From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions

©2009 Gao, Skolnick. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.doi:10.1371/journal.pcbi.1000341DNA–protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of DNA–protein interactions is a challenging problem. Here, we present a novel computational approach for predicting DNA-binding protein residues and DNA–protein interaction modes without knowing its specific DNA target sequence. Given the structure of a DNA-binding protein, the method first generates an ensemble of complex structures obtained by rigid-body docking with a nonspecific canonical B-DNA. Representative models are subsequently selected through clustering and ranking by their DNA–protein interfacial energy. Analysis of these encounter complex models suggests that the recognition sites for specific DNA binding are usually favorable interaction sites for the nonspecific DNA probe and that nonspecific DNA–protein interaction modes exhibit some similarity to specific DNA–protein binding modes. Although the method requires as input the knowledge that the protein binds DNA, in benchmark tests, it achieves better performance in identifying DNA-binding sites than three previously established methods, which are based on sophisticated machine-learning techniques. We further apply our method to protein structures predicted through modeling and demonstrate that our method performs satisfactorily on protein models whose root-mean-square Ca deviation from native is up to 5 Å from their native structures. This study provides valuable structural insights into how a specific DNA-binding protein interacts with a nonspecific DNA sequence. The similarity between the specific DNA–protein interaction mode and nonspecific interaction modes may reflect an important sampling step in search of its specific DNA targets by a DNA-binding protein

Protein–DNA electrostatics

Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in the absence of any active process. It has been rapidly recognized that, to achieve this task, these proteins should be efficient at both searching (i.e., sampling fast relevant parts of DNA) and finding (i.e., recognizing the specific site). A two-mode search and variants of it have been suggested since the 1970s to explain either a fast search or an efficient recognition. Combining these two properties at a phenomenological level is, however, more difficult as they appear to have antagonist roles. To overcome this difficulty, one may simply need to drop the dichotomic view inherent to the two-mode search and look more thoroughly at the set of interactions between DNA-binding proteins and a given DNA segment either specific or nonspecific. This chapter demonstrates that, in doing so in a very generic way, one may indeed find a potential reconciliation between a fast search and an efficient recognition. Although a lot remains to be done, this could be the time for a change of paradigm

Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains

A major obstacle towards elucidating the molecular basis of transcriptional regulation is the lack of a detailed understanding of the interplay between non-specific and specific protein–DNA interactions. Based on molecular dynamics simulations of C2H2 zinc fingers (ZFs) and engrailed homeodomain transcription factors (TFs), we show that each of the studied DNA-binding domains has a set of highly constrained side chains in preset configurations ready to form hydrogen bonds with the DNA backbone. Interestingly, those domains that bury their recognition helix into the major groove are found to have an electrostatic hot spot for Cl− ions located on the same binding cavity as the most buried DNA phosphate. The spot is characterized by three protein hydrogen bond donors, often including two basic side chains. If bound, Cl− ions, likely mimicking phosphates, steer side chains that end up forming specific contacts with bases into bound-like conformations. These findings are consistent with a multi-step DNA-binding mechanism in which a pre-organized set of TF side chains assist in the desolvation of phosphates into well defined sites, prompting the re-organization of specificity determining side chains into conformations suitable for the recognition of their cognate sequence

Computational models for large-scale simulations of facilitated diffusion

The binding of site-specific transcription factors to their genomic target sites is a key step in gene regulation. While the genome is huge, transcription factors belong to the least abundant protein classes in the cell. It is therefore fascinating how short the time frame is that they require to home in on their target sites. The underlying search mechanism is called facilitated diffusion and assumes a combination of three-dimensional diffusion in the space around the DNA combined with one-dimensional random walk on it. In this review, we present the current understanding of the facilitated diffusion mechanism and identify questions that lack a clear or detailed answer. One way to investigate these questions is through stochastic simulation and, in this manuscript, we support the idea that such simulations are able to address them. Finally, we review which biological parameters need to be included in such computational models in order to obtain a detailed representation of the actual process. © 2012 The Royal Society of Chemistry

The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics

The flexibility in the structure of calmodulin (CaM) allows its binding to over 300 target proteins in the cell. To investigate the structure-function relationship of CaM, we combined methods of computer simulation and experiments based on circular dichroism (CD) to investigate the structural characteristics of CaM that influence its target recognition in crowded cell-like conditions. We developed a unique multiscale solution of charges computed from quantum chemistry, together with protein reconstruction, coarse-grained molecular simulations, and statistical physics, to represent the charge distribution in the transition from apoCaM to holoCaM upon calcium binding. Computationally, we found that increased levels of macromolecular crowding, in addition to calcium binding and ionic strength typical of that found inside cells, can impact the conformation, helicity and the EF hand orientation of CaM. Because EF hand orientation impacts the affinity of calcium binding and the specificity of CaM's target selection, our results may provide unique insight into understanding the promiscuous behavior of calmodulin in target selection inside cells.Comment: Accepted to PLoS Comp Biol, 201

The suitability of Award Fee contracts for the Israeli Ministry of Defense (MOD).

The primary objective of this thesis was to analyze the suitability for use of the Award Fee Types of Contracts in the Israeli Ministry of Defense. The researcher used the Navy's Supervisor of Shipbuilding, Conversion and Repair award fee monitoring organization as a sample for comparison with the Israeli Ministry of Defense organization. The purpose for this comparison was to determine if there was an organization structure barrier that would prevent implementation of the Award Fee Types of Contracts. Other barriers were identified and discussed through the use of a written survey conducted with key personnel within the Israeli Ministry of Defense. A guide was developed for use when implementing the Award Fee Types of Contracts. The analysis revealed that there were no barriers that could not be overcome and that the benefits to be gained by incorporating the Award Fee Types of Contracts far outweigh any impediments. It was recommended that the Israeli Ministry of Defense consider incorporating these types of contracts into their procurement regulations after evaluating the results of a test case.http://archive.org/details/suitabilityofawa00givaIsraeli Ministry of Defense (MOD)Approved for public release; distribution is unlimited

Psychophysics tests on the internet: an evaluation

Conducting psychophysical experiments on the internet might constitute a useful addition to the existing spectrum of experimental methods in behavioural and cognitive sciences. Web-experiments allow access to a huge number of anonymous subjects that spend a short amount of time on an experiment. The technique is therefore suitable for experiments that (i) need few data per subject (eg, one-shot recognition experiments), (ii) need data from many subjects to get a significant result, (iii) cover a large parameter space, (iv) are designed to catalogue possible behaviours (eg, identification of exploration strategies in navigation), or (v) have a demand for subject diversity. We have implemented five web-experiments that investigate gender perception, perception of face orientation, visual encoding of scenes, canonical views, and memory for faces (http://exp.kyb.tuebingen.mpg.de/web-experiment/). In the first few months we had up to 200 subjects for the shortest and most attractive experiments, whereas experiments that took more time or required additional browser plug-ins (VRML) attracted only 20 - 50 subjects. The performance of a control group (n=20) that ran the same experiments on a computer in our laboratory confirmed the validity of our web-experiment data. Feedback from this group allowed us to improve the design of the experiments. We conclude that web-experiments can form a valuable method for accessing large groups of subjects, provided careful thought is given to the limitations of using anonymous subjects on remote locations. The technique is especially well suited for performing quick pilot studies and for validating laboratory experiments on larger numbers of subjects. Experiments that require precise control of timing, colour, display characteristics, etc (low-level psychophysics) should not be considered for internet implementation

Psychophysical experiments on the internet

Psychologists have recently discovered the Internet for demonstrating visual illusions and for education. We have examined the feasibility of using the Internet for another purpose, namely large-scale data collection in visual psychophysics. Web-experiments promise access to a huge number of subjects. The technique is therefore potentially suitable for experiments that either (1) need few data per subject (e.g., one-shot recognition experiments), (2) cover a large parameter space, (3) need data from many subjects to get a significant result, (4) are designed to catalogue possible behaviors (e.g., identification of exploration strategies in navigation), or (5) have a demand for subject diversity. Some disadvantages one has to deal with are that Internet subjects are anonymous, spend only a short amount of time on an experiment, and use unknown equipment. We have implemented five web-experiments that investigate gender perception, perception of face orientation, visual encoding of scenes, canonical views, and memory for faces (http://exp.kyb.tuebingen.mpg.de/web-experiment/). In the first year more than 2000 subjects participated in one or more web-experiments. The number of subjects per experiment varied from roughly 100 to more than 1500. Some of these experiments were derived from published experiments conducted previously in our lab, which allowed us to make direct comparisons between data obtained in the lab and on the Internet. The results of these comparisons plus a further comparison with the performance of a control group (n=20) that ran the Internet experiments using a computer in our lab strongly confirmed the general validity of our web-experiment data. We conclude that web-experiments form a valuable method for accessing large groups of subjects, provided careful thought is given to the limitations of using anonymous subjects and loosely specified experimental conditions. The technique is especially well suited for performing quick pilot-studies and for validating lab-experiments using larger numbers of subjects. Experiments that require precise control of timing, color, or display characteristics (often required for low-level psychophysics) should not be considered for Internet implementation