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Over the last decade, and especially after the advent of fluorescent in situ hybridization imaging and chromosome conformation capture methods, the availability of experimental data on genome three-dimensional organization has dramatically increased. We now have access to unprecedented details of how genomes organize within the interphase nucleus. Development of new computational approaches to leverage this data has already resulted in the first three-dimensional structures of genomic domains and genomes. Such approaches expand our knowledge of the chromatin folding principles, which has been classically studied using polymer physics and molecular simulations. Our outlook describes computational approaches for integrating experimental data with polymer physics, thereby bridging the resolution gap for structural determination of genomes and genomic domains., Spain. Ministerio de Ciencia e Innovación (BFU2010-19310), National Cancer Institute (U.S.), David H. Koch Institute for Integrative Cancer Research at MIT

Protein knots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Seven distinctly knotted folds have already been identified. It is by and large unclear how these exceptional structures actually fold, and only recently, experiments and simulations have begun to shed some light on this issue. In checking the new protein structures submitted to the Protein Data Bank, we encountered the most complex and the smallest knots to date: A recently uncovered α-haloacid dehalogenase structure contains a knot with six crossings, a so-called Stevedore knot, in a projection onto a plane. The smallest protein knot is present in an as yet unclassified protein fragment that consists of only 92 amino acids. The topological complexity of the Stevedore knot presents a puzzle as to how it could possibly fold. To unravel this enigma, we performed folding simulations with a structure-based coarse-grained model and uncovered a possible mechanism by which the knot forms in a single loop flip., Author Summary Knots are ubiquitous in many aspects of our life, but remain elusive in proteins. The multitude of protein structures archived in the Protein Data Bank can be grouped into several hundred patterns, but only a handful are folded into knots. Combing through the recently added structures we found several novel knotted proteins. A microbial enzyme that catalyzes the breakdown of pollutants is the most complex protein knot encountered so far (similar to a knot used by stevedores for lifting cargo). The smallest knotted protein on the other hand consists of only 92 amino acids. The existence of these complex motifs demonstrates that the ability of self assembly goes far beyond normal expectations. Aided by computer simulations we present evidence which suggests that the Stevedore protein knot, despite its topological complexity, may actually form in a single flipping movement.

The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a complex network of looping interactions. Here we use a polymer model of chromatin fiber to investigate whether, and to what extent, looping interactions between elements in the vicinity of an enhancer-promoter pair can influence their contact frequency. Our equilibrium polymer simulations show that a chromatin loop, formed by elements flanking either an enhancer or a promoter, suppresses enhancer-promoter interactions, working as an insulator. A loop formed by elements located in the region between an enhancer and a promoter, on the contrary, facilitates their interactions. We find that different mechanisms underlie insulation and facilitation; insulation occurs due to steric exclusion by the loop, and is a global effect, while facilitation occurs due to an effective shortening of the enhancer-promoter genomic distance, and is a local effect. Consistently, we find that these effects manifest quite differently for in silico 3C and microscopy. Our results show that looping interactions that do not directly involve an enhancer-promoter pair can nevertheless significantly modulate their interactions. This phenomenon is analogous to allosteric regulation in proteins, where a conformational change triggered by binding of a regulatory molecule to one site affects the state of another site., National Cancer Institute (U.S.). Physical Sciences-Oncology Center (U54-CA143874-04), Massachusetts Institute of Technology. Undergraduate Research Opportunities Program, National Science Foundation (U.S.). Massachusetts Institute of Technology. Program for Research in Mathematics, Engineering and Science for High School Students (PRIMES)