Mechanism Of Conformational Change Research Articles

METHODS OF REGULATING PHYSICAL PROPERTIES OF DOUGH USING PHYTOEXTRACTS

This paper considers the prospects of using phytomaterials to solve the problems of baking industry, caused by the instability and defects of wheat flour, and analyses the main methods of regulating structural and mechanical properties of wheat dough and improving the quality of products made from weak flour. The prospects of using phytomaterials as natural alternatives to synthetic additives and baking improvers are presented. The chemical composition and the content of active substances in rosehips (the dogrose fruit) and hawthorn fruit are analyzed as to their effect on increasing the nutritional value and improving the protective properties of products as well as their effect on the course of the technological process, the quality of semi-finished and finished products. The methods of processing the phytomaterials have been suggested, and the optimum parameters of their extraction have been determined as to their effect on the protein-proteinase complex. Water and milk whey are suggested as extractants with the 1:10 ratio between the raw materials and the extractant, while the optimal temperature (100°C) and duration (60 minutes) of extraction were determined experimentally. Rational doses of phytoextracts have been found on the basis of their influence on gluten elasticity and the physical properties of wheat dough during its mixing and fermentation (30% of the rosehip water extract, 45% of hawthorn water extract, and 15% of whey extracts to the weight of flour). It has been established that proposed phytoextracts can increase the water absorption capacity of flour with weak and medium-strength gluten during dough mixing, improve its formation, stability, and elasticity, and decrease the degree of dilution according to the study of rheological properties of the dough using farinograph and extensograph. The mechanism of interactions and conformational changes in the structure of gluten proteins with the active substances of phytoextracts, especially pectins, polyphenols, and organic acids, has been suggested. It has been proven that fruit phytoextracts can be used as alternatives to synthetic improvers to process weak flour. Their usage allows solving the problems of regulating the properties of the gluten network and obtaining baked products with high physical, chemical, and sensory qualities. The proposed methods are effective and relatively easy to implement, which is important for small bakeries and restaurant establishments.

How graphene affects the misfolding of human prion protein: A combined experimental and molecular dynamics simulation study

As the broad application of graphene in the biomedical field, it is urgent and important to evaluate how the graphene affects the structure and function of the proteins in our body, especially the amyloid-related proteins. Prion protein, as a typical amyloid protein, it misfolding and aggregation will lead to serious prion diseases. To explore if graphene promotes or inhibits the formation of amyloid, here, we combined the experimental and molecular dynamics (MD) simulation methods to study the influence of graphene on the globular domain of prion protein (PrP117–231). The results from fluorescence quenching and circular dichroism spectrum showed that the addition of graphene changed the secondary structure of prion protein largely, mainly reflecting in the reduced α-helix structure and the increased coil structure, indicating graphene may strengthen the misfolding inclination of prion. To further uncover the mechanism of conformational change of prion under the induction of graphene, the all-atoms MD simulations in explicit solvent were performed. Our simulations suggest that prion protein can be quickly and tightly adsorbed onto graphene together with the weak conformational rearrangement and may reorient when approaching the surface. The Van der Waals' force drive the adsorption process. In the induction of graphene, H1 and S2-H2 loop regions of prion become unstable and prion begins to misfold partially. Our work shows that graphene can induce the misfolding of prion protein and may cause the potential risk to biosystems.

Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes.

Interest in atomically detailed simulations has grown significantly with recent advances in computational hardware and Markov state modeling (MSM) methods, yet outstanding questions remain that hinder their widespread adoption. Namely, how do alternative sampling strategies explore conformational space and how might this influence predictions generated from the data? Here, we seek to answer these questions for four commonly used sampling methods: (1) a single long simulation, (2) many short simulations run in parallel, (3) adaptive sampling, and (4) our recently developed goal-oriented sampling algorithm, FAST. We first develop a theoretical framework for analytically calculating the probability of discovering select states on simple landscapes, where we uncover the drastic effects of varying the number and length of simulations. We then use kinetic Monte Carlo simulations on a variety of physically inspired landscapes to characterize the probability of discovering particular states and transition pathways for each of the four methods. Consistently, we find that FAST simulations discover each target state with the highest probability, while traversing realistic pathways. Furthermore, we uncover the potential pathology that short parallel simulations sometimes predict an incorrect transition pathway by crossing large energy barriers that long simulations would typically circumnavigate. We refer to this pathology as "pathway tunneling". To protect against this phenomenon when using adaptive-sampling and FAST simulations, we introduce the FAST-string method. This method enhances sampling along the highest-flux transition paths to refine an MSMs transition probabilities and discriminate between competing pathways. Additionally, we compare the performance of a variety of MSM estimators in describing accurate thermodynamics and kinetics. For adaptive sampling, we recommend simply normalizing the transition counts out of each state after adding small pseudocounts to avoid creating sources or sinks. Lastly, we evaluate whether our insights from simple landscapes hold for all-atom molecular dynamics simulations of the folding of the λ-repressor protein. Remarkably, we find that FAST-contacts predicts the same folding pathway as a set of long simulations but with orders of magnitude less simulation time.

Conformational changes in a multidrug resistance ABC transporter DrrAB: Fluorescence-based approaches to study substrate binding

Bacterial multidrug transporter DrrAB exhibits overlapping substrate specificity with mammalian P-glycoprotein. DrrA hydrolyzes ATP, and the energy is transduced to carrier DrrB resulting in export of drugs. Previous studies suggested that DrrB contains a large and flexible drug-binding pocket made of aromatic residues contributed by several transmembrane helices with different drugs binding to both specific and shared residues in this pocket. However, direct binding of drugs to DrrAB or the mechanism of substrate-induced conformational changes between DrrA and DrrB has so far not been investigated. We used two fluorescence-based approaches to determine substrate binding to purified DrrAB. Our analysis shows that DrrB binds drugs with variable affinities and contains multiple drug binding sites. This work also provides evidence for two asymmetric nucleotide binding sites in DrrA with strikingly different binding affinities. Using targeted fluorescence labeling, we provide clear evidence of long-range conformational changes occurring between DrrA and DrrB. It is proposed that the transduction pathway from the nucleotide-binding DrrA subunit to the substrate binding DrrB subunit includes Q-loop and CREEM motifs in DrrA and EAA-like motif in DrrB. This study lays a solid groundwork for examining roles of various conserved regions of DrrA and DrrB in transduction of conformational changes.

Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias.

Energy landscape theory suggests that native interactions are a major determinant of the folding mechanism of a protein. Thus, structure-based (Go̅) models have, aided by coarse-graining techniques, shown great success in capturing the mechanisms of protein folding and conformational changes. In certain cases, however, non-native interactions and atomic details are also essential to describe the protein dynamics, prompting the development of a variety of structure-based models that include non-native interactions, and differentiate between different types of attractive potentials. Here, we describe an all-protein-atom hybrid model, termed ProfasiGo, that integrates an implicit solvent all-atom physics-based model (called Profasi) and a structure-based Go̅ potential and its implementation in two software packages (PHAISTOS and ProFASi) that are developed for Monte Carlo sampling of protein molecules. We apply the ProfasiGo model to study the folding free energy landscapes of four topologically similar proteins, one of which can be folded by the simplified potential Profasi and two that have been folded by explicit solvent, all-atom molecular dynamics simulations with the CHARMM22* force field. Our results reveal that the hybrid ProfasiGo model is able to capture many of the details present in the physics-based potentials while retaining the advantages of Go̅ models for sampling and guiding to the native state. We expect that the model will be widely applicable to the study of the folding of more complex proteins or to the study of conformational dynamics and integration with experimental data.

Molecular mechanism of D816X mutation-induced c-Kit activation and -mediated inhibitor resistance in gastrointestinal stromal tumor

The D816X (X = V, H, Y or F) missense mutation constitutively activates c-Kit kinase in gastrointestinal stromal tumor (GIST) and has been observed to cause acquired resistance against first-line and second-line kinase inhibitors. In the present study, the allosteric mechanism of D816X-induced c-Kit conformational change is investigated at molecular level. The Asp816 residue is located at the activation loop (A-loop) of c-Kit and the mutation can eliminate a negative formal charge from the loop region by substituting the acidic asparagic acid residue with neutral valine, histidine, tyrosine or phenylalanine. Here, we classify the c-Kit kinase into four states in terms of its mutation (wild type or mutant) and conformation (DFG-in or DFG-out). The wild-type kinase is electrostatically stabilized in inactive DFG-out conformation, whereas the D816X mutation can promote the conformational conversion to active DFG-in and then activate the kinase. Structural analysis reveals that the Asp816 residue in DFG-out is surrounded by a number of polar and positively charged residues within its first and second shells of protein context, and kinase conformational change to DFG-in brings this residue into a negative electrostatic potential environment. Dynamics simulation characterizes that the c-Kit conformational conversion from DFG-out to DFG-in can cause local unfavorable effect to type-II inhibitor, while the mutation-induced global structural rearrangement would participate in the favorable interaction of c-Kit with type-I inhibitor.

Binding thermodynamics of metal ions to HIV-1 ribonuclease H domain.

Metal-protein interactions are not necessarily tight in many transient biological processes, such as cellular signaling, enzyme regulation, and molecular recognition. Here, we analyzed the binding thermodynamics and characterized the structural effect of divalent metal ions, i.e. Mn2+, Zn2+, and Mg2+, to the isolated ribonuclease H (RNH) of human immunodeficiency virus (HIV) using isothermal titration calorimetry (ITC) and circular dichroism. The binding thermodynamics of Mg2+ to RNH was determined using competition ITC experiments, and the binding affinity of Mg2+ was found to be about 40- and 400-times lower than those of Mn2+ and of Zn2+, respectively. The structural analysis showed that Mg2+ binding had little effect on the thermal stability of RNH, while Zn2+ and Mn2+ binding increased the stability. The thermodynamic characteristics of RNH metal binding, compared to intact HIV reverse transcriptase, and a possible mechanism of conformational change induced upon metal ion binding, in correlation with the structure-function relationship, are discussed.

Length-Dependent Manifestation of Vibration Modes Regulates a Specific Intermediate Morphology of Aβ17-42 in Different Environments.

Various cytotoxic mechanisms for neurodegenerative disease are induced by specific conformations of Aβ intermediates. The efforts to understand the diverse intermediate forms of amyloid oligomers have been focused on understanding the aggregation mechanism of specific morphologies for Aβ intermediates. However, these are still not easy tasks to be accomplished because the diverse conformations of Aβ intermediates can be altered during the aggregation process, even though the same Aβ monomers are present. Thus, efforts to reveal the conformational change mechanism could be a fundamental process to understand the formation of diverse Aβ intermediate conformations. Here, we evaluate the conformational characteristics of Aβ17-42 fibrillar oligomers in different environments according to the length. We observed that Aβ fibrillar oligomers optimize their inherent hydrogen bonds and configurational entropy to stabilize their structure according to the simulation time and their length increase. In addition, we revealed the role of the expressed vibration mode shape in the fibrillar oligomers' elongation and deformation processes. Our results suggest that limitations in amyloid oligomer growth and transformations of their morphologies can be regulated and controlled by modifying the vibration features.

Molecular Dynamics studies of DNA polymerase kappa, a human protein involved in translesion synthesis

Y family DNA polymerases are a class of enzymes characterized by their ability to copy damaged DNA in a process known as translesion synthesis. They do not eliminate the damage per se, but at least they are able to bypass a stalled replication, avoiding cell death. These polymerases bypass a wide variety of DNA damage, including thymine‐thymine dimers, inter‐strand DNA crosslinks, and other damage caused by reactive oxygen species. Unfortunately, they do not replicate the DNA with high fidelity and some polymerases are more error prone than others. In addition, the kinds of lesions that this group of enzymes can bypass are dependent on the enzyme itself, despite the general architectural similarities of all these enzymes. Human DNA polymerase kappa (pol k) is a member of the Y‐family of DNA polymerases involved in translesion synthesis in humans. Kinetics students have shown that this enzyme can bypass minor groove lesions such as O6‐methylated guanine (O‐metG) but not major groove lesions such as N2‐furfuryl‐guanine (N‐fG). Hydrogen exchange experiments have suggested solvent accessibility changes in various systems, hinting at a mechanism of conformational change upon substrate binding. Through molecular dynamics simulations, we tested the validity of the conformational change hypothesis by comparing the structural changes undergone by pol k in the presence of different templating lesions and with correct and incorrect incoming nucleotides. In addition, binary systems, comprised of just the DNA and the protein without the incoming nucleotide, were examined. Our results show that pol k does not attain a close, catalytically competent state in both the binary and the O‐metG systems, as evidenced by the few contacts between the protein and the incoming nucleotides. We have also identified key residues important for the stabilization of the incoming nucleotide as well as formulated a hypothesis to why the O‐metG lesion does not get bypassed as efficiently as other damages.Support or Funding InformationThis work was supported in part by the Rose M. Badgeley Residuary Charitable Trust Award and the Colette Mahoney Award to BSB.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Thermodynamic Stability of Polar and Non-polar Fibrils

Protein aggregation into fibril-like structures is the hallmark of amyloid diseases that included Alzheimer's, Parkinson's and type 2 diabetes. An understanding of the molecular forces driving fibril formation may provide insights into strategies to prevent these diseases. Thermodynamics has played an important role in unraveling the molecular mechanisms of different conformational changes in proteins, e.g., protein folding. However, equilibrium thermodynamic quantities of amyloid fibrils are not easily accessible experimentally and they remain largely unknown. In this work, we discuss results from all-atom molecular dynamics simulations in which we measured equilibrium thermodynamic quantities related to addition/dissociation of a peptide to/from a fibril. In particular, we will highlight differences in the thermodynamic properties of polar (IAPP28-33) and non-polar (Aβ16-21) fibrils. We also study the effect of a small molecule inhibitor on stability of these fibrils. Simulations were performed using an umbrella sampling protocol combined with replica exchange molecular dynamics to compute potential of mean force (PMF) of peptide addition as a function of temperature. The PMF corresponds to the free-energy to ad a peptide to a fibril. The temperature dependence of the PMF is used to compute changes in entropy (ΔS), enthalpy (ΔH) and heat capacity (ΔC) of peptide addition/dissociation. We find that the non-polar fibril becomes more stable with increasing temperature and its stability is dominated by entropy. In contrast, the polar fibril becomes less stable with increasing temperature while it is stabilized by enthalpy. These behaviors are consistent with the nature of the interactions in their dry core and they highlight the importance of side chains accounting for stability of amyloid fibrils.

Studying compaction-decompaction of DNA molecules induced by surfactants

The mechanism and detailed processes of DNA compaction and decompaction are essential for the life activities, as well as for the researches in the molecular biology, genetics and biomedicine. The compaction of two kinds of DNA molecules caused by Cetyltrimethyl Ammonium Bromide (CTAB) and their decompaction induced with sodium dodecyl sulfate (SDS) or excessive amount of CTAB have been investigated with multiple perspectives such as the UV-VIS spectrophotometry, dynamic light scattering, and zeta potential. The compaction phenomenon of DNA can easily be observed when the CTAB combines with the DNA, not just when the molar ratio QCTAB/QDNA is approximately equal to 1 as the conventional recognition, but also when QCTAB/QDNA <1,DNA can be compacted; Molecular state of DNA is only changed in the conformational structure, but not in the chemical structure. Finally, a model is suggested to help catch on the biophysical mechanism of DNA chain conformational change.

Phosphorylation-Dependent Effects on the Structural Flexibility of Phosphoglucosamine Mutase from Bacillus anthracis.

Phosphoglucosamine mutase (PNGM) is an evolutionarily conserved bacterial enzyme in the peptidoglycan biosynthetic pathway, catalyzing the reversible conversion between glucosamine 1- and 6-phosphate. Previous structural studies of PNGM from the pathogen Bacillus anthracis revealed its dimeric assembly and highlighted the rotational mobility of its C-terminal domain. Recent studies of two other enzymes in the same superfamily have demonstrated the long-range effects on the conformational flexibility associated with phosphorylation of the conserved, active site phosphoserine involved in phosphoryl transfer. Building on this work, we use a combination of experimental and computational studies to show that the active, phosphorylated version of B. anthracis PNGM has decreased flexibility relative to its inactive, dephosphorylated state. Limited proteolysis reveals an enhanced and accelerated cleavage of the dephosphorylated enzyme. 15N transverse relaxation-optimized NMR spectra corroborate a conformational adjustment with broadening and shifts of peaks relative to the phospho-enzyme. Electrostatic calculations indicate that residues in the mobile, C-terminal domain are linked to the phosphoserine by lines of attraction that are absent in the dephosphorylated enzyme. Phosphorylation-dependent changes in protein flexibility appear linked with the conformational change and enzyme mechanism in PNGM, establishing this as a conserved theme in multiple subgroups of the diverse α-d-phosphohexomutase superfamily.

Network of Conformational Transitions Revealed by Molecular Dynamics Simulations of the Carbonic Anhydrase II Apo-Enzyme.

Human carbonic anhydrase II (HCA II) is an enzyme that catalyzes the reversible hydration of CO2 into bicarbonate (HCO3–) and a proton (H+) as well as other reactions at an extremely high rate. This enzyme plays fundamental roles in human physiology/pathology, such as controlling the pH level in cells and so on. However, the binding mechanism between apo-HCA II and CO2 or other ligands as well as related conformational changes remains poorly understood, and atomic investigation into it could promote our understanding of related internal physiological/pathological mechanisms. In this study, long-time atomic molecular dynamics simulations as well as the clustering and free-energy analysis were performed to reveal the dynamics of apo-HCA II as well as the mechanism upon ligand binding. Our simulations indicate that the crystallographic B-factors considerably underestimate the loop dynamics: multiple conformations can be adopted by loops 1 and 2, especially for loop 1 because loop 1 is one side of the binding pocket, and its left-to-right movement can compress or extend the binding pocket, leading to one inactive (closed) state, three intermediate (semiopen) states, and one active (open) state; CO2 cannot get into the binding pocket of the inactive state but can get into those of intermediate and active states. The coexistence of multiple conformational states proposes a possible conformational selection model for the binding mechanism between apo-HCA II and CO2 or other ligands, revising our previous view of its functional mechanism of conformational change upon ligand binding and offering valuable structural insights into the workings of HCA II.

Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways

The catalytic subunit of PKA (PKAc) exhibits three major conformational states (open, intermediate, and closed) during the biocatalysis process. Both ATP and substrate/inhibitor can effectively induce the conformational changes of PKAc from open to closed states. Aiming to explore the mechanism of this allosteric regulation, we developed a coarse-grained model and analyzed the dynamics of conformational changes of PKAc during binding by performing molecular dynamics simulations for apo PKAc, binary PKAc (PKAc with ATP, PKAc with PKI), and ternary PKAc (PKAc with ATP and PKI). Our results suggest a mixed binding mechanism of induced fit and conformational selection, with the induced fit dominant. The ligands can drive the movements of Gly-rich loop as well as some regions distal to the active site in PKAc and stabilize them at complex state. In addition, there are two parallel pathways (pathway with PKAc-ATP as an intermediate and pathway PKAc-PKI as an intermediate) during the transition from open to closed states. By molecular dynamics simulations and rate constant analyses, we find that the pathway through PKAc-ATP intermediate is the main binding route from open to closed state because of the fact that the bound PKI will hamper ATP from successful binding and significantly increase the barrier for the second binding subprocess. These findings will provide fundamental insights of the mechanisms of PKAc conformational change upon binding.

Timing and Reset Mechanism of GTP Hydrolysis-Driven Conformational Changes of Atlastin

The endoplasmic reticulum (ER) forms a branched, dynamic membrane tubule network that is vital for cellular function. Branching arises from membrane fusion facilitated by the GTPase atlastin (ATL). Many metazoan genomes encode for three ATL isoforms that appear to fulfill partially redundant function despite differences in their intrinsic GTPase activity and localization within the ER; however, the underlying mechanistic differences between the isoforms are poorly understood. Here, we identify discrete temporal steps in the catalytic cycle for thetwo most dissimilar isoforms, ATL1 and ATL3, revealing an overall conserved progression of molecular events from nucleotide binding and hydrolysis to ATL dimerization and phosphate release. A crystal structure of ATL3 suggests a mechanism for the displacement of the catalytic Mg2+ ion following guanosine triphosphate (GTP) hydrolysis. Together, the data extend the mechanistic framework for howGTP hydrolysis drives conformational changes in ATL and how the cycle is reset for subsequent rounds of catalysis.

Critical Role of Interdomain Interactions in the Conformational Change and Catalytic Mechanism of Endoplasmic Reticulum Aminopeptidase 1.

Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that is important for the generation of antigenic epitopes and major histocompatibility class I-restricted adaptive immune responses. ERAP1 processes a vast variety of different peptides but still shows length and sequence selectivity, although the mechanism behind these properties is poorly understood. X-ray crystallographic analysis has revealed that ERAP1 can assume at least two distinct conformations in which C-terminal domain IV is either proximal or distal to active site domain II. To improve our understanding of the role of this conformational change in the catalytic mechanism of ERAP1, we used site-directed mutagenesis to perturb key salt bridges between domains II and IV. Enzymatic analysis revealed that these mutations, although located away from the catalytic site, greatly reduce the catalytic efficiency and change the allosteric kinetic behavior. The variants were more efficiently activated by small peptides and bound a competitive inhibitor with weaker affinity and faster dissociation kinetics. Molecular dynamics analysis suggested that the mutations affect the conformational distribution of ERAP1, reducing the population of closed states. Small-angle X-ray scattering indicated that both the wild type and the ERAP1 variants are predominantly in an open conformational state in solution. Overall, our findings suggest that electrostatic interactions between domains II and IV in ERAP1 are crucial for driving a conformational change that regulates the structural integrity of the catalytic site. The extent of domain opening in ERAP1 probably underlies its specialization for antigenic peptide precursors and should be taken into account in inhibitor development efforts.

Thermally tunable grating using thermo-responsive magnetic fluid

We report a thermally tunable grating prepared using poly(N-isopropylacrylamide) and super paramagnetic iron oxide nanoparticles. The array spacing is reversibly tuned by varying the temperature between 5 and 38 °C. Here, the ability of thermo-responsive polymer brushes to alter their conformation at an interface is exploited to control the grating spacing in nanoscale. The underlying mechanism for the temperature dependent conformational changes are studied by measuring the subtle intermolecular forces between the polymer covered interfaces. It is observed that the interparticle forces are repulsive and exponentially decaying with distance. The thermo-responsive grating is simple to use and offers a wide range of applications.

Exercise Training and Epigenetic Regulation: Multilevel Modification and Regulation of Gene Expression.

Exercise training elicits acute and adaptive long term changes in human physiology that mediate the improvement of performance and health state. The responses are integrative and orchestrated by several mechanisms, as gene expression. Gene expression is essential to construct the adaptation of the biological system to exercise training, since there are molecular processes mediating oxidative and non-oxidative metabolism, angiogenesis, cardiac and skeletal myofiber hypertrophy, and other processes that leads to a greater physiological status. Epigenetic is the field that studies about gene expression changes heritable by meiosis and mitosis, by changes in chromatin and DNA conformation, but not in DNA sequence, that studies the regulation on gene expression that is independent of genotype. The field approaches mechanisms of DNA and chromatin conformational changes that inhibit or increase gene expression and determine tissue specific pattern. The three major studied epigenetic mechanisms are DNA methylation, Histone modification, and regulation of noncoding RNA-associated genes. This review elucidates these mechanisms, focusing on the relationship between them and their relationship with exercise training, physical performance and the enhancement of health status. On this chapter, we clarified the relationship of epigenetic modulations and their intimal relationship with acute and chronic effect of exercise training, concentrating our effort on skeletal muscle, heart and vascular responses, that are the most responsive systems against to exercise training and play crucial role on physical performance and improvement of health state.

Understanding the Phosphorylation Mechanism by Using Quantum Chemical Calculations and Molecular Dynamics Simulations

Phosphorylation is one of the most frequent post-translational modifications on proteins. It regulates many cellular processes by modulation of phosphorylation on protein structure and dynamics. However, the mechanism of phosphorylation-induced conformational changes of proteins is still poorly understood. Here, we report a computational study of three representative groups of tyrosine in ADP-ribosylhydrolase 1, serine in BTG2, and serine in Sp100C by using six molecular dynamics (MD) simulations and quantum chemical calculations. Added phosphorylation was found to disrupt hydrogen bond, and increase new weak interactions (hydrogen bond and hydrophobic interaction) during MD simulations, leading to conformational changes. Quantum chemical calculations further indicate that the phosphorylation on tyrosine, threonine, and serine could decrease the optical band gap energy (Egap), which can trigger electronic transitions to form or disrupt interactions easily. Our results provide an atomic and electronic description of how phosphorylation facilitates conformational and dynamic changes in proteins, which may be useful for studying protein function and protein design.

Molecular assembly and structure of the bacteriophage T4 tail.

The tail of bacteriophage T4 undergoes large structural changes upon infection while delivering the phage genome into the host cell. The baseplate is located at the distal end of the contractile tail and plays a central role in transmitting the signal to the tail sheath that the tailfibers have been adsorbed by a host bacterium. This then triggers the sheath contraction. In order to understand the mechanism of assembly and conformational changes of the baseplate upon infection, we have determined the structure of an in vitro assembled baseplate through the three-dimensional reconstruction of cryo-electron microscopy images to a resolution of 3.8Å from electron micrographs. The atomic structure was fitted to the baseplate structure before and after sheath contraction in order to elucidate the conformational changes that occur after bacteriophage T4 has attached itself to a cell surface. The structure was also used to investigate the protease digestion of the assembly intermediates and the mutation sites of the tail genes, resulting in a number of phenotypes.