Chromatin fibers encountered in various species and tissues are characterized by different nucleosome repeat lengths (NRL) of the linker DNA connecting the nucleosomes. While single cellular organisms and rapidly growing cells with high protein production have short NRL ranging from 160 to 189 base pairs (bp), mature cells usually have longer NRL ranging between 190 and 220 bp. Recently, various experimental studies have examined the effect of NRL on the internal organization of chromatin fiber. Here we investigate by mesoscale modeling of oligonucleosomes the folding patterns for different NRL, with and without linker histone, under typical monovalent salt conditions using both one-start solenoid and two-start zigzag starting configurations. We find that short to medium NRL chromatin fibers (173 to 209 bp) with linker histone condense into irregular zigzag structures, and that solenoid-like features are viable only for longer NRL (226 bp). We suggest that medium NRL are more advantageous for packing and various levels of chromatin compaction throughout the cell cycle than their shortest and longest brethren; the former (short NRL) fold into narrow fibers, while the latter (long NRL) arrays do not easily lead to high packing ratios due to possible linker DNA bending. Moreover, we show that the linker histone has a small effect on the condensation of short-NRL arrays but an important condensation effect on medium-NRL arrays which have linker lengths similar to the linker histone lengths. Finally, we suggest that the medium-NRL species, with densely packed fiber arrangements, may be advantageous for epigenetic control because their histone tail modifications can have a greater effect compared to other fibers due to their more extensive nucleosome interaction network.

It is recognized that shear topology of two directly connected force-bearing terminal ␤-strands is a common feature among the vast majority of mechanically stable proteins known so far. However, these proteins belong to only two distinct protein folds, Ig-like ␤ sandwich fold and ␤-grasp fold, significantly hindering delineating molecular determinants of mechanical stability and rational tuning of mechanical properties. Here we combine singlemolecule atomic force microscopy and steered molecular dynamics simulation to reveal that the de novo designed Top7 fold [Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D (2003) Science 302:1364 -1368] represents a mechanically stable protein fold that is distinct from Ig-like ␤ sandwich and ␤-grasp folds. Although the two force-bearing ␤ strands of Top7 are not directly connected, Top7 displays significant mechanical stability, demonstrating that the direct connectivity of force-bearing ␤ strands in shear topology is not mandatory for mechanical stability. This finding broadens our understanding of the design of mechanically stable proteins and expands the protein fold space where mechanically stable proteins can be screened. Moreover, our results revealed a substructure-sliding mechanism for the mechanical unfolding of Top7 and the existence of two possible unfolding pathways with different height of energy barrier. Such insights enabled us to rationally tune the mechanical stability of Top7 by redesigning its mechanical unfolding pathway. Our study demonstrates that computational biology methods (including de novo design) offer great potential for designing proteins of defined topology to achieve significant and tunable mechanical properties in a rational and systematic fashion.atomic force microscopy ͉ computational design ͉ mechanical unfolding ͉ unfolding pathway P rotein mechanics is an important aspect of biology. Many proteins have evolved to sense, generate and bear mechanical forces (1) in a variety of biological processes, such as cellular adhesion (2), muscle contraction (3), and ligand-receptor interactions (4). Elastomeric proteins constitute a unique class of mechanical proteins with diverse functions ranging from molecular springs to structural materials of superb mechanical properties. Recent development in single-molecule force spectroscopy has made it possible to study the mechanical properties of proteins at singlemolecule level (5, 6). These studies not only revealed rich information about the architectural design of elastomeric proteins and shed light on the biophysical principles underpinning various biological processes, but also revealed promising prospect of using engineered elastomeric proteins for nanomechanical applications (7-9). However, in comparison to chemical and thermodynamic properties of proteins, experimental data on mechanical properties of proteins remains rather limited and molecular determinants of mechanical properties of proteins are less well understood. These factors have made it difficult or impossible to predict...

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