Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Modeling the biomolecular self-assembly and interaction

textWhat materials designers most envy is nature’s building design. It has long been a dream for scientists to mimic and further engineer the behaviors, interactions, and reactions of biomolecules beyond experimental limits. To interpret and facilitate novel materials’ design, a hierarchical approach is presented in this dissertation. With the advent of molecular modeling, many biomolecular interactions can be studied. Using both computational and experimental approaches, we investigated the self-assembly of fluorenylmethoxycarbonyl-conjugated dipeptides (which are called “biomimetic materials”) including Fmoc-dialanine (Fmoc-AA) and Fmoc-Alanine-Lactic acid (Fmoc-ALac) molecules. We simulated the assembly of Fmoc-dipeptides and compared with experiments. We illustrated not only the angstrom-scale self-assembled structures, but also a prevalent polyproline II conformation with β-sheet-like hydrogen bonding pattern among short peptides. Further, simulations to calculate the potential of mean force (PMF) and melting temperatures were performed to gain deeper insights into the inter-fibril interaction. An energetic preference for fibril-fibril surface contact was demonstrated for the first time, which arises from a fibril-level amphiphilicity. From our study, a hierarchical self-assembly process mediated by the balance between hydrophobicity and hydrophilicity of fibril structures was unveiled. The next major topic in this dissertation involves the development of a chemically accurate polarizable multipole-based molecular mechanics model with the investigation of a series of chloromethanes. The ability of molecular modeling to make prediction is determined by the accuracy of underlying physical model. The traditional fixed-charge based force field is severely limited when applied to highly charged systems, halogen, phosphate and sulfate compounds. Via a sophisticated electrostatic model, an accurate description of electrostatics in organochlorine compounds and halogen bonds were achieved. Our model demonstrated its advantages by reproducing the experimental density and heat of vaporization; besides, the calculated hydration free energy, solvent reaction fields, and interaction energies of several homo- and heterodimer of chloromethanes were all in good agreement with experimental and ab initio data.Biomedical Engineerin

Experimental and Computational Studies Reveal an Alternative Supramolecular Structure for Fmoc-Dipeptide Self-Assembly

We have investigated the self-assembly of fluorenylmethoxycarbonyl-conjugated dialanine (Fmoc-AA) molecules using combined computational and experimental approaches. Fmoc-AA gels were characterized using transmission electron microscopy (TEM), circular dichroism (CD), Fourier transform infrared (FTIR), and wide-angle X-ray scattering (WAXS). Computationally, we simulated the assembly of Fmoc-AA using molecular dynamics techniques. All simulations converged to a condensed fibril structure in which the Fmoc groups stack mostly within in the center of the fibril. However, the Fmoc groups are partially exposed to water, creating an amphiphilic surface, which may be responsible for the aggregation of fibrils into nanoscale fibers observed in TEM. From the fibril models, radial distribution calculations agree with <i>d</i>-spacings observed in WAXS for the fibril diameter and π-stacking interactions. Our analyses show that dialanine, despite its short length, adopts a mainly extended polyproline II conformation. In contrast to previous hypotheses, these results indicate that β-sheet-like hydrogen bonding is not prevalent. Rather, stacking of Fmoc groups, inter-residue hydrogen bonding, and hydrogen bonding with water play the important roles in stabilizing the fibril structure of supramolecular assemblies of short conjugated peptides

Experimental and Computational Studies Reveal an Alternative Supramolecular Structure for Fmoc-Dipeptide Self-Assembly

We have investigated the self-assembly of fluorenylmethoxycarbonyl-conjugated dialanine (Fmoc-AA) molecules using combined computational and experimental approaches. Fmoc-AA gels were characterized using transmission electron microscopy (TEM), circular dichroism (CD), Fourier transform infrared (FTIR), and wide-angle X-ray scattering (WAXS). Computationally, we simulated the assembly of Fmoc-AA using molecular dynamics techniques. All simulations converged to a condensed fibril structure in which the Fmoc groups stack mostly within in the center of the fibril. However, the Fmoc groups are partially exposed to water, creating an amphiphilic surface, which may be responsible for the aggregation of fibrils into nanoscale fibers observed in TEM. From the fibril models, radial distribution calculations agree with <i>d</i>-spacings observed in WAXS for the fibril diameter and π-stacking interactions. Our analyses show that dialanine, despite its short length, adopts a mainly extended polyproline II conformation. In contrast to previous hypotheses, these results indicate that β-sheet-like hydrogen bonding is not prevalent. Rather, stacking of Fmoc groups, inter-residue hydrogen bonding, and hydrogen bonding with water play the important roles in stabilizing the fibril structure of supramolecular assemblies of short conjugated peptides

Experimental and Computational Studies Reveal an Alternative Supramolecular Structure for Fmoc-Dipeptide Self-Assembly

We have investigated the self-assembly of fluorenylmethoxycarbonyl-conjugated dialanine (Fmoc-AA) molecules using combined computational and experimental approaches. Fmoc-AA gels were characterized using transmission electron microscopy (TEM), circular dichroism (CD), Fourier transform infrared (FTIR), and wide-angle X-ray scattering (WAXS). Computationally, we simulated the assembly of Fmoc-AA using molecular dynamics techniques. All simulations converged to a condensed fibril structure in which the Fmoc groups stack mostly within in the center of the fibril. However, the Fmoc groups are partially exposed to water, creating an amphiphilic surface, which may be responsible for the aggregation of fibrils into nanoscale fibers observed in TEM. From the fibril models, radial distribution calculations agree with <i>d</i>-spacings observed in WAXS for the fibril diameter and π-stacking interactions. Our analyses show that dialanine, despite its short length, adopts a mainly extended polyproline II conformation. In contrast to previous hypotheses, these results indicate that β-sheet-like hydrogen bonding is not prevalent. Rather, stacking of Fmoc groups, inter-residue hydrogen bonding, and hydrogen bonding with water play the important roles in stabilizing the fibril structure of supramolecular assemblies of short conjugated peptides

β Sheets Not Required: Combined Experimental and Computational Studies of Self-Assembly and Gelation of the Ester-Containing Analogue of an Fmoc-Dipeptide Hydrogelator

In our work toward developing ester-containing self-assembling peptides as soft biomaterials, we have found that a fluorenylmethoxycarbonyl (Fmoc)-conjugated alanine-lactic acid (Ala-Lac) sequence self-assembles into nanostructures that gel in water. This process occurs despite Fmoc-Ala-Lac’s inability to interact with other Fmoc-Ala-Lac molecules via β-sheet-like amide–amide hydrogen bonding, a condition previously thought to be crucial to the self-assembly of Fmoc-conjugated peptides. Experimental comparisons of Fmoc-Ala-Lac to its self-assembling peptide sequence analogue Fmoc-Ala-Ala using a variety of microscopic, spectroscopic, and bulk characterization techniques demonstrate distinct features of the two systems and show that while angstrom-scale self-assembled structures are similar, their nanometer-scale size and morphological properties diverge and give rise to different bulk mechanical properties. Molecular dynamics simulations were performed to gain more insight into the differences between the two systems. An analysis of the hydrogen-bonding and solvent-surface interface properties of the simulated fibrils revealed that Fmoc-Ala-Lac fibrils are stronger and less hydrophilic than Fmoc-Ala-Ala fibrils. We propose that this difference in fibril amphiphilicity gives rise to differences in the higher-order assembly of fibrils into nanostructures seen in TEM. Importantly, we confirm experimentally that β-sheet-type hydrogen bonding is not crucial to the self-assembly of short, conjugated peptides, and we demonstrate computationally that the amide bond in such systems may act mainly to mediate the solvation of the self-assembled single fibrils and therefore regulate a more extensive higher-order aggregation of fibrils. This work provides a basic understanding for future research in designing highly degradable self-assembling materials with peptide-like bioactivity for biomedical applications

β Sheets Not Required: Combined Experimental and Computational Studies of Self-Assembly and Gelation of the Ester-Containing Analogue of an Fmoc-Dipeptide Hydrogelator

In our work toward developing ester-containing self-assembling peptides as soft biomaterials, we have found that a fluorenylmethoxycarbonyl (Fmoc)-conjugated alanine-lactic acid (Ala-Lac) sequence self-assembles into nanostructures that gel in water. This process occurs despite Fmoc-Ala-Lac’s inability to interact with other Fmoc-Ala-Lac molecules via β-sheet-like amide–amide hydrogen bonding, a condition previously thought to be crucial to the self-assembly of Fmoc-conjugated peptides. Experimental comparisons of Fmoc-Ala-Lac to its self-assembling peptide sequence analogue Fmoc-Ala-Ala using a variety of microscopic, spectroscopic, and bulk characterization techniques demonstrate distinct features of the two systems and show that while angstrom-scale self-assembled structures are similar, their nanometer-scale size and morphological properties diverge and give rise to different bulk mechanical properties. Molecular dynamics simulations were performed to gain more insight into the differences between the two systems. An analysis of the hydrogen-bonding and solvent-surface interface properties of the simulated fibrils revealed that Fmoc-Ala-Lac fibrils are stronger and less hydrophilic than Fmoc-Ala-Ala fibrils. We propose that this difference in fibril amphiphilicity gives rise to differences in the higher-order assembly of fibrils into nanostructures seen in TEM. Importantly, we confirm experimentally that β-sheet-type hydrogen bonding is not crucial to the self-assembly of short, conjugated peptides, and we demonstrate computationally that the amide bond in such systems may act mainly to mediate the solvation of the self-assembled single fibrils and therefore regulate a more extensive higher-order aggregation of fibrils. This work provides a basic understanding for future research in designing highly degradable self-assembling materials with peptide-like bioactivity for biomedical applications

Syntheses, Structures, and Catalytic Activities of the Anionic Heterobimetallic Rare-Earth Metal Complexes Supported by Pyrrolyl-Substituted 1,2-Diimino Ligands

A series of the anionic heterobimetallic rare-earth metal complexes supported by <i>trans-</i> or chiral pyrrolyl-substituted 1,2-diimino ligands were synthesized in good yields via reactions of [(Me₃Si)₂N]₃RE­(μ-Cl)­Li­(THF)₃ with the corresponding 1,2-diimino proligands. Reactions of [(Me₃Si)₂N]₃RE­(μ-Cl)­Li­(THF)₃ with 2 equiv of <i>trans</i>-1,2-bis­(pyrrol-2-ylmethylene)-1,2-diphenylethanediamine (<b>H</b>_<b>2</b><b>L</b>^<b>1</b>) afforded the discrete ion-pair rare-earth metal complexes [Li­(THF)₄]⁺[(<b>L</b>^<b>1</b>)₂RE]⁻ (RE = Sm­(<b>5</b>), Dy­(<b>6</b>), Er­(<b>7</b>)). Reactions of [(Me₃Si)₂N]₃RE­(μ-Cl)­Li­(THF)₃ with 2 equiv of (<i>R</i>,<i>R</i>)-1,2-bis­(pyrrol-2-ylmethylene)-1,2-diphenylethanediamine (<b>H</b>_<b>2</b><b>L</b>^<b>2</b>) gave the heterobimetallic rare-earth metal complexes (<b>L</b>^<b>2</b>)₂RELi­(THF)₂ (RE = Sm­(<b>8</b>), Y­(<b>9</b>)). When the rare-earth metal is Er, the chiral linear rare-earth coordination polymer {(<b>L</b>^<b>2</b>)₂ErLi}_<i>n</i> (<b>10</b>) was obtained. Reactions of [(Me₃Si)₂N]₃RE­(μ-Cl)­Li­(THF)₃ with 2 equiv of <i>trans</i>-1,2-bis­(pyrrol-2-ylmethyleneamino)­cyclohexane (H₂<b>L</b>^<b>3</b>) gave the heterobimetallic rare-earth metal complexes (<b>L</b>^<b>3</b>)₂RELi­(THF)₂ (RE = Pr (<b>11</b>), Sm­(<b>12</b>), Eu­(<b>13</b>)). Reactions of [(Me₃Si)₂N]₃RE­(μ-Cl)­Li­(THF)₃ with 2 equiv of (<i>R</i>,<i>R</i>)-1,2-bis­(pyrrol-2-ylmethyleneamino)­cyclohexane (H₂<b>L</b>^<b>4</b>) also gave the heterobimetallic rare-earth metal complexes (<b>L</b>^<b>4</b>)₂RELi­(THF)₂ (Ln = Pr­(<b>14</b>), Sm­(<b>15</b>)). All complexes were characterized by spectroscopic methods and elemental analyses, and complexes <b>5</b>–<b>11</b>, <b>13</b>, and <b>14</b> were further determined by single-crystal X-ray diffraction. The catalytic properties of racemic rare-earth metal complexes on cyanosilylation of ketones were examined, and results showed that the above complexes could effectively catalyze the cyanosilylation of ketones. Chiral rare-earth metal complexes as catalysts for the enantioselective epoxidation of α,β-unsaturated ketones were also examined to afford the chiral epoxides in high yields with moderate enantioselectivities