Chloromethyl-oxirane and chloromethyl-thiirane in liquid phase: A joint experimental and quantum chemical study
Contributors: M. Campetella, L. Bencivenni, R. Caminiti, C. Zazza, S. Di Trapani, A. Martino, L. Gontrani
... The X-ray diffraction spectra of liquid chloromethyl-oxirane (ClMO) and chloromethyl-thiirane (ClMT) have been recorded for the first time. The interpretation of X-ray measurements was based on ab initio molecular dynamics simulations at finite temperature conditions. Both liquids show conformational equilibrium, which is discussed in terms of Gauche-2, Gauche-1 and Cis structures. The occurrence of the various forms estimated from X-ray and AIMD data has been compared with spectroscopy data from the literature, with the FTIR spectra of the liquids newly recorded in this work, and with theoretical in vacuo calculations.
Structural and biochemical characterization of bacterial YpgQ protein reveals a metal-dependent nucleotide pyrophosphohydrolase
Contributors: Ye Ji Jeon, Sun Cheol Park, Wan Seok Song, Ok-Hee Kim, Byung-Chul Oh, Sung-il Yoon
... The optimal balance of cellular nucleotides and the efficient elimination of non-canonical nucleotides are critical to avoiding erroneous mutation during DNA replication. One such mechanism involves the degradation of excessive or abnormal nucleotides by nucleotide-hydrolyzing enzymes. YpgQ contains the histidine-aspartate (HD) domain that is involved in the hydrolysis of nucleotides or nucleic acids, but the enzymatic activity and substrate specificity of YpgQ have never been characterized. Here, we unravel the catalytic activity and structural features of YpgQ to report the first Mn2+-dependent pyrophosphohydrolase that hydrolyzes (deoxy)ribonucleoside triphosphate [(d)NTP] to (deoxy)ribonucleoside monophosphate and pyrophosphate using the HD domain. YpgQ from Bacillus subtilis (bsYpgQ) displays a helical structure and assembles into a unique dimeric architecture that has not been observed in other HD domain-containing proteins. Each bsYpgQ monomer accommodates a metal ion and a nucleotide substrate in a cavity located between the N- and C-terminal lobes. The metal cofactor is coordinated by the canonical residues of the HD domain, namely, two histidine residues and two aspartate residues, and is positioned in close proximity to the β-phosphate group of the nucleotide, allowing us to propose a nucleophilic attack mechanism for the nucleotide hydrolysis reaction. YpgQ enzymes from other bacterial species also catalyze pyrophosphohydrolysis but exhibit different substrate specificity. Comparative structural and mutational studies demonstrated that residues outside the major substrate-binding site of bsYpgQ are responsible for the species-specific substrate preference. Taken together, our structural and biochemical analyses highlight the substrate-recognition mode and catalysis mechanism of YpgQ in pyrophosphohydrolysis.
Structural Fine-Tuning of MIT-Interacting Motif 2 (MIM2) and Allosteric Regulation of ESCRT-III by Vps4 in Yeast
Contributors: Rieko Kojima, Takayuki Obita, Kousuke Onoue, Mineyuki Mizuguchi
... The endosomal sorting complex required for transport (ESCRT) facilitates roles in membrane remodeling, such as multivesicular body biogenesis, enveloped virus budding and cell division. In yeast, Vps4 plays a crucial role in intraluminal vesicle formation by disassembling ESCRT proteins. Vps4 is recruited by ESCRT-III proteins to the endosomal membrane through the interaction between the microtubule interacting and trafficking (MIT) domain of Vps4 and the C-terminal MIT-interacting motif (MIM) of ESCRT-III proteins. Here, we have determined the crystal structure of Vps4–MIT in a complex with Vps20, a member of ESCRT-III, and revealed that Vps20 adopts a unique MIM2 conformation. Based on structural comparisons with other known MIM2s, we have refined the consensus sequence of MIM2. We have shown that another ESCRT-III protein, Ist1, binds to Vps4–MIT via its C-terminal MIM1 with higher affinity than Vps2, but lacks MIM2 by surface plasmon resonance. Surprisingly, the Ist1 MIM1 competed with the MIM2 of Vfa1, a regulator of Vps4, for binding to Vps4–MIT, even though these MIMs bind in non-overlapping sites on the MIT. These findings provide insight into the allosteric recognition of MIMs of ESCRT-III by Vps4 and also the regulation of ESCRT machinery at the last step of membrane remodeling.
Crystal structures of Apo and GMP bound hypoxanthine–guanine phosphoribosyltransferase from Legionella pneumophila and the implications in gouty arthritis
Contributors: Nannan Zhang, Xiaojian Gong, Min Lu, Xiaofang Chen, Ximing Qin, Honghua Ge
... Hypoxanthine–guanine phosphoribosyltransferase (HGPRT) (EC 18.104.22.168) reversibly catalyzes the transfer of the 5-phophoribosyl group from 5-phosphoribosyl-alpha-1-pyrophosphate (PRPP) to hypoxanthine or guanine to form inosine monophosphate (IMP) or guanosine monophosphate (GMP) in the purine salvage pathway. To investigate the catalytic mechanism of this enzyme in the intracellular pathogen Legionella pneumophila, we determined the crystal structures of the L. pneumophila HGPRT (LpHGPRT) both in its apo-form and in complex with GMP. The structures reveal that LpHGPRT comprises a core domain and a hood domain which are packed together to create a cavity for GMP-binding and the enzymatic catalysis. The binding of GMP induces conformational changes of the stable loop II. This new binding site is closely related to the Gout arthritis-linked human HGPRT mutation site (Ser103Arg). Finally, these structures of LpHGPRT provide insights into the catalytic mechanism of HGPRT.
Structural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B
Contributors: Grégoire Rondelet, Thomas Dal Maso, Luc Willems, Johan Wouters
... DNA methylation is an important epigenetic modification involved in chromatin organization and gene expression. The function of DNA methylation depends on cell context and is correlated with histone modification patterns. In particular, trimethylation of Lys36 on histone H3 tail (H3K36me3) is associated with DNA methylation and elongation phase of transcription. PWWP domains of the de novo DNA methyltransferases DNMT3A and DNMT3B read this epigenetic mark to guide DNA methylation. Here we report the first crystal structure of the DNMT3B PWWP domain–H3K36me3 complex. Based on this structure, we propose a model of the DNMT3A PWWP domain–H3K36me3 complex and build a model of DNMT3A (PWWP-ADD-CD) in a nucleosomal context. The trimethylated side chain of Lys36 (H3K36me3) is inserted into an aromatic cage similar to the “Royal” superfamily domains known to bind methylated histones. A key interaction between trimethylated Lys36 and a conserved water molecule stabilized by Ser270 explains the lack of affinity of mutated DNMT3B (S270P) for the H3K36me3 epigenetic mark in the ICF (Immunodeficiency, Centromeric instability and Facial abnormalities) syndrome. The model of the DNMT3A-DNMT3L heterotetramer in complex with a dinucleosome highlights the mechanism for recognition of nucleosome by DNMT3s and explains the periodicity of de novo DNA methylation.
Experimental and theoretical investigation on the structural characterization and orientation preferences of 2-hydroxy-1-naphthoic acid/β-cyclodextrin host-guest inclusion complex
Contributors: K. Sivakumar, T.R. Ragi, D. Prema, T. Stalin
... The inclusion complex formation between 2-hydroxy-1-naphthoic acid (2H1NA) and β-cyclodextrin (β-CD) in liquid, solid and virtual states was investigated. The binding constant of 2H1NA:β-CD complex is estimated in liquid state using cyclic voltammetry (CV) analysis at pH2.75. Drastic increase in the anodic peak current and peak potential with the increase in β-CD concentration is attributed to the inclusion complex formation between β-CD and 2H1NA. The diffusion coefficient, and the electron transfer rate constant (ko) of the 2H1NA:β-CD complex are also estimated using CV studies. The solid 2H1NA:β-CD complex prepared by co-precipitation method is characterized by FTIR, and NMR techniques. The estimated stabilization energies, EHOMO-ELUMO, and MEP maps of complexes infer that guest molecule prefers the orientation in which it experiences lesser steric repulsion effect and scores as a highly stable and energetically favourable. Results of computational studies, semiempirical analysis and experimental investigations correlate well with each other.
The molecular organization of the beta-sheet region in Corneous beta-proteins (beta-keratins) of sauropsids explains its stability and polymerization into filaments
Contributors: Matteo Calvaresi, Leopold Eckhart, Lorenzo Alibardi
... The hard corneous material of avian and reptilian scales, claws, beak and feathers is mainly derived from the presence of proteins formerly known as beta-keratins but now termed Corneous beta-proteins of sauropsids to distinguish them from keratins, which are members of the intermediate filament protein family. The modeling of the conserved 34 amino acid residues long central beta-sheet region of Corneous beta-proteins using an ab initio protein folding and structure prediction algorithm indicates that this region is formed by four antiparallel beta-sheets. Molecular dynamic simulations and Molecular Mechanics/Poisson Boltzmann Surface Area (MM–PBSA) analysis showed that the disposition of polar and apolar amino acids within the beta-region gives rise to an amphipathic core whose stability is further increased, especially in an aqueous environment, by the association into a dimer due to apolar interactions and specific amino-acid interactions. The dimers in turn polymerize into a 3nm thick linear beta-filament due to van der Waals and hydrogen-bond interactions. It is suggested that once this nuclear core of anti-parallel sheets evolved in the genome of a reptilian ancestor of the extant reptiles and birds about 300 millions years ago, new properties emerged in the corneous material forming scales, claws, beaks and feathers in these amniotes based on the tendency of these unique corneous proteins to form stable filaments different from keratin intermediate filaments or sterical structures formed by other corneous proteins so far known.
Contributors: Hila Nudelman, Carmen Valverde-Tercedor, Sofiya Kolusheva, Teresa Perez Gonzalez, Marc Widdrat, Noam Grimberg, Hilla Levi, Or Nelkenbaum, Geula Davidov, Damien Faivre
... Magnetotactic bacteria are Gram-negative bacteria that navigate along geomagnetic fields using the magnetosome, an organelle that consists of a membrane-enveloped magnetic nanoparticle. Magnetite formation and its properties are controlled by a specific set of proteins. MamC is a small magnetosome-membrane protein that is known to be active in iron biomineralization but its mechanism has yet to be clarified. Here, we studied the relationship between the MamC magnetite-interaction loop (MIL) structure and its magnetite interaction using an inert biomineralization protein-MamC chimera. Our determined structure shows an alpha-helical fold for MamC-MIL with highly charged surfaces. Additionally, the MamC-MIL induces the formation of larger magnetite crystals compared to protein-free and inert biomineralization protein control experiments. We suggest that the connection between the MamC-MIL structure and the protein’s charged surfaces is crucial for magnetite binding and thus for the size control of the magnetite nanoparticles.
Structural and molecular basis of cellulase Cel48F by computational modeling: Insight into catalytic and product release mechanism
Contributors: Mengdan Qian, Shanshan Guan, Yaming Shan, Hao Zhang, Song Wang
... As a processive cellulase, Cel48F from Clostridium cellulolyticum plays a crucial role in cellulose fiber degradation. It has been confirmed in experiment that residue Glu44 will greatly affect the catalytic activity but the mechanism is still unknown. In this study, conventional molecular dynamics, steered molecular dynamics and free energy calculation were integrated to simulate the hydrolysis and product release process to gain insights into the factors that influence catalytic activity. Analysis of simulation results indicated that Glu44 could maintain the proper conformation of its substrate to ensure successful cleavage reaction or serve as a base required in the inverting mechanism in hydrolysis. After hydrolysis is completed, residues Glu44, Asp494, Trp611 and Glu55 participate in hydrogen bond rearrangement during product releasing process. This rearrangement can reduce the sliding barrier and stimulate the product to move toward the exit in the initial release stage. Dependent on the rearrangement, the product moves toward the exit and is exposed to an increasing amount of solvent molecules, which makes solvent effect more and more notable. With the assistance of solvent interaction, product can get rid of the enzyme more easily. However, the subsequent release process remains uncertain because of the disordered motion of solvent molecules. This work provides theoretical data as a basis of cellulase modification or mutation.
First principles investigation on the electronic, magnetic and optical properties of Bi0.8M0.2Fe0.9Co0.1O3 (M=La, Gd, Er, Lu)
Contributors: Ning Gao, Wei Chen, Ren Zhang, Jian Zhang, Zhenli Wu, Weiwei Mao, Jianping Yang, Xing’ao Li, Wei Huang
... The effect of La, Gd, Er and Lu dopings (0.2 per unit cell) on the electronic, magnetic and optical properties of BiFe0.9Co0.1O3 (BFCO) were investigated by first-principles calculations. It is found that the La- and Er-dopings reduce the band gaps to 1.72 and 0.81eV and convert the systems to half-metallic, while the Lu and Gd dopings convert the systems to metallic. Notably, the rare-earth element dopings can increase the total magnetic moments by ∼0.2μB per cell. The static dielectric function ε1(0) is equal to 9.0, 7.0, 7.4, 9.2 and 10.5 for the pristine Er-, La-, Gd- and Lu-doped BFCOs respectively. Moreover, the dopings significantly increase the optical reflectivity and the reflection index. Our results show that electronic, magnetic and optical properties in BFCO could be effectively modulated by rare-earth element dopings.