Computational Studies of Protein Folding

Figure 1: CRISPR–Cas9-mediated DNA interference in bacterial adaptive immunity. (a) A typical CRISPR locus in a type II CRISPR–Cas system comprises an array of repetitive sequences (repeats, brown dia...

Figure 2: The mechanism of CRISPR–Cas9–mediated genome engineering. The synthetic sgRNA or crRNA–tracrRNA structure directs a Cas9 endonuclease to almost arbitrary DNA sequence in the genome through a...

Figure 3: Overall structure of Streptococcus pyogenes Cas9 (SpyCas9) in the apo state. (a) Ribbon representation of the crystal structure of SpyCas9 (PDB ID 4CMP). Individual Cas9 domains are colored ...

Figure 4: Guide RNA loading enables Cas9 to form a DNA recognition–competent conformation for target search. (a) Ribbon diagram showing the apo structure of SpyCas9 aligned in the same orientation as ...

Figure 5: Structures of CRISPR–Cas9 bound to DNA substrates, showing the same view as in Figure 4c after superposition. (a) Crystal structure of SpyCas9 (surface representation) in complex with sgRNA ...

Figure 6: Schematic representations of the proposed mechanisms of CRISPR–Cas9-mediated target DNA recognition and cleavage. Upon sgRNA loading, Cas9 undergoes a large conformational rearrangement to r...

Figure 7: Structures of Cas9 orthologs reveal both the conserved and divergent structural features among orthologous CRISPR–Cas9 systems. Individual Cas9 domains are colored according to the scheme in...

Figure 1: A schematic illustration of an antibody. Abbreviations: Fab, fragment, antigen-binding; Fc, fragment, crystallizable.

Figure 2: A schematic illustration of antibody therapy. Abbreviations: ACE2, angiotensin-converting enzyme 2; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Figure 3: The alignment of the available 3D structures of the SARS-CoV-2 S-protein RBD in binding complexes with antibodies, as well as with ACE2. Abbreviations: ACE2, angiotensin-converting enzyme 2;...

Figure 4: The alignment of the available 3D structures of the SARS-CoV S-protein RBD in binding complexes with antibodies, as well as with ACE2. Abbreviations: ACE2, angiotensin-converting enzyme 2; R...

Figure 5: Illustration of the contact positions of antibody and ACE2 epitopes with SARS-CoV-2 and SARS-CoV S-protein RBDs on RBD 2D sequences. The proteins in the structures of 6M0J, 6WPS, 6W41, 7C01,...

Figure 6: An illustration of the binding affinities of antibodies with SARS-CoV and SARS-CoV-2 RBDs. The molecular names of these antibodies are 80R (2GHW) ACE2 (3D0G), VHH-72 (6WAQ), m396 (2DD8), S23...

Figure 7: Overall binding affinity changes following mutations of the S-protein RBD from SARS-CoV to SARS-CoV-2 for molecules 80R, ACE2, and VHH-72. The x axis records the wild type to the mutant type...

Figure 8: Overall binding affinity changes following mutations of S-protein RBD from SARS-CoV to SARS-CoV-2 for molecules m396, S230, and F26G19. The x axis records the wild type to the mutant type at...

Figure 9: Cα network analysis of three antibody–antigen complexes. Circles indicate antigen (spike-protein receptor-binding domain), and squares represent antibody or angiotensin-converting enzyme 2. ...

Figure 10: An illustration of the TopNetTree model (77). Protein structure shown in the plot is an antibody (PDB 7BZ5) (blue indicates heavy chain, orange indicates light chain) and SARS-CoV-2 S-prote...

Figure 1: Overview of cellular bodies that are well described as biomolecular condensates. These bodies include large, well-studied structures such as the nucleolus, nuclear speckles, and P-bodies, bu...

Figure 2: Schematic of different types of stickers and spacers for different systems. (a) For folded domains, the mapping of the stickers and spacers is achieved via the physics of patchy colloids, wh...

Figure 3: Schematic of sticker patterning and effective solvation volume. (a) Three distinct sequences of intrinsically disordered proteins with identical numbers of sticker residues distributed in di...

Figure 4: Four examples of multiphase assemblies formed for different multicomponent systems. (a) Three-phase assembly of nucleoli is readily reproduced using a simple stickers-and-spacers model, as s...

Figure 5: General model for emergent stickers formed through oligomerization, linear polymerization, and/or clustering. (a) Depiction of monomers of ARF19 (solid shapes) that correspond to the PB1 dom...

Figure 1: G-tetrad structure with a potassium cation.

Figure 2: G-quadruplex structure formed by three stacked G-tetrads and metallic cations.

Figure 3: Representation of different binding modes between a ligand and a G-quadruplex DNA. (a) End stacking. (b) Groove binding mode. (c) Loop binding mode.

Figure 4: Chemical structure of TMPyP4 (left) and the overlapping of its porphyrin ring with terminal DNA bases (right).

Figure 5: Scheme of ion penetration into the central binding site. Figure adapted with permission from Reference 135.

Figure 6: Molecular dynamics simulations of 15-TBA during Na+ penetration. The letter P in the figure and the dashed vertical lines indicate the simulation step where the cation penetrates the G-quadr...

Figure 7: RMSD (Å) of all nonhydrogen atoms (black) and guanine atoms (red) for the molecular dynamics simulation on the interaction between N,N′-bis-salicylidene-1,2-phenylenediaminato (a) NiII and (...

Figure 8: The free energy surface (FES) of the 3′ end opening of TBA shows three main energy minima: (a) TBA occurs in the G-quadruplex structure, (b) an intermediate state occurs, and (c) the G-tripl...

Figure 9: Representation of the G-triad structure for the G-triplex.

Figure 10: The free energy landscape and the representative structures of the basins of attraction. The units of the free energies are kcal mol−1. Figure adapted with permission from Reference 16.

Figure 11: Mapping scheme used to generate the coarse-grained model. Red indicates the core, green indicates the loop, cyan indicates K+ in solution, and yellow indicates K+ in the ion channel. Figure...

Figure 12: Reduction of degrees of freedom for the 1KF1 and the structure consisting of 20 blocks of 1KF1. The structure is shown without potassium ions. Figure adapted with permission from Reference ...

Figure 13: Coarse-grained model representation of a guanine nucleotide. Figure adapted with permission from Reference 157.

Figure 14: PES curves for three G-tetrad and one-ion system with K+, Na+, or Li+. The vertical lines mark passage of the ion through the quartet plane. Figure adapted with permission from Reference 52...

Figure 1: Structures of actin and actin complexes. The structures of actin complexes are shown to scale and in chronological order of publication. (a) Classical view of the structure of the actin mono...

Figure 2: The helical structure of F-actin derived from cryo-electron microscopy (16). The molecules are arranged on a single helix with 13 molecules repeating in almost exactly six left-handed turns....

Figure 3: The essence of the G-actin to F-actin transition is a flattening of the actin molecule by a propeller-twist of the outer and inner domains about an axis roughly at right angles to the actin ...

Figure 4: Intermolecule bonding in F-actin. Shown are five actin molecules labeled −2 to +2. The run of the protein chain is shown as a secondary structure schematic color-coded from blue (N terminus)...

Figure 5: Precursor helix assembled by the formin FH2 domain. The left view shows the precursor helix assembled by FH2 subunits along the crystallographic C2 axis. The formin FH2 domain is shown gray ...