosphorylated human STAT5a core domain unambiguously identifies the simultaneous presence of a monomer and a dimer. The dimer is the minor species but could be structurally characterized by SAXS in the presence of the monomer using appropriate computational tools and shown to correspond to the antiparallel assembly. The equilibrium is governed by a moderate dissociation constant of Kd ∼ 90 μM. Integration of these results with previous knowledge of the N‐terminal domain structure and dissociation constants allows the modeling of the full‐length protein. A complex network of intermolecular interactions of low or medium affinity is suggested. These contacts can be eventually formed or broken to trigger the dramatic modifications in the dimeric arrangement needed for STAT regulation and activity.
Jasmonate‐ and salicylate‐mediated plant defense responses to insect herbivores, pathogens and parasitic plants
Authors: Smith Jordan L , De Moraes Consuelo M , Mescher Mark C 
Published: February 2009

AbstractWhile extensive research has examined plant defense responses to attack by herbivores and pathogens, plant responses to parasitism by other plants are not well characterized. The expression of induced plant defenses is mediated by complex signaling networks in which the plant hormones jasmonic acid (JA) and salicylic acid (SA) play key roles. In general, JA‐mediated signaling pathways are implicated in the regulation of antiherbivore defenses, while the SA pathway is associated with defense responses against pathogens. However, there are many exceptions to this basic framework, and recent work suggests that interactions between the JA and SA pathways may play important roles in fine‐tuning defense responses. The few studies that have addressed plant responses to parasitism by other plants suggest that both salicylates and jasmonates can mediate effective defenses. Here, a review is given of recent work on these defense signaling molecules with relevance for understanding their role in plant responses to parasitism. Copyright © 2009 Society of Chemical Industry
The Year of the Rat ends—time to fight hunger!
Authors: Meerburg Bastiaan G , Singleton Grant R , Leirs Herwig 
Published: February 2009

AbstractThis paper investigates the importance of ecologically based rodent management in the light of the current food crisis, and the potential effects of this approach on the position of the undernourished. Hunger and food prices are on the rise owing to shortages that can be traced to reasons such as climatic extremes, use of crops for biofuels, reduced growth in yields which lag behind population growth, reduced world stocks and lack of sufficient investment in maintaining the irrigation infrastructure. For the undernourished this is problematic as they are most vulnerable to the rise in food prices. Very often, agricultural experts focus on an increase in agricultural production to reduce food prices. It is postulated in this article that almost 280 million undernourished could additionally benefit if more attention were paid to reducing pre‐ and post‐harvest losses by rodents. Moreover, rodent‐borne diseases would decrease, diseases that can be catastrophic to the livelihoods of the poorest of the poor. Copyright © 2009 Society of Chemical Industry
Inheritance mode and realized heritability of resistance to imidacloprid in the brown planthopper, Nilaparvata lugens (Stål) (Homoptera: Delphacidae)
Authors: Wang Yan Hua , Liu Xu Gan , Zhu Yu Cheng , Wu Sheng Gan , Li Shu Yong , Chen Wen Ming , Shen Jin Liang 
Published: February 2009

AbstractBACKGROUND: The brown planthopper, Nilaparvata lugens (Stål), is a serious pest that causes enormous losses to the rice crop in Asia. The genetic basis of imidacloprid resistance was investigated in N. lugens.RESULTS: The resistant strain, selected for imidacloprid resistance from a field population of N. lugens collected from Nanjing, Jiangsu Province, China, showed a 964‐fold resistance compared with the laboratory strain. Progenies of reciprocal crosses (F1 and F1′) showed similar dose–mortality responses (LC50) to imidacloprid, and also exhibited a similar degree of dominance (D), 0.58 for F1 and 0.63 for F1′. Chi‐square analyses of self‐bred and backcross progenies (F2, F2′ and BC respectively) rejected the hypothesis for a single gene control of the resistance. The estimated realized heritability (h2) of imidacloprid resistance was 0.1141 in the resistant strain of N. lugens.CONCLUSION: The results showed that imidacloprid resistance in N. lugens was autosomal and was expressed as an incompletely dominant trait, probably controlled by multiple genes. Copyright © 2009 Society of Chemical Industry
Acute diarrhoea: recommended management in general practice
Authors: Banks Matthew , Farthing Michael 
Published: February 2009

AbstractIn most cases, acute diarrhoea presenting in general practice is self‐limiting; it is important, however, to recognise when further treatment is required. Here, the authors discuss the causes and recommended management, followed by a review of prescription data, sources of further information and the Datafile. Copyright © 2006 Wiley Interface Ltd