Molecular Insight into the Effect of HIV-TAT Protein on Amyloid-ß Peptides.

Increased deposition of amyloid-ß (Aß) plaques in the brain is a frequent pathological feature observed in human immunodeficiency virus (HIV)-positive patients. Emerging evidence indicates that HIV regulatory proteins, particularly the transactivator of transcription (TAT) protein, could interact with Aß peptide, accelerating the formation of Aß plaques in the brain and potentially contributing to the onset of Alzheimer's disease in individuals with HIV infection. Nevertheless, the molecular mechanisms underlying these processes remain unclear. In the present study, we have used long all-atom molecular dynamics simulations to probe the direct interactions between the TAT protein and Aß peptide at the molecular level. Sampling over 28.0 µs, our simulations show that TAT protein induces a shift in the Aß monomer ensemble toward elongated conformations, exposing aggregation-prone regions on the surface and thereby inducing subsequent aggregation. TAT protein also appears to enhance the stability of preformed Aß fibrils, while increasing the ß-sheet content within these fibrils. Our atomistically detailed simulations qualitatively agree with previous in vitro and in vivo studies. Importantly, our simulations identify key interactions between Aß and the TAT protein that drive the Aß aggregation process and stabilize the preformed Aß aggregates, which are particularly challenging to obtain through current experimental techniques.

The stability and dynamics of the Aß40/Aß42 interlaced mixed fibrils.

The accumulation of fibrillar amyloid-ß (Aß) aggregates in the brain, predominantly comprising 40- and 42-residue amyloid-ß (Aß40 and Aß42), is a major pathological hallmark of Alzheimer's disease (AD). Aß40 and Aß42 naturally coexist in the brain under normal physiological conditions, and their interplay is generally considered to be a critical factor in the progression of AD. In addition to forming homogeneous oligomers and fibrils, Aß40 and Aß42 are also reported to co-assemble into hetero-oligomers and interlaced mixed fibrils, as evidenced by solid-state nuclear magnetic resonance spectroscopy (NMR), high molecular weight mass spectrometry and cross-seeding experiments. However, the exact molecular mechanisms underlying these processes remain unclear. In this study, we have used a recently resolved structurally uniform 1:1 mixture of Aß40/Aß42 interlaced mixed fibril as a prototype to gain insights into the molecular-level interactions between Aß40 and Aß42. We employed fully atomistic molecular dynamics simulation and compared the results with a homogeneous U-shaped Aß40 fibrillar model. Our simulations using two different force fields provide conclusive evidence that the Aß40/Aß42 interlaced mixed fibril is energetically more favorable than the homogeneous Aß40 fibrillar model. Furthermore, we also show that the increase in stability observed in the mixed model stems primarily from the packing interfaces and the stacking interfaces between C-termini. Our simulation results provide valuable mechanistic insights that are not readily accessible in experiment and could have significant implications for both the pathogenesis of AD and the development of current therapeutic strategies.Communicated by Ramaswamy H. Sarma.

Catalytic Reaction Mechanism of Bacterial GH92 α-1,2-Mannosidase: A QM/MM Metadynamics Study.

The catalytic mechanism of a C a + 2 ${C{a}^{+2}}$ -dependent family 92 α ${{\rm \alpha }}$ -mannosidase, which is abundantly present in human gut flora and malfunctions leading to the lysosomal storage disease α-mannosidosis, has been investigated using quantum mechanics/molecular mechanics and metadynamics methods. Computational efforts show that the enzyme follows a conformational itinerary of and the C a + 2 ${C{a}^{+2}}$ ion serves a dual purpose, as it not only distorts the sugar ring but also plays a crucial role in orchestrating the arrangement of catalytic residues. This orchestration, in turn, contributes to the facilitation of O S 2 ${{{\rm \ }}^{{\rm O}}{{\rm S}}_{2}}$ conformers for the ensuing reaction. This mechanistic insight is well-aligned with the experimental predictions of the catalytic pathway, and the computed energies are of the same order of magnitude as the experimental estimations. Hence, our results extend the mechanistic understanding of glycosidases.

Resolution exchange with tunneling for enhanced sampling of protein landscapes.

Simulations of protein folding and protein association happen on timescales that are orders of magnitude larger than what can typically be covered in all-atom molecular dynamics simulations. Use of low-resolution models alleviates this problem but may reduce the accuracy of the simulations. We introduce a replica-exchange-based multiscale sampling technique that combines the faster sampling in coarse-grained simulations with the potentially higher accuracy of all-atom simulations. After testing the efficiency of our Resolution Exchange with Tunneling (ResET) in simulations of the Trp-cage protein, an often used model to evaluate sampling techniques in protein simulations, we use our approach to compare the landscape of wild-type and A2T mutant Aß_{1-42} peptides. Our results suggest a mechanism by that the mutation of a small hydrophobic alanine (A) into a bulky polar threonine (T) may interfere with the self-assembly of Aß fibrils.

Interconversion between Serum Amyloid A Native and Fibril Conformations.

Overexpression of serum amyloid A (SAA) can lead to a form of amyloidosis where the fibrils are made of SAA fragments, most often SAA1-76. Using Replica Exchange with Tunneling, we study the conversion of a SAA1-76 chain between the folded conformation and a fibril conformation. We find that the basins in the free energy landscape corresponding to the two motifs are separated by barriers of only about 2-3 k B T. Crucial for the assembly into the fibril structure is the salt bridge 26E-34K that provides a scaffold for forming the fibril conformation.

Role of Notch, IL-1 and leptin expression in colorectal cancer.

An increasing number of studies have shown that angiogenesis has an important role in the progression of cancer. The growth of a new network of blood vessels is crucial for tumor growth and metastasis, which is promoted by several proangiogenic factors. Leptin, an essential adipokine that is secreted from fat tissue, is one of these pro-angiogenic factors. It has been shown that the inhibition of leptin-induced angiogenesis resulted in decreased levels of vascular endothelial growth factor (VEGF)/VEGFR2, hypoxia inducible factor (HIF) 1α, NF-κB, IL-1 and Notch and reduced the tumor growth in breast cancer. Leptin induces angiogenesis in breast cancer either by upregulating VEGFR2 in endothelial cells or by increasing VEGF/VEGFR2 expression through the Notch, IL-1 and leptin crosstalk outcome (NILCO) pathway. NILCO is a novel mechanism that interacts with proinflammatory and proangiogenic signals, which are critical for cell proliferation and angiogenesis in cancer. Several studies have shown that components of NILCO may affect human cancer incidence and progression. However, to the best of our knowledge, the interactions between Notch, IL-1 and leptin in human colorectal cancer have not been yet studied at the molecular level. The aim of the present study was to investigate the expression levels of genes related to the NILCO pathway in human colorectal cancer specimens. The current results demonstrated that leptin, leptin receptor (ObR) b, Notch-1, Notch-4, IL-1α, IL-1ß, IL-1R, IL-6, JAK-2, STAT-1, STAT-3, VEGFA, VEGFR1, VEGFR2, TNF-α and NF-κB mRNA expression levels in the cancer tissue were increased compared with the normal tissue. No significant changes in the mRNA expression levels of Jagged-1, HIF-1α and TNF receptor 1 were observed. Western blotting revealed that the protein expression levels of IκB were increased in the cancer tissue compared with normal tissue, whereas HIF-1α and phosphorylated STAT-1 levels were decreased. IL-6 and VEGFA plasma concentrations were statistically raised and the leptin plasma concentration was also raised, although significantly, patients with cancer compared with control individuals. Together, the present findings indicated that Notch, IL-1 and leptin may serve a crucial role in the development of colorectal cancer.

Replica-exchange-with-tunneling for fast exploration of protein landscapes.

While the use of replica-exchange molecular dynamics in protein simulations has become ubiquitous, its utility is limited in many practical applications. We propose to overcome some shortcomings that hold back its use in settings such as multi-scale or explicit solvent simulations by integrating ideas of hybrid MC/MD into the replica-exchange protocol. This Replica-Exchange-with-Tunneling method is tested by simulating the Trp-cage protein, a system often used in molecular biophysics for testing sampling techniques.

Freestyle Perforator-Based Fasciocutaneous Flap Reconstruction in Nicolau Syndrome-Related Tissue Necrosis.

The actual pathology of the Nicolau syndrome (NS) is still unknown. It is thought to involve direct vascular damage and vasospasm. Many NS cases were reported in the literature but a treatment protocol is still not established. However, after demarcation of the necrotic tissue, surgical intervention is mandatory. Five NS cases with extensive tissue necrosis on the upper lateral gluteal region were analyzed retrospectively. Operative technique was described in details for freestyle perforator-based fasciocutaneous flaps from the gluteal region to reconstruct defects of NS-related tissue necrosis. Freestyle perforator-based fasciocutaneous flaps were used for defect closure in all patients. All flaps survived totally. No complications occurred during the follow-up period. Although rare, NS is a serious complication of inadvertent intramuscular injections. Prevention is the best treatment. However, in case of large-tissue necrosis, freestyle perforator-based fasciocutaneous flaps harvested from the gluteal region is a satisfactory option for reconstruction.

Multicanonical Molecular Dynamics Simulations of the N-terminal Domain of Protein L9.

We describe multicanonical molecular dynamic simulations of the N-terminal domain of the protein L9. Analyzing free energy landscapes and thermal ordering, we propose a possible folding mechanism for the protein. By comparing our results with that of molecular dynamics runs of the protein at constant temperature, we find that multicanonical molecular dynamics leads to orders of magnitude higher sampling of folding transitions.

Folding and self-assembly of a small heterotetramer.

Designed miniproteins offer a possibility to study folding and association of protein complexes, both experimentally and in silico. Using replica exchange molecular dynamics and the coarse-grain UNRES force field, we have simulated the folding and self-assembly of the heterotetramer BBAThet1, comparing it with that of the homotetramer BBAT1 which has the same size and ßßα-fold. For both proteins, association of the tetramer precedes and facilitates folding of the individual chains.

Sampling of Protein Folding Transitions: Multicanonical Versus Replica Exchange Molecular Dynamics.

We compare the efficiency of multicanonical and replica exchange molecular dynamics for the sampling of folding/unfolding events in simulations of proteins with end-to-end ß-sheet. In Go-model simulations of the 75-residue MNK6, we observe improvement factors of 30 in the number of folding/unfolding events of multicanonical molecular dynamics over replica exchange molecular dynamics. As an application, we use this enhanced sampling to study the folding landscape of the 36-residue DS119 with an all-atom physical force field and implicit solvent. Here, we find that the rate-limiting step is the formation of the central helix that then provides a scaffold for the parallel ß-sheet formed by the two chain ends.

In silico cross seeding of Aß and amylin fibril-like oligomers.

Recent epidemiological data have shown that patients suffering from Type 2 Diabetes Mellitus have an increased risk to develop Alzheimer's disease and vice versa. A possible explanation is the cross-sequence interaction between Aß and amylin. Because the resulting amyloid oligomers are difficult to probe in experiments, we investigate stability and conformational changes of Aß-amylin heteroassemblies through molecular dynamics simulations. We find that Aß is a good template for the growth of amylin and vice versa. We see water molecules permeate the ß-strand-turn-ß-strand motif pore of the oligomers, supporting a commonly accepted mechanism for toxicity of ß-rich amyloid oligomers. Aiming for a better understanding of the physical mechanisms of cross-seeding and cell toxicity of amylin and Aß aggregates, our simulations also allow us to identify targets for the rational design of inhibitors against toxic fibril-like oligomers of Aß and amylin oligomers.

Enhancing the affinity of SEB-binding peptides by repeating their sequence.

The utilization of peptide ligands in biosensors and bioassays is dependent on achieving high affinity of these peptides toward their targets. In a previous report, we identified 12-mer peptides that could selectively bind to Staphylococcal enterotoxin B (SEB) using a phage-display library. In this study, we explore for new modification approaches to enhance the affinity of two different SEB-binding peptides. In order to identify the binding regions of selected peptides, the charged residues and the ones, critical for the structure of peptide, were replaced with alanine. However, a specific binding region could not be suggested as all mutant peptides have lost their affinities toward SEB completely. The modifications for the affinity enhancement were done by repeating the 12-mer peptide sequences. A 10-fold increase was observed in the binding affinity of one of the two-repeated peptides, while this modification did not affect the affinity of the other tested peptide. The peptide, with enhanced affinity, was further modified as three repeats; however the affinity of the peptide decreased. The structural basis of the affinity difference between modified peptides was examined by molecular dynamics simulation. The results showed that the conformational differences hold the key for affinity of peptides modified by repeating the sequence. This high affinity peptide with increased affinity is a promising molecular recognition agent to be used in the detection of SEB to be utilized in biosensing systems.

Perforated mixed carcinoid-adenocarcinoma in transverse colon and at gastroenterostomy site: case report.

Goblet cell carcinoid of the large intestine is a rare neoplasm, usually located in ascending colon and rectum. A 60-year-old male patient underwent surgery after the diagnosis of acute abdomen. Exploratory laparotomy revealed perforation with a diameter of 1 cm at the site of the previously performed gastroenterostomy and dilatation of the right colic flexure, secondary to a solid obstructive mass located in the mid-portion of transverse colon. Histopathological investigation of the biopsies, taken from the gastroenterostomy site and the tumor, revealed mixed carcinoid-adenocarcinoma with carcinoid component, predominantly composed of goblet cells. Three cycles of FOLFOX-4 protocol was administered. Following respiratory distress secondary to pulmonary metastasis, the patient's condition deteriorated and subsequently died in the fourth postoperative month. Our aim with this paper is to point out that more cases should be reported for more effective diagnosis, histopathological study, clinical investigation, treatment and prognosis of this specific neoplasm.

Thermodynamic and structural analysis of interactions between peptide ligands and SEB.

Staphylococcal enterotoxin B (SEB) is an exotoxin produced by Staphylococcus aureus and commonly associated with food poisoning. In this study, SEB-binding peptides were identified by screening a phage displayed peptide library. The binding of peptides to SEB was tested with isothermal titration calorimetry (ITC) and of the five selected peptides, three showed affinity to SEB, with one measured to have the highest affinity constant (10(5) M(-1)). ITC revealed that the interaction of peptide ligands with SEB was driven entropically and the binding was dominated by hydrophobic interactions. Circular dichroism (CD) measurements and molecular dynamics (MD) simulations, together, give a structural insight into the interaction of peptides with SEB. While SEB binding peptides showed random coil structure before binding, after complex formation they had more ordered structures. The peptide with highest affinity to SEB showed stable conformation during MD simulation. Taken together, our approach about thermodynamic and structural characterization of peptide ligands can be used to develop aptamers, with high affinity and selectivity, for biosensor applications.

Molecular modeling of various peptide sequences of gliadins and low-molecular-weight glutenin subunits.

The contribution of the three-dimensional structures of one heptapeptide (PQPQPFP) sequence and one pentapeptide (PQQPY) repeat sequence of alpha/beta-gliadins, one heptapeptide (PQQPFPQ) repeat sequence of gamma-gliadins, two heptapeptide (PQQPPFS and QQQQPVL) repeat motifs of low-molecular-weight (LMW) subunits and a tetrapeptide sequence in polyQ region of S-rich prolamins to their conformations are investigated by using the recently developed multicanonical simulation procedure. Ramachandran plots were prepared and analysed to predict the relative occurrence probabilities of gamma-tutn, gamma-turn, and helical structures. The probability of inverse 7-turn was generally higher than that of beta-turns in all sequences investigated. Occurrence probability of helical structure in the repetitive domain of gliadins was low. Structural predictions of QQQQPVL sequence of LMW-glutenin subunits and QQQQ sequence in the polyQ region of S-rich prolamins indicate the presence of helical structures with the probability of >20%. The probability of helical structure significantly decreased around 100 degrees C.

Efficiency of the multicanonical simulation method as applied to peptides of increasing size: the heptapeptide deltorphin.

The advantage of the multicanonical (MUCA) simulation method of Berg and coworkers over the conventional Metropolis method is in its ability to move a system effectively across energy barriers thereby providing results for a wide range of temperatures. However, a MUCA simulation is based on weights (related to the density of states) that should be determined prior to a production run and their calculation is not straightforward. To overcome this difficulty a procedure has been developed by Berg that calculates the MUCA weights automatically. In a previous article (Yasar et al. J Comput Chem 2000, 14, 1251-1261) we extended this procedure to continuous systems and applied it successfully to the small pentapeptide Leu-enkephalin. To investigate the performance of the automated MUCA procedure for larger peptides, we apply it here to deltorphin, a linear heptapeptide with bulky side chains (H-Tyr(1)-D-Met(2)-Phe(3)-His(4)-Leu(5)-Met(6)-Asp(7)-NH(2)). As for Leu-enkephalin, deltorphin is modeled in vacuum by the potential energy function ECEPP. MUCA is found to perform well. A weak second peak is seen for the specific heat, which is given a special attention. By minimizing the energy of structures along the trajectory it is found that MUCA provides a good conformational coverage of the low energy region of the molecule. These latter results are compared with conformational coverage obtained by the Monte Carlo minimization method of Li and Scheraga.