Protein Chain Research Articles

Effect of synovial fluid constituent on the tribological behaviors of UHMWPE-CoCrMo alloy contact pair

PurposeThis study aims to systematically investigate the tribological behaviors of metal and polyethylene using lubricants composed of four synovial fluid (SF) components. In addition, the changes in protein conformation during wear were analyzed to establish the correlation between protein conformation and tribological properties.Design/methodology/approachA pin-on-disk tester with multidirectional sliding motion was used for tribological properties observation between metal and polyethylene pairs. Simulated SFs with four main constituents were used as the testing lubricants. Differential scanning calorimetry and Raman were used to characterize the changes in protein conformation during wear.FindingsThe coupling of lipids and hyaluronic acid further suppressed protein denaturation. The protein structures of the adsorption film and the ensnared protein chains in the friction zone were maintained to a certain extent, thus improving the friction and wear of polyethylene.Originality/valueThese findings established the correlation between protein conformation and friction and wear, promoting the understanding of the lubrication mechanism of artificial joints.

Effects of representative point mutations on dynamic behavior of the DISC1–Ndel1 complex: a molecular dynamics study

It has been found that the development of schizophrenia and some other psychiatric disorders is related to defects in the normal functioning of Disrupted-In-Schizophrenia 1 (DISC1). It is a large-sized protein containing 855 residues and acts as an active hub at the core of many interactions with various proteins. On the other hand, NudE Neurodevelopment Protein 1 Like 1 (Ndel1) plays a role in nervous system development via interaction with the DISC1. It was shown that some point mutations on DISC1 have clinical implications. In line with these reports, here we have used the NMR structure of the wild-type (WT) C-terminal tail of DISC1 in complex with the N-terminal fragment of Ndel1, and have constructed the three-dimensional structures of L62Q and L29Q mutants, as the pathologic variants of the complex. The time-dependent interaction of DISC1 with Ndel1 in the WT complex and mutants was simulated by performing molecular dynamics (MD) simulation using programs in the GROMACS package. It was found that the flexibility of residues in some regions of the protein chains increases, and secondary structural changes from ordered toward unordered one leads to destabilizing of the complex in mutants. Destabilization of the complex upon substitution of Leu by Gln was also confirmed by analysis of the contact map plot. Communicated by Ramaswamy H. Sarma

Conformational aspects in the formation of structures of the backbone of polypeptide chains in proteins. Relationship between conformational stability/lability and β-turns

To assess the nature of the relationship between the integral conformational stability of tetrapeptides and the main types of β-turns (which are also tetrapeptides), calculations were performed using spectrum diagrams and asymmetry in the distribution of conformationally stable and unstable tetrapeptides. It was shown that type I', II, and II' β-turns are comprised of predominantly conformationally labile peptides, that is consistent with the predetermined nature of their structure as described earlier. As previously shown in our study, in this case the conformation is imposed by external conditions (namely the cycle closuring) and the prevalence of conformationally labile peptides facilitates the formation of the structure by virtue of external factors. Type I β-turn is an exception: peptides with different conformational lability are fairly evenly distributed. Most likely, this indicates that the formation of the type I β-turn is not predetermined.

Predicting amyloid PET and tau PET stages with plasma biomarkers.

Staging the severity of Alzheimer's disease pathology using biomarkers is useful for therapeutic trials and clinical prognosis. Disease staging with amyloid and tau PET has face validity; however, this would be more practical with plasma biomarkers. Our objectives were, first, to examine approaches for staging amyloid and tau PET and, second, to examine prediction of amyloid and tau PET stages using plasma biomarkers. Participants (n = 1136) were enrolled in either the Mayo Clinic Study of Aging or the Alzheimer's Disease Research Center; had a concurrent amyloid PET, tau PET and blood draw; and met clinical criteria for cognitively unimpaired (n = 864), mild cognitive impairment (n = 148) or Alzheimer's clinical syndrome with dementia (n = 124). The latter two groups were combined into a cognitively impaired group (n = 272). We used multinomial regression models to estimate discrimination [concordance (C) statistics] among three amyloid PET stages (low, intermediate, high), four tau PET stages (Braak 0, 1-2, 3-4, 5-6) and a combined amyloid and tau PET stage (none/low versus intermediate/high severity) using plasma biomarkers as predictors separately within unimpaired and impaired individuals. Plasma analytes, p-tau181, Aβ1-42 and Aβ1-40 (analysed as the Aβ42/Aβ40 ratio), glial fibrillary acidic protein and neurofilament light chain were measured on the HD-X Simoa Quanterix platform. Plasma p-tau217 was also measured in a subset (n = 355) of cognitively unimpaired participants using the Lilly Meso Scale Discovery assay. Models with all Quanterix plasma analytes along with risk factors (age, sex and APOE) most often provided the best discrimination among amyloid PET stages (C = 0.78-0.82). Models with p-tau181 provided similar discrimination of tau PET stages to models with all four plasma analytes (C = 0.72-0.85 versus C = 0.73-0.86). Discriminating a PET proxy of intermediate/high from none/low Alzheimer's disease neuropathological change with all four Quanterix plasma analytes was excellent but not better than p-tau181 only (C = 0.88 versus 0.87 for unimpaired and C = 0.91 versus 0.90 for impaired). Lilly p-tau217 outperformed the Quanterix p-tau181 assay for discriminating high versus intermediate amyloid (C = 0.85 versus 0.74) but did not improve over a model with all Quanterix plasma analytes and risk factors (C = 0.85 versus 0.83). Plasma analytes along with risk factors can discriminate between amyloid and tau PET stages and between a PET surrogate for intermediate/high versus none/low neuropathological change with accuracy in the acceptable to excellent range. Combinations of plasma analytes are better than single analytes for many staging predictions with the exception that Quanterix p-tau181 alone usually performed equivalently to combinations of Quanterix analytes for tau PET discrimination.

Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations.

Replica exchange with solute tempering (REST) is a highly effective variant of replica exchange for enhanced sampling in explicit solvent simulations of biomolecules. By scaling the Hamiltonian for a selected "solute" region of the system, REST effectively applies tempering only to the degrees of freedom of interest but not the rest of the system ("solvent"), allowing fewer replicas for covering the same temperature range. A key consideration of REST is how the solute-solvent interactions are scaled together with the solute-solute interactions. Here, we critically evaluate the performance of the latest REST2 protocol for sampling large-scale conformation fluctuations of intrinsically disordered proteins (IDPs). The results show that REST2 promotes artificial protein conformational collapse at high effective temperatures, which seems to be a designed feature originally to promote the sampling of reversible folding of small proteins. The collapse is particularly severe with larger IDPs, leading to replica segregation in the effective temperature space and hindering effective sampling of large-scale conformational changes. We propose that the scaling of the solute-solvent interactions can be treated as free parameters in REST, which can be tuned to control the solute conformational properties (e.g., chain expansion) at different effective temperatures and achieve more effective sampling. To this end, we derive a new REST3 protocol, where the strengths of the solute-solvent van der Waals interactions are recalibrated to reproduce the levels of protein chain expansion at high effective temperatures. The efficiency of REST3 is examined using two IDPs with nontrivial local and long-range structural features, including the p53 N-terminal domain and the kinase inducible transactivation domain of transcription factor CREB. The results suggest that REST3 leads to a much more efficient temperature random walk and improved sampling efficiency, which also further reduces the number of replicas required. Nonetheless, our analysis also reveals significant challenges of relying on tempering alone for sampling large-scale conformational fluctuations of disordered proteins. It is likely that more efficient sampling protocols will require incorporating more sophisticated Hamiltonian replica exchange schemes in addition to tempering.

Melatonin Activation by Cytochrome P450 Isozymes: How Does CYP1A2 Compare to CYP1A1?

Cytochrome P450 enzymes are versatile enzymes found in most biosystems that catalyze mono-oxygenation reactions as a means of biosynthesis and biodegradation steps. In the liver, they metabolize xenobiotics, but there are a range of isozymes with differences in three-dimensional structure and protein chain. Consequently, the various P450 isozymes react with substrates differently and give varying product distributions. To understand how melatonin is activated by the P450s in the liver, we did a thorough molecular dynamics and quantum mechanics study on cytochrome P450 1A2 activation of melatonin forming 6-hydroxymelatonin and N-acetylserotonin products through aromatic hydroxylation and O-demethylation pathways, respectively. We started from crystal structure coordinates and docked substrate into the model, and obtained ten strong binding conformations with the substrate in the active site. Subsequently, for each of the ten substrate orientations, long (up to 1 μs) molecular dynamics simulations were run. We then analyzed the orientations of the substrate with respect to the heme for all snapshots. Interestingly, the shortest distance does not correspond to the group that is expected to be activated. However, the substrate positioning gives insight into the protein residues it interacts with. Thereafter, quantum chemical cluster models were created and the substrate hydroxylation pathways calculated with density functional theory. These relative barrier heights confirm the experimental product distributions and highlight why certain products are obtained. We make a detailed comparison with previous results on CYP1A1 and identify their reactivity differences with melatonin.

Serum Glial Fibrillary Acidic Protein Compared With Neurofilament Light Chain as a Biomarker for Disease Progression in Multiple Sclerosis

There is a lack of validated biomarkers for disability progression independent of relapse activity (PIRA) in multiple sclerosis (MS). To determine how serum glial fibrillary acidic protein (sGFAP) and serum neurofilament light chain (sNfL) correlate with features of disease progression vs acute focal inflammation in MS and how they can prognosticate disease progression. Data were acquired in the longitudinal Swiss MS cohort (SMSC; a consortium of tertiary referral hospitals) from January 1, 2012, to October 20, 2022. The SMSC is a prospective, multicenter study performed in 8 centers in Switzerland. For this nested study, participants had to meet the following inclusion criteria: cohort 1, patients with MS and either stable or worsening disability and similar baseline Expanded Disability Status Scale scores with no relapses during the entire follow-up; and cohort 2, all SMSC study patients who had initiated and continued B-cell-depleting treatment (ie, ocrelizumab or rituximab). Patients received standard immunotherapies or were untreated. In cohort 1, sGFAP and sNfL levels were measured longitudinally using Simoa assays. Healthy control samples served as the reference. In cohort 2, sGFAP and sNfL levels were determined cross-sectionally. This study included a total of 355 patients (103 [29.0%] in cohort 1: median [IQR] age, 42.1 [33.2-47.6] years; 73 female patients [70.9%]; and 252 [71.0%] in cohort 2: median [IQR] age, 44.3 [33.3-54.7] years; 156 female patients [61.9%]) and 259 healthy controls with a median [IQR] age of 44.3 [36.3-52.3] years and 177 female individuals (68.3%). sGFAP levels in controls increased as a function of age (1.5% per year; P < .001), were inversely correlated with BMI (-1.1% per BMI unit; P = .01), and were 14.9% higher in women than in men (P = .004). In cohort 1, patients with worsening progressive MS showed 50.9% higher sGFAP levels compared with those with stable MS after additional sNfL adjustment, whereas the 25% increase of sNfL disappeared after additional sGFAP adjustment. Higher sGFAP at baseline was associated with accelerated gray matter brain volume loss (per doubling: 0.24% per year; P < .001) but not white matter loss. sGFAP levels remained unchanged during disease exacerbations vs remission phases. In cohort 2, median (IQR) sGFAP z scores were higher in patients developing future confirmed disability worsening compared with those with stable disability (1.94 [0.36-2.23] vs 0.71 [-0.13 to 1.73]; P = .002); this was not significant for sNfL. However, the combined elevation of z scores of both biomarkers resulted in a 4- to 5-fold increased risk of confirmed disability worsening (hazard ratio [HR], 4.09; 95% CI, 2.04-8.18; P < .001) and PIRA (HR, 4.71; 95% CI, 2.05-9.77; P < .001). Results of this cohort study suggest that sGFAP is a prognostic biomarker for future PIRA and revealed its complementary potential next to sNfL. sGFAP may serve as a useful biomarker for disease progression in MS in individual patient management and drug development.

Folding of the nascent polypeptide chain of a histidine phosphocarrier protein in vitro

The phosphotransferase system (PTS), a metabolic pathway formed by five proteins, modulates the use of sugars in bacteria. The second protein in the chain is the histidine phosphocarrier, HPr, with the binding site at His15. The HPr kinase/phosphorylase (HPrK/P), involved in the bacterial use of carbon sources, phosphorylates HPr at Ser46, and it binds at its binding site. The regulator of sigma D protein (Rsd) also binds to HPr at His15. We have designed fragments of HPr, growing from its N-terminus and containing the His15. In this work, we obtained three fragments, HPr38, HPr58 and HPr70, comprising the first thirty-eight, fifty-eight and seventy residues of HPr, respectively. All fragments were mainly disordered, with evidence of a weak native-like, helical population around the binding site, as shown by fluorescence, far-ultraviolet circular dichroism, size exclusion chromatography and nuclear magnetic resonance. Although HPr38, HPr58 and HPr70 were disordered, they could bind to: (i) the N-terminal domain of first protein of the PTS, EIN; (ii) Rsd; and, (iii) HPrK/P, as shown by fluorescence and biolayer interferometry (BLI). The association constants for each protein to any of the fragments were in the low micromolar range, within the same range than those measured in the binding of HPr to each protein. Then, although acquisition of stable, native-like secondary and tertiary structures occurred at the last residues of the polypeptide, the ability to bind protein partners happened much earlier in the growing chain. Binding was related to the presence of the native-like structure around His15.

Conformational Aspects in the Formation of Structures of the Backbone of Polypeptide Chains in Proteins: the Relationship between Conformational Stability/Lability and β-Turns

Conformational Aspects in the Formation of Structures of the Backbone of Polypeptide Chains in Proteins: the Relationship between Conformational Stability/Lability and β-Turns

Engineering electro-osmotic flow through biological channels for nanopore protein sequencing

Reading the amino acid sequence of individual proteins with high precision and throughput holds promise to deliver the most detailed portrait of a biological cell. In the absence of natural mechanisms to copy, read, or transcribe protein sequences, abiological approaches to protein sequencing have taken a lead. One such approach is nanopore sequencing, where the amino acid sequence of a protein is read as the protein chain is moved through a nanopore reader. In contrast to DNA strand which carries a uniform negative charge regardless of its nucleotide sequence, capturing and keeping an unevenly charged peptide taut through the nanopore's constriction is a major challenge in nanopore sequencing of protein. Here, we use all-atom molecular dynamics simulations to explore the effective force experienced by heterogeneously charged peptides in a biological nanopore and the means to increase the force through protein engineering. We accomplish that by applying an external hydrostatic pressure that generates the water flow required to keep polypeptide chain under tension through the nanopore. The effective force on the peptide is measured by harmonically restraining one end of the peptide to a point in the pore vestibule. Our simulations have compared the effective force on the peptide applied by water flow in the most common biological nanopores used for sequencing: the truncated MspA, CsgG, alpha-hemolysin. Our results revealed the magnitude of the effective force applied to a peptide by a water flow, its dependence on the flow profile, and the amino acid composition of the peptide. The results of our simulations suggest a possibility of creating a high-performance engineered nanopore by increasing the electro-osmotic force introduced as a result of point mutations to the MspA structure.

Mapping inhomogeneous network structures within biomolecular condensate using single-molecule imaging and tracking of fluorogenic probes.

Biomolecular condensates form via phase separation coupled to percolation. These phase transitions are driven by multivalent macromolecules. Network structures within condensates and the interfaces of condensates are difficult to interrogate experimentally. Here, we leverage single-molecule (SM) techniques and three fluorogenic probes, Nile blue (NB), Nile red (NR), and merocyanine 540 (MC540), to study the network structures within biomolecule condensates of the low-complexity domain of the hnRNPA1 protein (A1-LCD). Importantly, the fluorescent probes are not covalently bound to A1-LCD but instead diffuse in solution and become fluorescent in response to inhomogeneities of the local chemical environments within condensates. Interestingly, epifluorescence microscopy shows that the three probes respond in unique ways within condensates: NB gives a uniform intensity distribution, MC540 shows a higher intensity at the interface, and NR highlights hot spots inside the condensates. We then use SM localization microscopy to correlate localizations of the three probes. Surprisingly, the high-resolution SM reconstructions all show inhomogeneous network structures but with different emphases: NR shows the largest number of hotspots, NB exhibits the most spatial uniformity, and MC540 shows the greatest spatial variation within each condensate. Further, NB and MC540 localizations are highly correlated within each condensate. SM tracking experiments show that slower-moving NB molecules form high-contrast inhomogeneous network structures with hot spots, in agreement with SMLM. On the other hand, highly diffusive NB molecules are uniformly distributed throughout the condensate. We therefore conclude that network structures within the condensate are heterogeneous; protein chains with strong connections to neighboring chains form a relatively stable inhomogeneous network with hot spots, while chains with weak interactions are diffusive throughout the condensates. The mesoscale and sub-mesoscale structural organizations of molecules within condensates inferred from SM measurements agree with recent computational studies.

Coherent exciton coupling in fluorescent protein dimers probed by two-photon polarization ratio

Coherent excitonic coupling of two chromophores in a dimer of a GFP-analogue, VenusA206, was discovered previously by using circular dichroism and a combination of photon antibunching and fluorescence correlation spectroscopy. To further elucidate this effect, here we use a new approach based on the measurements of two-photon polarization ratio (Ω) as a function of excitation wavelength. Theoretically, Ω depends on the angle between the vectors of absorption transition dipole moment and permanent dipole moment change upon excitation. Generally, excitonic coupling of two chromophores should provide a change of this angle. We measured Ω for the tandem dimer of Venus (tdV) with two chromophores per protein chain and, as a control - for the tandem dimer with one of the chromophores knocked out by point mutation (tdVx). Compared to tdVx, we observe in tdV a significant increase of Ω in the red side of the pure electronic transition and a significant decrease of Ω in the blue side. At the same time, the two-photon absorption spectra of the two systems virtually coincide. Our observations are consistent with a model where only a minority of dimers are coupled coherently and the two permanent dipoles are oriented in an oblique head-to-head arrangement with an angle ∼400 between them. For multiphoton microscopy applications, it is interesting to investigate if the coherently coupled GFP dimer can provide a cooperative enhancement of the two-photon cross section, i.e., absorb stronger than two uncoupled monomers. This possibility can come from the “motional narrowing” of excitonic transition and will be discussed.

Lipid backmapping and its application to membrane builder.

I will present a novel lipid backmapping methodology that uses mapping scheme and isomerchemical properties of a molecule. The method randomly places atoms around their corresponding coarse-grained bead and relaxes a system heavily based on bonded interactions while softened nonbonded interactions ensure no overlap between atoms during energy minimization. The developed method is simple to use with minimal input and powerful enough to construct a whole lipid structure from a single point. The method also imposes a set of dihedrals to keep the known isomerchemical properties of molecules during relaxation. I will also present an automated membrane builder based on our lipid backmapping scheme. The membrane builder constructs a plane bilayer membrane with protein chains embedded if given at Martini resolution. A series of short Martini simulations is carried out to equilibrate a membrane system. Lipids are transformed into atomistic resolutions based on the developed backmapping method, and proteins are replaced with the given input structures. Finally, phase separation examples inside membranes, prepared with the membrane builder, are shown at the atomistic level.

Elucidating the dynamics of individual IDPs in a biomolecular condensate using single-molecule FRET and molecular simulation.

A wide range of biomolecules in solution can phase-separate and form membraneless organelles in the cell. These assemblies often have liquid-like properties, and the corresponding dynamics and exchange of molecules with the environment are important for biological function. The dynamics and materials properties of these systems are commonly assessed based on translational diffusion or rheological properties, typically covering timescales of milliseconds and longer. However, information on the structure and dynamics at the molecular level is lacking. We have studied coacervates of two intrinsically disordered highly oppositely charged nuclear proteins as a prototypical example of heterotypic liquid-liquid phase separation of components abundant in the cell nucleus. Using single-molecule fluorescence spectroscopy, we show that the proteins in the condensates remain disordered, and that their chain dynamics occur on timescale surprisingly close to the ∼100-nanosecond dynamics of the 1:1 complex in dilute solution, even though the condensate is almost three orders of magnitude more viscous than the dilute solution and translational diffusion of the same proteins is ∼50 times slower in the dense than in the dilute phase. The experimental results are in good agreement with large-scale all-atom explicit-solvent molecular dynamics simulations consisting of ∼200 proteins and ∼4 million atoms in total, which can thus provide detailed insights into the protein interactions and dynamics within the condensate. The simulations indicate that the rapid protein chain dynamics in the dense phase are linked to the similarity of the local environment experienced by the proteins in the dilute and dense phases and the short lifetime of intermolecular contacts in the dense phase.

Nascent-chain interaction networks and their effect on the bacterial ribosome.

In order to become bioactive, proteins need to be biosynthesized and protected from aggregation during translation. Remarkably, the ribosome contributes to both of these tasks. Some ribosomal proteins (r-proteins) are known to noncovalently interact with ribosome-bound nascent chains (RNCs). Yet, specific interaction networks and their role within the ribosomal machinery remain poorly characterized. Here, we found that empty ribosomes are more sensitive to urea denaturation than ribosomes harboring nascent protein chains, including aminoacyl or short peptidyl-tRNA (snc-tRNA). This result suggests that snc-tRNAs play a ribosome-stabilizing role. On the other hand, RNCs of variable sequence and length do not significantly modify the apparent stability of the peptidyl-transferase center (PTC) and r-proteins, suggesting that RNC/r-protein interaction networks close to the PTC have a negligible effect on the apparent ribosome stability. Fluorescence anisotropy decay, chemical-crosslinking and Western blots show that 140-residue-long RNCs of the foldable protein apoHmp have an N-terminal compact region (63-94 residues) and interact with r-protein L23 but not with L24 or L29. Longer RNCs bear a similar compact region and interact either with L23 or with L23 and another unidentified r-protein or with molecular chaperones. Interestingly, the apparent stability of RNC/r-protein complexes does not depend on RNC sequence or length. Taken together, our findings show that RNCs establish preferential interactions with the L23 ribosomal protein whose strength does not depend on RNC amino-acid sequence and length. As the nascent chain elongates, the interaction network extends to additional r-proteins and chaperones. It follows that the ribosome provides uniform, indiscriminate support to nascent proteins regardless of their sequence and foldability. This result highlights the mode of action of this unbiased molecular machine for cellular health.

Membrane protein structural symmetry and assembly patterns.

The evolution of membrane proteins depends on the physicochemical constraints imposed by the lipid bilayer, and by extension, their folding mechanisms. Repetition of well-folded motifs following these rules is frequently observed within protein sequences and has allowed efficient creation of larger macromolecules capable of more complex functions. Such repeated elements within individual protein chains can result in structural symmetry, as does association of subunits into higher-order assemblies. Nevertheless, much remains to be learned about interplay between folding, assembly, symmetry, and evolution. Structural data obtained by crystallography or electron cryo-microscopy provides an evolutionary snapshot with which to examine these questions in greater detail. At the time of writing, almost 8000 membrane protein structures have been collated into our structure and symmetry database, EncoMPASS. We present a systematic analysis of these data and discuss the implications for folding, function, and evolution.

ProtNA-ASA data base: new version including information about electrostatic potential of DNA minor groove

Background: In the past decades, the rapid development of molecular biology has led to a generation of an unprecedented amount of biological data obtained by the scientific community. Therefore, there is a significant and unmet need to store, process, and make sense of such a vast amount of data. There are currently available a number of databases, that cover different fields of molecular biology. Objectives: In this paper, we describe Protein-Nucleic Acid Structural Database with Information on Accessible Surface Area, ProtNA-ASA, http://www.ire.kharkov.ua/ProtNA-ASA/index.php. The main aim of ProtNA-ASA is to provide quick and convenient access to structural information about DNA and protein-DNA complexes, that can be used for comprehensive study of protein-DNA recognition. Materials and Methods: ProtNA-ASA database comprise information based on X-ray or NMR structures derived from Nucleic Acids Data Bank: 973 structures of protein-DNA complexes, 129 structures of naked А- and 403 of B-DNA ones; following structural parameters for each structure: conformational DNA parameters calculated with the 3DNA/CompDNA analyzer; DNA accessible surface area calculated using the modified algorithm of Higo and Go; DNA electrostatic potential calculated with DelPhi package. Results: The recent update of ProtNA-ASA includes the electrostatic potential of the DNA minor groove since it plays an essential role in the indirect protein-DNA recognition process. The update also includes an advanced search, which serves to ease the use of the database and contribute to a more accurate structure selection. Advanced search allows finding structures by PDB/NDB ID, citation, length and sequence of a protein or DNA chain, type of structure, method of structure obtaining and resolution. All these queries can be used in different combinations with and/or statements. Conclusion: The combination of structural information and physical characteristics from the ProtNA-ASA database is particularly useful to scientists studying the indirect readout, that based on DNA deformability. The detail analyzes of protein-DNA complexes and mechanisms of protein-DNA recognition is essential for implications in understanding cellular processes, DNA metabolism, transcriptional regulation, and developing therapeutic drugs.

Starch Chemical Composition and Molecular Structure in Relation to Physicochemical Characteristics and Resistant Starch Content of Four Thai Commercial Rice Cultivars Differing in Pasting Properties.

Variations in starch pasting properties, considered an alternative potential quality classification parameter for rice starches, are directly controlled by the diverse starch molecular composition and structural features. Here, the starch characteristics of four rice cultivars (i.e., RD57, RD29, KDML105, and RD6) differing in pasting properties were assessed, and their relationship was determined. The results revealed that protein and moisture contents and their crystalline type were similar among the four rice starches. However, their molecular compositions and structures (i.e., reducing sugar and amylose contents, amylopectin branch chain-length distributions, granule size and size distribution, and degree of crystallinity) significantly varied among different genotypes, which resulted in distinct swelling, solubility, gelatinization, retrogradation, and hydrolytic resistance properties. The swelling power and gelatinization enthalpy (∆H) were positively correlated with C-type granule and relative crystallinity, but were negatively correlated with amylose content, B-type granule and median particle size (d(0.5)). Conversely, the water solubility and resistant starch content negatively correlated with C-type granule, but positively correlated with amylose content, B-type granule, and d(0.5). The gelatinization onset temperature (To(g)), and retrogradation concluding temperatures (Tc(r)), enthalpy (∆H(r)), and percentage (R%) were positively impacted by the amount of protein, amylose, and B1 chains (DP 13-24), while they were negatively correlated with short A chains (DP 6-12). Collectively, the starch physicochemical and functional properties of these Thai rice starches are attributed to an interplay between compositional and structural features. These results provide decisive and crucial information on rice cultivars' suitability for consumption as cooked rice and for specific industrial applications.

Mesoscale Confinement in Bagworm Silk: A Hidden Structural Organization.

While silk fibers produced by silkworms and spiders are frequently described as a network of amorphous protein chains reinforced by crystalline β-sheet nanodomains, the importance of higher-order, self-assembled structures has been recognized for advanced modeling of mechanical properties. General acceptance of hierarchical structural models is, however, currently limited by lack of experimental results. Indeed, X-ray scattering studies of spider's dragline-type fibers have been particularly limited by low crystallinities. Here we are reporting on probing the local structure of exceptionally crystalline bagworm silk fibers by X-ray nanobeam scattering. Probing the comparable thickness of cross sections with an X-ray nanobeam allows removing the strong scattering background from the outer sericin layer and reveals a hidden structural organization due to a radial gradient in diameters of mesoscale nanofibrillar bundles in the fibroin phase. Our results provide direct support for lateral interactions between nanofibrils.

Analogue and structure based approaches for modelling HIV-1 integrase inhibitors

A set of 220 inhibitors belonging to different structure classes and having HIV-1 integrase activity were collected along with their experimental pIC50 values. Geometries of all the inhibitors were fully optimized using B3LYP/6-31 + G(d) level of theory. These ligands were docked against 4 different HIV-1 integrase receptors (PDB IDs: 4LH5, 5KRS, 3ZSQ and 3ZSV). 30 docked poses were generated for all 220 inhibitors and ligand interaction of the first docked pose and the docked pose with the highest score were analysed. Residue GLU170 of 4LH5 receptor shows the highest number of interactions followed by ALA169, GLN168, HIS171 and ASP167 residues. Hydrogen bonding and stacking are mainly responsible for the interactions of these inhibitors with the receptor. We performed Molecular Dynamics (MD) simulation to observe the root-mean-square deviation (RMSD), for measure the average change of displacement between the atoms for a particular frame with respect to a reference and The Root Mean Square Fluctuation (RMSF) for characterization of local changes along the protein chain of the docked complexes. Analogue based models were generated to predict the pIC50 values for integrase inhibitors using various types of descriptors such as constitutional, geometrical, topological, quantum chemical and docking based descriptors. The best models were selected on the basis of statistical parameters and were validated by training and test set division. A few new inhibitors were designed on the basis of structure activity relationship and their pIC50 values were predicted using the generated models. All the designed new inhibitors a very high potential and may be used as potent inhibitors of HIV integrase. These models may be useful for further design and development of new and potent HIV integrase inhibitors. Communicated by Ramaswamy H. Sarma