Past

PAST GROUP MEETINGS
May 9, 2005	Andrew	Replica-exchange molecular dynamics method for protein folding
April 22, 2005	Jose	Amyloid &beta -protein monomer structure: a computational and experimental study
Apr 08 2005	Andrew	Interneuron Diversity series: Circuit complexity and axon wiring economy of cortical interneurons
Apr 01 2005	Sijung	Water as a conformational editor in protein folding
Mar 11 2005	Brigita	In silico study of amyloid beta-protein folding and oligomer formation
Mar 04 2005	Shouyong	The protein structure prediction problem could be solved using the current PDB library
Feb 25 2005	Alfonso	Probing the Initial Stage of Aggregation of the Abeta10-35-protein: Assessing the Propensity for Peptide Dimerization
Feb 11 2005	Jose	Optimized Monte Carlo Data Analysis
Feb 04 2005	Sijung	Recent results of our DMD simulation on aggregation
Jan 28 2005	Brigita	Curcumin inhibits formation of A&beta oligomers and fibrils, binds plaques and reduces amyloid in vivo
Jan 21 2005	Shouyong	Intrinsic versus mutation dependent instability/flexibility: a comparative analysis of the structure and dynamics of wild-type transthyretin and its pathogenic variants
Jan 14 2005	Alfonso	Stabilities and Conformations of Alzheimer's Beta Amyloid Peptide Olygomers (AB16-22, AB16-35 and AB10-35): Sequence Effects

Jan 07 2005	Jose	Propagating structure of Alzheimer's &beta -amyloid(10-35) is parallel &beta -sheet with residues in exact register
Dec 17 2004	Sijung	Kinetic control of dimer structure formation in amyloid fibrillogenesis
Dec 10 2004	Brigita	Alzheimer's A&beta 40 studied by NMR at low pH reveals that DSS binds and promotes &beta -ball oligomerization
Dec 03 2004	Shouyong	Solid state NMR reveals a pH-dependent antiparallel beta-sheet registry in fibrils formed by a beta-amyloid peptide
Nov 19 2004	Alfonso	Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides
Nov 12 2004	Jose	In Silico studies of amyloid beta-protein decapeptide Abeta(21-30)

Replica-exchange molecular dynamics method for protein folding

(Abstract of the article) We have developed a formulation for molecular dynamics algorithm for the replica-exchange method. The effectiveness of the method for the protein-folding problem is tested with the penta-peptide Met-enkephalin. The method can overcome the multiple-minima problem by exchanging non-interacting replicas of the system at several temperatures. From only one simulation run, one can obtain probability distributions in canonical ensemble for a wide temperature range using multiple-histogram reweighting techniques, which allows the calculation of any thermodynamic quantity as a function of temperature in that range. (PDF).

Amyloid &beta -protein monomer structure: a computational and experimental study

(Abstract of the article) The structural properties of the A&beta 42 peptide, a main constituent of the amyloid plaques formed in Alzheimer's disease, were investigated through a combination of ion-mobility mass spectrometry and theoretical modeling. Replica exchange molecular dynamics simulations using a fully atomic description of the peptide and implicit water solvent were performed on the -3 charge state of the peptide, its preferred state under experimental conditions. Equilibrated structures at 300K were clustered into three distinct families with similar structural features within a family and with significant root mean square deviations between families. An analysis of secondary structure indicates the A&beta 42 peptide conformations are dominated by loops and turns but show some helical structure in the C-terminal hydrophobic tail. A second calculation on A&beta 42 in a solvent- free environment yields compact structures turned "inside out" from the solution structures (hydrophobic parts on the outside, polar parts on the inside). Ion mobility experiments on the A&beta 42 -3 charge state electrosprayed from solution yield a bimodal arrival time distribution. This distribution can be quantitatively fit using cross-sections from dehydrated forms of the three families of calculated solution structures and the calculated solvent-free family of structures. Implications of the calculations on the early stages of aggregation of A&beta 42 are discussed. (PDF, PPT).

Interneuron Diversity series: Circuit complexity and axon wiring economy

(Abstract of the article) The performance of the brain is constrained by wiring length and maintenance costs. The apparently inverse relationship between number of neurons in the various interneuron classes and the spatial extent of their axon trees suggests a mathematically definable organization, reminiscent of `small-world' or scale-free networks observed in other complex systems. The wiring-econ- omy-based classification of cortical inhibitory inter- neurons is supported by the distinct physiological patterns of class members in the intact brain. The com- plex wiring of diverse interneuron classes could rep- resent an economic solution for supporting global synchrony and oscillations at multiple timescales with minimum axon length. (PDF).

The protein structure prediction problem could be solved using the current PDB library

(Abstract of the article) As molecules approach one another in aqueous solution, desolvation free energy barriers to association are encountered. Experiments suggest these (de)solvation effects contribute to the free energy barriers separating the folded and unfolded states of protein molecules. To explore their influence on the energy landscapes of protein folding reactions, we have incorporated desolvation barriers into a semi-realistic, off-lattice protein model that uses a simplified physico-chemical force-field determined solely by the sequence of amino acids. Monte Carlo sampling techniques were used to study the effects on the thermodynamics and kinetics of folding of a number of systems, diverse in structure and sequence. In each case, desolvation barriers increase the stability of the native conformation and the cooperativity of the major folding/unfolding transition. The folding times of these systems are reduced significantly upon inclusion of desolvation barriers, demonstrating that the particulate nature of the solvent engenders a more defined route to the native fold. (PDF)

In silico study of amyloid beta-protein folding and oligomer formation

Brigita will be presenting her scheduled talk for the FASEB conference.

The protein structure prediction problem could be solved using the current PDB library

(Abstract of the article) For single-domain proteins, we examine the completeness of the structures in the current Protein Data Bank (PDB) library for use in full-length model construction of unknown sequences. To address this issue, we employ a comprehensive benchmark set of 1,489 medium-size proteins that cover the PDB at the level of 35% sequence identity and identify templates by structure alignment. With homologous proteins excluded, we can always find similar folds to native with an average rms deviation (RMSD) from native of 2.5 Angs with {approx}82% alignment coverage. These template structures often contain a significant number of insertions/deletions. The TASSER algorithm was applied to build full-length models, where continuous fragments are excised from the top-scoring templates and reassembled under the guide of an optimized force field, which includes consensus restraints taken from the templates and knowledge-based statistical potentials. For almost all targets (except for 2/1,489), the resultant full-length models have an RMSD to native below 6 Angs (97% of them below 4 Angs). On average, the RMSD of full-length models is 2.25 Angs, with aligned regions improved from 2.5 Angs to 1.88 Angs, comparable with the accuracy of low-resolution experimental structures. Furthermore, starting from state-of-the-art structural alignments, we demonstrate a methodology that can consistently bring template-based alignments closer to native. These results are highly suggestive that the protein-folding problem can in principle be solved based on the current PDB library by developing efficient fold recognition algorithms that can recover such initial alignments. (PDF)

Probing the Initial Stage of Aggregation of the Abeta10-35-protein: Assessing the Propensity for Peptide Dimerization

(Abstract of the article) Characterization of the early stages of peptide aggregation is of fundamental importance in elucidating the mechanism of the formation of deposits associated with amyloid disease. The initial step in the pathway of aggregation of the Ab-protein, whose monomeric NMR structure is known, was studied through the simulation of the structure and stability of the peptide dimer in aqueous solution. A protocol based on shape complementarity was used to generate an assortment of possible dimer structures. The structures generated based on shape complementarity were evaluated using rapidly computed estimates of the desolvation and electrostatic interaction energies to identify a putative stable dimer structure. The potential of mean force associated with the dimerization of the peptides in aqueous solution was computed for both the hydrophobic and the electrostatic driven forces using umbrella sampling and classical molecular dynamics simulation at constant temperature and pressure with explicit solvent and periodic boundary conditions. The comparison of the two free energy profiles suggests that the structure of the peptide dimer is determined by the favorable desolvation of the hydrophobic residues at the interface. Molecular dynamics trajectories originating from two putative dimer structures indicate that the peptide dimer is stabilized primarily through hydrophobic interactions, while the conformations of the peptide monomers undergo substantial structural reorganization in the dimeriza- tion process. The finding that the 4-dimer may constitute the ensemble of stable Ab10-35 dimer has important implications for fibril formation. In particular, the expulsion of water molecules at the interface might be a key event, just as in the oligomerization of Ab16-22 fragments. We conjecture that events prior to the nucleation process themselves might involve crossing free energy barriers which depend on the peptidepeptide and peptidewater interactions. Consistent with existing experimental studies, the peptides within the ensemble of aggregated states show no signs of formation of secondary structure. (PDF)

Optimized Monte Carlo Data An alysis

(Abstract of the article) We present a new method for optimizing the anal ysis of data from multiple Monte Carlo computer simulations over wide ranges of parameter values. Explicit error estimates allow objective planning of the lengt hs of runs and the parameter values to be simulated. The method is applicable to simulations in lattice gauge theories, chemistry, and biology, as well as stati stical mechanics. (PDF)

Recent results of our DMD simulation on aggregation

Sijung will present his latest results and we'll discuss the data for ideas and directions.

Curcumin inhibits formation of A&beta oligomers and fibrils, binds plaques and reduces amyloid in vivo

(Abstract of the article)Alzheimer's disease (AD) involves amyloid (A&beta ) accumulation, oxidative damage and inflammation; and risk is reduced with increased antioxidant and anti-inflammatory consumption. The phenolic yellow curry pigment curcumin has potent anti-inflammatory and antioxidant activities and can suppress oxidative damage, inflammation, cognitive deficits, and amyloid accumulation. Since the molecular structure of curcumin suggested potential Aß-binding, we investigated whether its efficacy in AD models could be explained by effects on Aß aggregation. Under aggregating conditions in vitro, curcumin inhibited aggregation (IC50 =0.8 µM) as well as disaggregated fibrillar Aß40 (IC50 =1 µM), indicating favorable stoichiometry for inhibition. Curcumin was a better A ² 40 aggregation inhibitor than ibuprofen and naproxen, and prevented A&beta 42 oligomer formation and toxicity between 0.1-1.0 µM. Under electron microscopy, curcumin decreased dose-dependently Aß fibril formation beginning with 0.125 µM. Curcumin's effects did not depend on A&beta sequence but on fibril-related conformation. AD and Tg2576 mice brain sections incubated with curcumin revealed preferential labeling of amyloid plaques. In vivo studies showed that curcumin injected peripherally into aged Tg mice, crossed the blood brain barrier and bound plaques. When fed to aged Tg2576 mice with advanced amyloid accumulation, curcumin labeled plaques and reduced amyloid levels and plaque burden. Hence, curcumin directly binds small &beta -amyloid species to block aggregation and fibril formation in vitro and in vivo. These data suggest that low dose curcumin effectively disaggregates Aß as well as prevents fibril and oligomer formation, supporting the rationale for curcumin use in clinical trials preventing or treating AD. (PDF)

Intrinsic versus mutation dependent instability/flexibility: a comparative analysis of the structure and dynamics of wild-type transthyretin and its pathogenic variants

(Abstract of the article) Transthyretin (TTR) is one of the about 20 known human proteins associated with amyloidosis which is characterized by the accumulation of amyloid fibrils in tissues or extracellular matrix surrounding vital organs. Unlike Alzheimer's fibrils that comprise a fragment of a large precursor protein, TTR amyloid fibrils are composed of both full-length protein and fragments of the molecule. The native state of TTR is a homotetramer with eight beta-strands organized into a beta-sandwich in each monomer. To elucidate the structural reorganization mechanisms preceding amyloid formation, it is important to characterize the dynamic features of the wild-type native state as well as to reveal the influence of disease-associated mutations on the structure and dynamics. Molecular dynamics (MD) simulations complement X-ray crystallography and D-H exchange to capture the intrinsically unstable/flexible sites of the wild-type as well as the mutation dependent unstable sites of the pathogenic variants. Our results of MD simulations have shown that the Leu55-->Pro (L55P) mutation occurs in an intrinsically unstable site, leading to substantial local and global structural changes. This observation supports the early speculation that the C-strand-loop-D-strand rearrangement leads to the formation of amyloidogenic intermediates. In addition to the D strand, the alpha-helical region and the strands at the monomer-monomer interface are also intrinsically unstable. The central channel of L55P-TTR undergoes opening and closing fluctuations, which may provide an explanation for the fact that while the mutation is far from the channel, the mutant shows a substantial low binding affinity of thyroxine (PDF).

Stabilities and Conformations of Alzheimer's Beta Amyloid Peptide Olygomers (AB16-22, AB16-35 and AB10-35): Sequence Effects

(Abstract of the article) Previously, we have studied the minimal oligomer size of an aggregate amyloid seed and the mechanism of seed growth with a multilayer beta-sheet model. Under high temperature simulation conditions, our approach can test the stability of possible amyloid forms. Here, we report our study of oligomers of Alzheimer's amyloid beta-peptide (Abeta) fragments 16-22, 16-35, and 10-35 (abbreviated Abeta(16-22), Abeta(16-35), and Abeta(10-35), respectively). Our simulations indicate that an antiparallel beta-sheet orientation is the most stable for the Abeta(16-22), in agreement with a solid state NMR-based model [Balbach, J. J., Ishii, Y., Antzutkin, O. N., Leapman, R. D., Rizzo, N. W., et al. (2000) Biochemistry 39, 13748-13759]. A model with twenty-four Abeta(16-22) strands indicates a highly twisted fibril. Whereas the short Abeta(16-22) and Abeta(24-36) may exist in fully extended form, the linear parallel beta-sheets for Abeta(16-35) appear impossible, mainly because of the polar region in the middle of the 16-35 sequence. However, a bent double-layered hairpin-like structure (called hook) with the polar region at the turn forms parallel beta-sheets with higher stability. An intra-strand salt-bridge (D23-K28) stabilizes the bent hairpin-like hook structure. The bent double-beta-sheet model for the Abeta(10-35) similarly offers oligomer stability (PDF).

Propagating structure of Alzheimer's &beta -amyloid(10-35) is parallel &beta -sheet with residues in exact register

(Abstract of the article) The pathognomonic plaques of Alzheimer's disease are composed primarily of the 39- to 43-aa beta -amyloid (Abeta ) peptide. Crosslinking of Abeta peptides by tissue transglutaminase (tTg) indicates that Gln15 of one peptide is proximate to Lys16 of another in aggregated Abeta . Here we report how the fibril structure is resolved by mapping interstrand distances in this core region of the Abeta peptide chain with solid-state NMR. Isotopic substitution provides the source points for measuring distances in aggregated Abeta . Peptides containing a single carbonyl 13C label at Gln15, Lys16, Leu17, or Val18 were synthesized and evaluated by NMR dipolar recoupling methods for the measurement of interpeptide distances to a resolution of 0.2 Angstroms. Analysis of these data establish that this central core of Abeta consists of a parallel beta -sheet structure in which identical residues on adjacent chains are aligned directly, i.e., in register. Our data, in conjunction with existing structural data, establish that the Abeta fibril is a hydrogen-bonded, parallel beta -sheet defining the long axis of the Abeta fibril propagation (PDF).

Kinetic control of dimer structure formation in amyloid fibrillogenesis

(Abstract of the article) Amyloid fibril formation involves nonfibrillar oligomeric intermediates, which are important as possible cytotoxic species in neurodegenerative diseases. However, their transient nature and polydispersity have made it difficult to identify their formation mechanism or structure. We have investigated the dimerization process, the first step in aggregate formation, by multiple molecular dynamics simulations of five beta-sheet-forming peptides. Contrary to the regular beta-sheet structure of the amyloid fibril, the dimers exhibit all possible combinations of beta-sheets, with an overall preference for antiparallel arrangements. Through statistical analysis of 1,000 dimerization trajectories, each 1 ns in length, we have demonstrated that the observed distribution of dimer configurations is kinetically determined; hydrophobic interactions orient the peptides so as to minimize the solvent accessible surface area, and the dimer structures become trapped in energetically unfavorable conformations. Once the hydrophobic contacts are present, the backbone hydrogen bonds form rapidly by a zipper-like mechanism. The initial nonequilibrium structures formed are stable during the 1-ns simulation time for all five peptides at room temperature. In contrast, at higher temperatures, where rapid equilibration among different configurations occurs, the distribution follows the global energies. The relaxation time of dimers at room temperature was estimated to be longer than the time for diffusional encounters with other oligomers at typical concentrations. These results suggest that kinetic trapping could play a role in the structural evolution of early aggregates in amyloid fibrillogenesis (PDF).

Alzheimer's A&beta 40 studied by NMR at low pH reveals that DSS binds and promotes &beta -ball oligomerization

(Abstract of the article) The Alzheimer's Abeta40 peptide forms soluble oligomers which are extremely potent neurotoxins and strongly impede synapses function. Here, the formation and structure of the large, soluble, neurotoxic A&beta 40 oligomer called &beta -ball have been characterized by 2D-NMR, circular dichroism, and fluorescence spectroscopies, hydrogen exchange and equilibrium sedimentation. In acidic aqueous solution, half the A&beta 40 molecules are in the &beta -ball state; the remainder are monomeric. The equilibrium between the two states is slow as judged by NMR linewidths, and is stable for months. The kinetics of &beta -ball formation from monomer are bi-phasic, with &tau _1= 7 min and &tau _2= 80 min, with no transient helix formation. Monomeric A&beta 40 is essentially devoid of stable secondary structure, although the central, L17-A21, and C-terminal, G29-V40, hydrophobic regions show propensity towards adopting extended structure and residues 22-25 tend to form a turn. We have found that sodium 4,4 dimethyl-4-silapentane-1- sulfonate, DSS 1 , binds to the central hydrophobic region of monomeric A&beta 40. DSS binds &beta -balls more strongly and causes them to double in size. Plausible micelle-like models for the &beta -ball structure with and without bound DSS are presented. (PDF).

Solid state NMR reveals a pH-dependent antiparallel &beta -sheet registry in fibrils formed by a &beta -amyloid peptide

(Abstract of the article) We report solid state nuclear magnetic resonance (NMR) measurements that probe the supramolecular organization of &beta -sheets in the cross-&beta motif of amyloid fibrils formed by residues 11-25 of the &beta -amyloid peptide associated with Alzheimer's disease (A&beta(11-25)). Fibrils were prepared at pH 7.4 and pH 2.4. The solid state NMR data indicate that the central hydrophobic segment of A&beta(11-25) (sequence LVFFA) adopts a &beta -strand conformation and participates in antiparallel &beta -sheets at both pH values, but that the registry of intermolecular hydrogen bonds is pH-dependent. Moreover, both registries determined for A&beta(11-25) fibrils are different from the hydrogen bond registry in the antiparallel &beta -sheets of A&beta(16-22) fibrils at pH 7.4 determined in earlier solid state NMR studies. In all three cases, the hydrogen bond registry is highly ordered, with no detectable "registry-shift" defects. These results suggest that the supramolecular organization of &beta -sheets in amyloid fibrils is determined by a sensitive balance of multiple side-chain-side-chain interactions. Recent structural models for A&beta(11-25) fibrils based on X-ray fiber diffraction data are inconsistent with the solid state NMR data at both pH values (PDF).

Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides

(Abstract of the article) Assembly of normally soluble proteins into amyloid fibrils is a cause or associated symptom of numerous human disorders, including Alzheimer's and the prion diseases. We report molecular-level simulation of spontaneous fibril formation. Systems containing 12 96 model polyalanine peptides form fibrils at temperatures greater than a critical temperature that decreases with peptide concentration and exceeds the peptide s folding temperature, consistent with experimental findings. Formation of small amorphous aggregates precedes ordered nucleus formation and subsequent rapid fibril growth through addition of beta-sheets laterally and monomeric peptides at fibril ends. The fibril s structure is similar to that observed experimentally (PDF).

In Silico studies of amyloid beta-protein decapeptide Abeta(21-30)

Oligomeric assemblies of the amyloid beta-protein (Abeta) have been implicated in the pathogenesis of Alzheimer's disease as a primary source of neurotoxicity. Recent {\em in vitro} studies have suggested that a ten-residue segment, Abeta(21--30), forms a turn-like structure that nucleates the folding of the full-length Abeta protein. To gain mechanistic insight into the folding of Abeta(21--30) and to determine the structure of its folded state, we simulate Abeta(21--30) folding using a discrete molecular dynamics algorithm and a united-atom model incorporating implicit solvent and variable electrostatic interaction strength. Independent of the electrostatic interaction strength, we find that A\beta(21--30) folds into a loop-like conformation driven by an effective hydrophobic attraction between Val24 and the butyl portion of the Lys28 side-chain. Varying the electrostatic interaction strength, we show that at medium strengths (1.5 Kcal/mol), the class of unfolded monomer conformations almost disappears, in agreement with experimental observations. Under conditions optimal for monomer folding, Glu22 and Asp23 form transient salt-bridges with Lys28 that stabilize the loop conformations. Glu22-Lys28 is the most favored salt-bridge interaction. High electrostatic interaction strengths, which usually occur in the interior of proteins, destabilize the packing of Val24 and Lys28. Analysis of the unpacked structures reveals the formation of strong salt-bridges---Glu22-Lys28 (23% frequency), Asp23-Lys28 (48%), or both (29%). Our observations suggest that when the electrostatic interaction is strong, the salt-bridge Asp23-Lys28 is more likely to form, in agreement with studies of molecular modeling of full-length Abeta fibrils. The binary nature of salt-bridge formation by Lys28 provides a mechanistic explanation for the linkage of amino acid substitutions at Glu22 and Asp23 with Alzheimer's disease or cerebral amyloid angiopathy. Substitutions may alter the frequency of Glu22 or Asp23 involvement in salt-bridge formation and affect the stability of the folding nucleus formed in the Abeta(21--30).