Time to face the fats : What can mass spectrometry reveal about the structure of lipids and their interactions with proteins?

Since the 1950s, X-ray crystallography has been the mainstay of structural biology, providing detailed atomic-level structures that continue to revolutionize our understanding of protein function. From recent advances in this discipline, a picture has emerged of intimate and specific interactions between lipids and proteins that has driven renewed interest in the structure of lipids themselves and raised intriguing questions as to the specificity and stoichiometry in lipid-protein complexes. Herein we demonstrate some of the limitations of crystallography in resolving critical structural features of ligated lipids and thus determining how these motifs impact protein binding. As a consequence, mass spectrometry must play an important and complementary role in unraveling the complexities of lipid-protein interactions. We evaluate recent advances and highlight ongoing challenges towards the twin goals of (1) complete structure elucidation of low, abundant, and structurally diverse lipids by mass spectrometry alone, and (2) assignment of stoichiometry and specificity of lipid interactions within protein complexes.

Contrast transfer function correction applied to cryo-electron tomography and sub-tomogram averaging

Cryo-electron tomography together with averaging of sub-tomograms containing identical particles can reveal the structure of proteins or protein complexes in their native environment. The resolution of this technique is limited by the contrast transfer function (CTF) of the microscope. The CTF is not routinely corrected in cryo-electron tomography because of difficulties including CTF detection, due to the low signal to noise ratio, and CTF correction, since images are characterised by a spatially variant CTF. Here we simulate the effects of the CTF on the resolution of the final reconstruction, before and after CTF correction, and consider the effect of errors and approximations in defocus determination. We show that errors in defocus determination are well tolerated when correcting a series of tomograms collected at a range of defocus values. We apply methods for determining the CTF parameters in low signal to noise images of tilted specimens, for monitoring defocus changes using observed magnification changes, and for correcting the CTF prior to reconstruction. Using bacteriophage PRDI as a test sample, we demonstrate that this approach gives an improvement in the structure obtained by sub-tomogram averaging from cryo-electron tomograms.

Identification of a BRCA1-mRNA splicing complex required for efficient DNA repair and maintenance of genomic stability

Mutations within BRCA1 predispose carriers to a high risk of breast and ovarian cancers. BRCA1 functions to maintain genomic stability through the assembly of multiple protein complexes involved in DNA repair, cell-cycle arrest, and transcriptional regulation. Here, we report the identification of a DNA damage-induced BRCA1 protein complex containing BCLAF1 and other key components of the mRNA-splicing machinery. In response to DNA damage, this complex regulates pre-mRNA splicing of a number of genes involved in DNA damage signaling and repair, thereby promoting the stability of these transcripts/proteins. Further, we show that abrogation of this complex results in sensitivity to DNA damage, defective DNA repair, and genomic instability. Interestingly, mutations in a number of proteins found within this complex have been identified in numerous cancer types. These data suggest that regulation of splicing by the BRCA1-mRNA splicing complex plays an important role in the cellular response to DNA damage.

Androgen receptor-dependent and independent functions of ARIP4

Androgen receptor (AR) is necessary for normal male phenotype development and essential for spermatogenesis. AR is a classical steroid receptor mediating actions of male sex steroids testosterone and 5-alpha-dihydrotestosterone. Numerous coregulators interact with the receptor and regulate AR activity on target genes. This study deals with the characterization of androgen receptor-interacting protein 4 (ARIP4). ARIP4 binds DNA, interacts with AR in vitro and in cultured yeast and mammalian cells, and modulates AR-dependent transactivation. ARIP4 is an active DNA-dependent ATPase, and this enzymatic activity is essential for the ability of ARIP4 to modulate AR function. On the basis of sequence homology in its ATPase domain, ARIP4 belongs to the SNF2 family of proteins involved in chromatin remodeling, DNA repair, and homologous recombination. Similar to its closest homologs ATRX and Rad54, ARIP4 does not seem to be a classical chromatin remodeling protein in that it does not appear to form large protein complexes in vivo or remodel mononucleosomes in vitro. However, ARIP4 is able to generate superhelical torsion on linear DNA fragments. ARIP4 is covalently modified by SUMO-1, and mutation of six potential SUMO attachment sites abolishes the ability of ARIP4 to bind DNA, hydrolyze ATP, and activate AR function. ARIP4 expression starts in early embryonic development. In mouse embryo ARIP4 is present mainly in the neural tube and limb buds. In adult mouse tissues ARIP4 expression is virtually ubiquitous. In mouse testis ARIP4 is expressed in the nuclei of Sertoli cells in a stage-dependent manner. ARIP4 is also present in the nuclei of Leydig cells, spermatogonia, pachytene and diplotene spermatocytes. Testicular expression pattern of ARIP4 does not differ significantly in wild-type, FSHRKO, and LuRKO mice. In the testis of hpg mice, ARIP4 is found mainly in interstitial cells and has very low, if any, expression in Sertoli and germ cells. Heterozygous Arip4+/ mice are fertile and appear normal; however, they are haploinsufficient with regard to androgen action in Sertoli cells. In contrast, Arip4 / embryos are not viable. They have significantly reduced body size at E9.5 and die by E11.5. Compared to wild-type littermates, Arip4 / embryos possess a higher percentage of apoptotic cells at E9.5 and E10.5. Fibroblasts derived from Arip4 / embryos cease growing after 2-3 passages and exhibit a significantly increased apoptosis and decreased proliferation rate than cells from wild-type embryos. Our findings demonstrate that ARIP4 plays an essential role in mouse embryonic development. In addition, testicular expression and AR coregulatory activity of ARIP4 suggest a role of ARIP4-AR interaction in the somatic cells of the testis.

Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks

The interdependence of the concept of allostery and enzymatic catalysis, and they being guided by conformational mobility is gaining increased prominence. However, to gain a molecular level understanding of llostery and hence of enzymatic catalysis, it is of utter importance that the networks of amino acids participating in allostery be deciphered. Our lab has been exploring the methods of network analysis combined with molecular dynamics simulations to understand allostery at molecular level. Earlier we had outlined methods to obtain communication paths and then to map the rigid/flexible regions of proteins through network parameters like the shortest correlated paths, cliques, and communities. In this article, we advance the methodology to estimate the conformational populations in terms of cliques/communities formed by interactions including the side-chains and then to compute the ligand-induced population shift. Finally, we obtain the free-energy landscape of the protein in equilibrium, characterizing the free-energy minima accessed by the protein complexes. We have chosen human tryptophanyl-tRNA synthetase (hTrpRS), a protein esponsible for charging tryptophan to its cognate tRNA during protein biosynthesis for this investigation. This is a multidomain protein exhibiting excellent allosteric communication. Our approach has provided valuable structural as well as functional insights into the protein. The methodology adopted here is highly generalized to illuminate the linkage between protein structure networks and conformational mobility involved in the allosteric mechanism in any protein with known structure.

Adiabatic eigenfunction-based approach for coherent excitation transfer: An almost analytical treatment of the Fenna-Matthews-Olson complex

We suggest a method of studying coherence in finite-level systems coupled to the environment and use it for the Hamiltonian that has been used to describe the light-harvesting pigment-protein complex. The method works with the adiabatic states and transforms the Hamiltonian to a form in which the terms responsible for decoherence and population relaxation are separated out. Decoherence is then accounted for nonperturbatively and population relaxation using a Markovian master equation. Almost analytical results can be obtained for the seven-level system, and the calculations are very simple for systems with more levels. We apply the treatment to the seven-level system, and the results are in excellent agreement with the exact numerical results of Nalbach et al. Nalbach, Braun, and Thorwart, Phys. Rev. E 84, 041926 (2011)]. Our approach is able to account for decoherence and population relaxation separately. It is found that decoherence causes only damping of oscillations and does not lead to transfer to the reaction center. Population relaxation is necessary for efficient transfer to the reaction center, in agreement with earlier findings. Our results show that the transformation to the adiabatic basis followed by a Redfield type of approach leads to results in good agreement with exact simulation.

TSpred: a web server for the rational design of temperature-sensitive mutants

Temperature sensitive (Ts) mutants of proteins provide experimentalists with a powerful and reversible way of conditionally expressing genes. The technique has been widely used in determining the role of gene and gene products in several cellular processes. Traditionally, Ts mutants are generated by random mutagenesis and then selected though laborious large-scale screening. Our web server, TSpred (http://mspc.bii.a-star.edu.sg/TSpred/), now enables users to rationally design Ts mutants for their proteins of interest. TSpred uses hydrophobicity and hydrophobic moment, deduced from primary sequence and residue depth, inferred from 3D structures to predict/identify buried hydrophobic residues. Mutating these residues leads to the creation of Ts mutants. Our method has been experimentally validated in 36 positions in six different proteins. It is an attractive proposition for Ts mutant engineering as it proposes a small number of mutations and with high precision. The accompanying web server is simple and intuitive to use and can handle proteins and protein complexes of different sizes.

Chemical specificity and conformational flexibility in proteinase-inhibitor interaction: Scaffolds for promiscuous binding

One of the most important roles of proteins in cellular milieu is recognition of other biomolecules including other proteins. Protein protein complexes are involved in many essential cellular processes. Interfaces of protein protein complexes are traditionally known to be conserved in evolution and less flexible than other solvent interacting tertiary structural surface. But many examples are emerging where these features do not hold good. An understanding of inter-play between flexibility and sequence conservation is emerging, providing a fresh dimension to the paradigm of sequence structure function relationship. The functional manifestation of the inter-relation between sequence conservation and flexibility of interface is exemplified in this review using proteinase inhibitor protein complexes. (C) 2014 Elsevier Ltd. All rights reserved.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated.We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard–Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

The Metabolic Core and Catalytic Switches Are Fundamental Elements in the Self-Regulation of the Systemic Metabolic Structure of Cells

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Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated. We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard-Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

Engineering multi-step electron tunneling systems in proteins

Multi-step electron tunneling, or “hopping,” has become a fast-developing research field with studies ranging from theoretical modeling systems, inorganic complexes, to biological systems. In particular, the field is exploring hopping mechanisms in new proteins and protein complexes, as well as further understanding the classical biological hopping systems such as ribonuclease reductase, DNA photolyases, and photosystem II. Despite the plethora of natural systems, only a few biologically engineered systems exist. Engineered hopping systems can provide valuable information on key structural and electronic features, just like other kinds of biological model systems. Also, engineered systems can harness common biologic processes and utilize them for alternative reactions. In this thesis, two new hopping systems are engineered and characterized.

The protein Pseudomonas aeruginosa azurin is used as a building block to create the two new hopping systems. Besides being well studied and amenable to mutation, azurin already has been used to successfully engineer a hopping system. The two hopping systems presented in this thesis have a histidine-attached high potential rhenium 4,7-dimethyl-1,10-phenanthroline tricarbonyl [Re(dmp)(CO)3] + label which, when excited, acts as the initial electron acceptor. The metal donor is the type I copper of the azurin protein. The hopping intermediates are all tryptophan, an amino acid mutated into the azurin at select sites between the photoactive metal label and the protein metal site. One system exhibits an inter-molecular hopping through a protein dimer interface; the other system undergoes intra-molecular multi-hopping utilizing a tryptophan “wire.” The electron transfer reactions are triggered by excitation of the rhenium label and monitored by UV-Visible transient absorption, luminescence decays measurements, and time-resolved Infrared spectroscopy (TRIR). Both systems were structurally characterized by protein X-ray crystallography.

牛耳草Bose hygrometrica 离体叶脱水-复水过程的光合作用及基因表达

本文以复苏植物牛耳草Boea hygrometrica成熟植株的离体叶片为试材，对比非复苏植物烟叶唇苣苔Chirita heterotricha, 以光合作用在脱水－复水过程中的变化为切入点，从生理水平上探讨其脱水保护位点：应用mRNA差异显示技术，从分子水平上探讨其脱水保护机制。 光合放氧速率、快速荧光诱导动力学、慢速荧光诱导动力学、荧光发射光谱、荧光激发谱的结果表明，相对于烟叶唇柱苣苔，脱水对牛耳草净光合速率、PS II和PS I光化学活性、电子传递、光合磷酸化及CO_2固定的影响有一个共同的特点，即脱水时迅速降低，复水后恢复能力强。通过非变性绿胶的研究牛耳草叶片类囊体膜叶绿素－蛋白复合体在脱水－复水过程中保持高度稳定。色素含量分析表明牛耳草的叶绿素含量在脱水－复水过程中也相对稳定。这些特征可能是牛耳草叶片光合作用脱水保护机制的一部分。 SDS－PAGE和IEF电泳结果表明，牛耳草脱水复苏过程中蛋白质表达有差异，或增或减，并分别发现了一条（SDS－PAGE）和两条（IEF）在脱水过程中特异出现的蛋白质。 本文以银染法代替放射自显影用于mRNA差异显示，不但简化了实验步骤，缩短了实验周期，而且在不降低灵敏度的前提下避免了放射性危害，降低了实验成本。本文证明了mRNA差异银染显示法用于复苏植物牛耳草脱水－复水过程中基因表达变化的研究是可行的。 mRNA差异银染显示法揭示牛耳草耐脱水复苏机制涉及到基因表达的调控。脱水－复水过程中差异表达的基因有6种，其中脱水特异诱导表达的13个cDNA所相应的基因、脱水上调节的15个cDNA所相应的基因可能参与牛耳草叶片脱水保护机制，复水特异诱导的8个cDNA的所相应基因可能参与牛耳草复水后的修复机制。2个脱水特异诱导表达的cDNA片段进行了克隆和测序。

高等植物PSI颗粒的分离提纯及其光破坏机理的初步探讨

从菠菜叶绿体中分离提纯PSI颗粒及其捕光天线色素蛋白复合物LHCI，对其光谱特性进行分析。对PSI颗粒中色素和蛋白的光破坏进程，并对外加组氨酸、Triton，以及温度对PSI颗粒光破坏的影响等进行了比较系统的研究，以探讨PSI光破坏的机理。其主要结果如下： 1. 对PSI颗粒和LHCI色素蛋白复合物的荧光光谱的研究，发现PSI中Chlb所吸收的光能主要传递给LHCI中的“长波组分”（吸收波长大于P700的Chla）。 2. 在PSI颗粒光破坏进程的研究中发现，Chla中吸收波长较长的组分首先发生光破坏;位于PSI颗粒外围的LHCI上的Chlb，也容易受到光破坏;Car先于Chlb发生光破坏。在光照处理过程中，PSI的天线色素蛋白复合物LHCI多肽降解程度大于反应中心多肽组分（PsaA，PsaB）的降解，其中LHCI-680首先由于光破坏而发生降解。PsaD也是容易受到光破坏而发生降解的一个多肽。另外，还发现在长时间光照后有蛋白聚合现象发生。 3. 在PSI颗粒中外加单线态氧的淬灭剂组氨酸，分析不同光强光照处理过程中组氨酸对PSI颗粒中色素和多肽光破坏的保护作用，发现外加组氨酸对强光照（2300μEm-2s-1）引起的叶绿素光吸收减少和CD信号减弱的有效抑制表现出一个明显的延迟期，但对强光诱导的荧光产量下降的效应却能立即表现出来;在强光照前期和弱光照（300μEm-2s-1）条件下，组氨酸不能抑制PSI颗粒的光吸收下降。另外，外加组氨酸除了对反应中心多肽有光保护作用以外，对PSI中其它多肽也有显著的保护作用。 4. 用不同浓度的Triton处理PSI颗粒，发现较低浓度的Triton可以增大叶绿素的光吸收和PSI颗粒的荧光产量，而不对PSI颗粒的多肽组成造成影响;当Triton浓度达到一定的程度时，虽然不会影响PSI颗粒的多肽组成，但是会使其光吸收减少，荧光产量下降;而当Triton浓度过高时，PSI颗粒的多肽会发生降解现象，同时其光吸收和荧光产量也迅速下降。Triton浓度较低时，PSI颗粒光破坏的程度随Triton浓度的增大而增大，当Triton浓度增大到一定的程度时，PSI颗粒的光破坏程度同Triton浓度不再呈明显的正相关。 5. 对PSI颗粒进行不同温度的热处理，其结果表明：温度较低（20 ℃～40 ℃）的热处理对PSI颗粒的多肽和叶绿素光吸收的影响程度很小，照光后不同温度热处理过的PSI颗粒光吸收减少和多肽降解的程度相近;温度较高（50 ℃～60 ℃）的热处理会对PSI颗粒的结构产生影响，使之稳定性减小，对光处理更敏感;温度更高（大于70 ℃）的热处理会破坏PSI颗粒的结构，引起多肽组分的降解。另外，不同的多肽对热处理的敏感性显著不同。 6. 低温（4 ℃）和常温（20 ℃）下PSI颗粒光破坏的比较发现，室温下PSI颗粒的光破坏程度明显大于低温下光破坏的程度，表明光处理过程中温度会影响到PSI颗粒光破坏的程度。 通过上述的研究结果，分析了PSI颗粒光破坏过程中色素和蛋白的变化及其外界因子的影响，对PSI颗粒光破坏的机制进行了初步的探讨。

Bayesian correlated clustering to integrate multiple datasets.

MOTIVATION: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct-but often complementary-information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured through parameters that describe the agreement among the datasets. RESULTS: Using a set of six artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real Saccharomyces cerevisiae datasets. In the two-dataset case, we show that MDI's performance is comparable with the present state-of-the-art. We then move beyond the capabilities of current approaches and integrate gene expression, chromatin immunoprecipitation-chip and protein-protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques-as well as to non-integrative approaches-demonstrate that MDI is competitive, while also providing information that would be difficult or impossible to extract using other methods.