bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular dynamics study of chemically engineered green fluorescent protein mutants: Comparison of intramolecular fluorescence resonance energy transfer rate
Authors: Mitchell Felicity L. , Frank Filipp , Marks Gabriel E. , Suzuki Miho , Douglas Kenneth T. , Bryce Richard A. 
Published: September 2008

AbstractBecause of its unusual spectroscopic properties, green fluorescent protein (GFP) has become a useful tool in molecular genetics, biochemistry and cell biology. Here, we computationally characterize the behavior of two GFP constructs, designed as bioprobes for enzymatic triggering using intramolecular fluorescence resonance energy transfer (FRET). These constructs differ in the location of an intramolecular FRET partner, an attached chemical chromophore (either near an N‐terminal or C‐terminal site). We apply the temperature replica exchange molecular dynamics method to the two flexible constructs in conjunction with a generalized Born implicit solvent model. The calculated rate of FRET was derived from the interchromophore distance, R, and orientational factor, κ2. In agreement with experiment, the construct with the C‐terminally attached dye was predicted to have higher energy transfer rate than observed for the N‐terminal construct. The molecular basis for this observation is discussed. In addition, we find that the orientational factor, κ2, deviates from the commonly assumed value, the implications of which are also considered. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Residue‐wise conformational stability of DLC8 dimer from native‐state hydrogen exchange
Authors: Mohan P. M. Krishna , Chakraborty Swagata , Hosur Ramakrishna V. 
Published: September 2008

AbstractDynein light chain (DLC8) is the smallest subunit of the dynein motor complex, which is known to act as a cargo adaptor in intracellular trafficking. The protein exists as a pure dimer at physiological pH and a completely folded monomer below pH 4. Here, we have determined the energy landscape of the dimeric protein using a combination of optical techniques and native‐state hydrogen exchange of amide groups, the former giving the global features and the latter yielding the residue level details. The data indicated the presence of intermediates along the equilibrium unfolding transition. The hydrogen exchange data suggested that the molecule has differential stability in its various segments. We deduce from the free energy data that the antiparallel β‐sheets (β4 and β5) that form the hydrophobic core of the protein and the α2 helix, all of which are highly protected with regard to hydrogen exchange, contribute significantly to the initial step of the protein folding mechanism. Denaturant‐dependent hydrogen exchange indicated further that some amides exchange via local fluctuations, whereas there are others which exchange via global unfolding events. Implications of these to cargo adaptability of the dimer are discussed. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Theoretical modeling of the O‐intermediate structure of bacteriorhodopsin
Authors: Watanabe Hiroshi C. , Ishikura Takakazu , Yamato Takahisa 
Published: September 2008

AbstractBacteriorhodopsin is a prototype of efficient molecular machinery functioning as a light‐activated proton pump. Among the five distinct intermediates (K, L, M, N, and O) of the photocycle, there is less structural information on the later stages compared with the early intermediates. Here, we report the structural modeling of the O‐intermediate for which the determination of experimental structure remains difficult. Hypothetical conformational change of the molecule from the light‐adapted state to the O‐intermediate state was simulated by gradually changing the protonation state of two residues. To achieve accurate molecular modeling, we carefully constructed a realistic system of the native purple membrane. The modeled structure of the O‐intermediate has some implications about proton transfer in the later stages of the photocycle and the structural response of bacteriorhodopsin to the inner charge distribution. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures
Authors: Labute Paul 
Published: September 2008

AbstractA new method, called Protonate3D, is presented for the automated prediction of hydrogen coordinates given the 3D coordinates of the heavy atoms of a macromolecular structure. Protonate3D considers side‐chain “flip,” rotamer, tautomer, and ionization states of all chemical groups, ligands, and solvent, provided suitable templates are available in a parameter file. The energy model includes van der Waals, Coulomb, solvation, rotamer, tautomer, and titration effects. The results of computational validation experiments suggest that Protonate3D can accurately predict the location of hydrogen atoms in macromolecular structures. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Structural analysis of fish versus mammalian hemoglobins: Effect of the heme pocket environment on autooxidation and hemin loss
Authors: Aranda Roman , Cai He , Worley Chad E. , Levin Elena J. , Li Rong , Olson John S. , Phillips George N. , Richards Mark P. 
Published: September 2008

AbstractThe underlying stereochemical mechanisms for the dramatic differences in autooxidation and hemin loss rates of fish versus mammalian hemoglobins (Hb) have been examined by determining the crystal structures of perch, trout IV, and bovine Hb at high and low pH. The fish Hbs autooxidize and release hemin ∼50‐ to 100‐fold more rapidly than bovine Hb. Five specific amino acid replacements in the CD corner and along the E helix appear to cause the increased susceptibility of fish Hbs to oxidative degradation compared with mammalian Hbs. Ile is present at the E11 helical position in most fish Hb chains whereas a smaller Val residue is present in all mammalian α and β chains. The larger IleE11 side chain sterically hinders bound O2 and facilitates dissociation of the neutral superoxide radical, enhancing autooxidation. Lys(E10) is found in most mammalian Hb and forms favorable electrostatic and hydrogen bonding interactions with the heme‐7‐propionate. In contrast, Thr(E10) is present in most fish Hbs and is too short to stabilize bound heme, and causes increased rates of hemin dissociation. Especially high rates of hemin loss in perch Hb are also due to a lack of electrostatic interaction between His(CE3) and the heme‐6 propionate in α subunits whereas this interaction does occur in trout IV and bovine Hb. There is also a larger gap for solvent entry into the heme crevice near β CD3 in the perch Hb (∼8 Å) compared with trout IV Hb (∼6 Å) which in turn is significantly higher than that in bovine Hb (∼4 Å) at low pH. The amino acids at CD4 and E14 differ between bovine and the fish Hbs and have the potential to modulate oxidative degradation by altering the orientation of the distal histidine and the stability of the E‐helix. Generally rapid rates of lipid oxidation in fish muscle can be partly attributed to the fact that fish Hbs are highly susceptible to oxidative degradation. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Computational insights into the interaction of the anthrax lethal factor with the N‐terminal region of its substrates
Authors: Joshi Manali , Ebalunode Jerry Osagie , Briggs James M. 
Published: September 2008

AbstractThe anthrax lethal factor is a zinc metalloprotease toxin secreted by Bacillus anthracis which cleaves at the N‐terminal region of six mitogen activated protein kinase kinases (MEKs) in the cell. Additionally, it is known to cleave a nine residue peptide “LF10,” 50‐fold more efficiently than nine residues of MEK1. There is very little sequence similarity between the MEK N‐termini, thus, it is unclear how the lethal factor can accommodate and cleave the diverse N‐termini of the MEKs and whether there is a hierarchy in this interaction, as there is between LF10 and MEK1. To investigate this problem, we carried out multiple molecular dynamics simulations of the lethal factor with nine residues of each of the substrates. Our simulations reveal that like LF10, certain MEK substrates have residue compositions that favor β‐sheet formation with the lethal factor over others. The formation of this secondary structure maintains a catalytic conformation. Binding energetics using the MM‐PBSA method was used to rank‐order the substrates for their affinity to LF (KM). On the basis of the results, we conclude that the LF does not equally accommodate the MEK substrates and further predict that there will be differences between rates of cleavage among the nine residue MEK N‐termini. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Identification of selectivity‐determining residues in cytochrome P450 monooxygenases: A systematic analysis of the substrate recognition site 5
Authors: Seifert Alexander , Pleiss Jürgen 
Published: September 2008

AbstractThe large and diverse family of cytochrome P450 monooxygenases (CYPs) was systematically analyzed to identify selectivity‐ and specificity‐determining residues in the substrate recognition site 5, which is located in close vicinity to the heme center. A positively charged heme‐interacting residue was identified in the structures of 29 monooxygenases and in 97.7% of the 6379 CYP sequences investigated here. This heme‐interacting residue restricts the conformation of the substrate recognition site 5 and is preferentially located at position 10 or 11 after the conserved ExxR motif (in 94.4% of the sequences), in 3.3% of the sequences at position 9 or 12. As a result, a classification by the position of the heme‐interacting residue allows to predict residues that are closest to the heme center and restrict its accessibility. In 98.4% of all CYP sequences a preferentially hydrophobic residue is located at position 5 after the ExxR motif that is predicted to point close to the heme center. Replacing this residue by hydrophobic residues of different size has been shown to change substrate specificity and regioselectivity for CYPs of different superfamilies. Twenty‐seven percent of all CYPs are predicted to contain a second selectivity‐determining residue at position 9 after the ExxR motif that can be identified by the pattern EXXR‐X(7)‐{P}‐x‐P‐[HKR]. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Mechanism for multiple‐substrates recognition of α‐aminoadipate aminotransferase fromThermus thermophilus
Authors: Tomita Takeo , Miyagawa Tomoharu , Miyazaki Takashi , Fushinobu Shinya , Kuzuyama Tomohisa , Nishiyama Makoto 
Published: September 2008

Abstractα‐Aminoadipate aminotransferase (AAA‐AT), a homolog of mammalian kynurenine aminotransferase II (Kat II), transfers an amino group to 2‐oxoadipate to yield α‐aminoadipate in lysine biosynthesis through the α‐aminoadipate pathway inThermus thermophilus. AAA‐AT catalyzes transamination against various substrates, including AAA, glutamate, leucine, and aromatic amino acids. To elucidate the structural change for recognition of various substrates, we determined crystal structures of AAA‐AT in four forms: with pyridoxal 5′‐phosphate (PLP) (PLP complex), with PLP and leucine (PLP/Leu complex), withN‐phosphopyridoxyl‐leucine (PPL) (PPL complex), and withN‐phosphopyridoxyl‐α‐aminoadipate (PPA) at 2.67, 2.26, 1.75, and 1.67 Å resolution, respectively. The PLP complex is in an open state, whereas PLP/Leu, PPL, and PPA complexes are in closed states with maximal displacement (over 7 Å) of the α2 helix and the β1 strand in the small domain to cover the active site, indicating that conformational change is induced by substrate binding. In PPL and PLP/Leu complexes, several hydrophobic residues on the α2 helix recognize the hydrophobic side chain of the bound leucine moiety whereas, in the PPA complex, the α2 helix rotates to place the guanidium moiety of Arg23 on the helix at the appropriate position to interact with the carboxyl side chain of the AAA moiety. These results indicate that AAA‐AT can recognize various kinds of substrates using the mobile α2 helix. The crystal structures and site‐directed mutagenesis revealed that intersubunit‐electrostatic interactions contribute to the elevated thermostability of this enzyme. Proteins 2009. © 2008 Wiley‐Liss, Inc.
AU‐rich RNA‐binding induces changes in the quaternary structure of AUH
Authors: Kurimoto Kazuki , Kuwasako Kanako , Sandercock Alan M. , Unzai Satoru , Robinson Carol V. , Muto Yutaka , Yokoyama Shigeyuki 
Published: September 2008

AbstractThe human AU RNA binding protein/enoyl‐Coenzyme A hydratase (AUH) is a 3‐hydroxy‐3‐methylglutaconyl‐CoA dehydratase in the leucine degradation pathway. It also possesses an RNA‐binding activity to AUUU repeats, which involves no known conserved RNA‐binding domains and is seemingly unrelated to the enzymatic activity. In this study, we performed mass spectrometric analyses to elucidate the oligomeric states of AUH in the presence and absence of RNA. With a short RNA (AUUU) or without RNA, AUH mainly exists as a trimer in solution. On the other hand, the AUH trimer dimerizes upon binding to one molecule of a long RNA containing 24 repeats of the AUUU motif, (AUUU)24A. AUH was crystallized with the long RNA. Although the RNA was disordered in the crystalline lattice, the AUH structure was determined as an asymmetric dimer of trimers with a kink in the alignment of the trimer axes, resulting in the formation of two clefts with significantly different sizes. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Ferric uptake regulator protein: Binding free energy calculations and per‐residue free energy decomposition
Authors: Ahmad Rafi , Brandsdal Bjørn Olav , Michaud‐Soret Isabelle , Willassen Nils‐Peder 
Published: September 2008

AbstractIron homeostasis is, in many bacterial species, mediated by the ferric uptake regulator (Fur). A regulatory site able to bind iron to activate Fur for DNA binding has been described, and a structural zinc site essential for the dimerization has also been proposed. They have been localized and named site 1 and site 2, respectively, from the crystal structure of a zinc‐substituted Pseudomonas aeruginosa Fur (PA‐Fur). Notwithstanding the studies on Fur proteins from various species, both the precise site of iron binding and the effect on DNA binding affinity are still controversial. These issues were investigated here by molecular dynamics simulations and free energy calculations. Simulations were performed for eight molecular systems represented by the three forms of Fur, that is, apo Fur, metal‐substituted Fur, and Fur complexed with DNA. Because of the lack of a Fur‐DNA complex crystal structure, the recently published model based on mass spectrometry experiments on Escherichia coli Fur (EC‐Fur), and the crystal structure of PA‐Fur, was used, after adjustment to adopt a symmetric conformation. The simulation results suggest that the formerly proposed site 2 is, in fact, the regulatory iron‐sensing site. The calculations also predict that Fe2+ at site 2 is hexacoordinated having an octahedral environment with only nitrogen and oxygen atoms, which is in accordance with previous spectroscopic characterizations. Energy decomposition pinpoints H87 as an additional amino acid that defines the regulatory metal site. Finally, free energy decomposition analysis reveals a number of amino acids potentially important in dimerization and in DNA binding. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Opening of the ADP‐bound active site in the ABC transporter ATPase dimer: Evidence for a constant contact, alternating sites model for the catalytic cycle
Authors: Jones Peter M. , George Anthony M. 
Published: September 2008

AbstractABC transporters are ubiquitous, ATP‐dependent transmembrane pumps. The mechanism by which ATP hydrolysis in the nucleotide‐binding domain (NBD) effects conformational changes in the transmembrane domain that lead to allocrite translocation remains largely unknown. A possible aspect of this mechanism was suggested by previous molecular dynamics simulations of the MJ0796 NBD dimer, which revealed a novel, nucleotide‐dependent intrasubunit conformational change involving the relative rotation of the helical and catalytic subdomains. Here, we find that in four of five simulations of the ADP/ATP‐bound dimer, the relative rotation of the helical and catalytic subdomains in the ADP‐bound monomer results in opening of the ADP‐bound active site, probably sufficient or close to sufficient to allow nucleotide exchange. We also observe that in all five simulations of the ADP/ATP‐bound dimer, the intimate contact of the LSGGQ signature sequence with the ATP γ‐phosphate is weakened by the intrasubunit conformational change within the ADP‐bound monomer. We discuss how these results support a constant contact model for the function of the NBD dimer in contrast to switch models, in which the NBDs are proposed to fully disassociate during the catalytic cycle. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Targeting the early steps of Aβ16–22 protofibril disassembly by N‐methylated inhibitors: A numerical study
Authors: Chebaro Yassmine , Derreumaux Philippe 
Published: September 2008

AbstractAggregation of the Aβ1–40/Aβ1–42 peptides is a key factor in Alzheimer's disease. Though the inhibitory effect of N‐methylated Aβ16–22 (mAβ16–22) peptides is well characterized in vitro, there is little information on how they disassemble full‐length Aβ fibrils or block fibril formation. Here, we report coarse‐grained implicit solvent molecular dynamics (MD) and replica exchange molecular dynamics (REMD) simulations on Aβ16–22 and mAβ16–22 monomers, and then a preformed six‐chain Aβ16–22 bilayer with either four copies of Aβ16–22 or four copies of mAβ16–22. Our simulations show that the effect of N‐methylation on mAβ16–22 monomer is to reduce the density of compact forms. While 100 ns MD trajectories do not reveal any significant differences between the two ten‐chain systems, the REMD simulations totaling 1 μs help understand the first steps of Aβ16–22 protofibril disassembly by N‐methylated inhibitors. Notably, we find that mAβ16–22 preferentially interacts with Aβ16–22 by blocking both β‐sheet extension and lateral association of layers, but also by intercalation of the inhibitors allowing sequestration of Aβ16–22 peptides. This third binding mode is particularly appealing for blocking Aβ fibrillogenesis. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Shape complementarity of protein–protein complexes at multiple resolutions
Authors: Zhang Qing , Sanner Michel , Olson Arthur J. 
Published: September 2008

AbstractBiological complexes typically exhibit intermolecular interfaces of high shape complementarity. Many computational docking approaches use this surface complementarity as a guide in the search for predicting the structures of protein–protein complexes. Proteins often undergo conformational changes to create a highly complementary interface when associating. These conformational changes are a major cause of failure for automated docking procedures when predicting binding modes between proteins using their unbound conformations. Low resolution surfaces in which high frequency geometric details are omitted have been used to address this problem. These smoothed, or blurred, surfaces are expected to minimize the differences between free and bound structures, especially those that are due to side chain conformations or small backbone deviations. Despite the fact that this approach has been used in many docking protocols, there has yet to be a systematic study of the effects of such surface smoothing on the shape complementarity of the resulting interfaces. Here we investigate this question by computing shape complementarity of a set of 66 protein–protein complexes represented by multiresolution blurred surfaces. Complexed and unbound structures are available for these protein–protein complexes. They are a subset of complexes from a nonredundant docking benchmark selected for rigidity (i.e. the proteins undergo limited conformational changes between their bound and unbound states). In this work, we construct the surfaces by isocontouring a density map obtained by accumulating the densities of Gaussian functions placed at all atom centers of the molecule. The smoothness or resolution is specified by a Gaussian fall‐off coefficient, termed “blobbyness.” Shape complementarity is quantified using a histogram of the shortest distances between two proteins' surface mesh vertices for both the crystallographic complexes and the complexes built using the protein structures in their unbound conformation. The histograms calculated for the bound complex structures demonstrate that medium resolution smoothing (blobbyness = −0.9) can reproduce about 88% of the shape complementarity of atomic resolution surfaces. Complexes formed from the free component structures show a partial loss of shape complementarity (more overlaps and gaps) with the atomic resolution surfaces. For surfaces smoothed to low resolution (blobbyness = −0.3), we find more consistency of shape complementarity between the complexed and free cases. To further reduce bad contacts without significantly impacting the good contacts we introduce another blurred surface, in which the Gaussian densities of flexible atoms are reduced. From these results we discuss the use of shape complementarity in protein–protein docking. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Nonrandom distribution of intramolecular contacts in native single‐domain proteins
Authors: Mounce Bryan C. , Kurt Neşe , Ellison Paul A. , Cavagnero Silvia 
Published: September 2008

AbstractThe interplay of short‐ and long‐range interactions in protein structure and folding is poorly understood. This study focuses on the distribution of intramolecular contacts across different regions of the polypeptide chain in soluble single‐domain proteins. We show that while the average number of intramolecular interactions per residue is similar across all regions of the sequence, the interaction counterparts are distributed nonrandomly. Two types of proteins are observed. The first class comprises structures that have the majority of their intramolecular contacts linking amino acids within the same region of the sequence (i.e., N‐/C‐terminal or intermediate portion of the chain). A second smaller class includes proteins that have extensive contacts between the N and C termini. Such extensive interactions involve primarily distal β‐strands and are detected via the NCR parameter, a descriptor of the number of contacts with interaction counterparts in specific regions of the sequence. In summary, the majority of single‐domain proteins (first class) is dominated by short‐range interactions between contiguous elements of secondary structure and has only sparse contacts among the N and C termini. This finding defies the common assumption that the chain termini, often spatially close in folded proteins, have to participate in a large number of mutual interactions. Finally, our results suggest that the C‐terminal region of Class 2 proteins may be particularly effective at promoting folding upon completion of protein biosynthesis in the cell. Proteins 2009. © 2008 Wiley‐Liss, Inc.