Predicting allosteric pockets in protein biological assemblages.

Motivation: Allostery enables changes to the dynamic behavior of a protein at distant positions induced by binding. Here, we present APOP, a new allosteric pocket prediction method, which perturbs the pockets formed in the structure by stiffening pairwise interactions in the elastic network across the pocket, to emulate ligand binding. Ranking the pockets based on the shifts in the global mode frequencies, as well as their mean local hydrophobicities, leads to high prediction success when tested on a dataset of allosteric proteins, composed of both monomers and multimeric assemblages.

Cooperative mechanics of PR65 scaffold underlies the allosteric regulation of the phosphatase PP2A.

PR65, a horseshoe-shaped scaffold composed of 15 HEAT (observed in Huntingtin, elongation factor 3, protein phosphatase 2A, and the yeast kinase TOR1) repeats, forms, together with catalytic and regulatory subunits, the heterotrimeric protein phosphatase PP2A. We examined the role of PR65 in enabling PP2A enzymatic activity with computations at various levels of complexity, including hybrid approaches that combine full-atomic and elastic network models. Our study points to the high flexibility of this scaffold allowing for end-to-end distance fluctuations of 40-50 Å between compact and extended conformations.

Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods.

Recent years have seen several hybrid simulation methods for exploring the conformational space of proteins and their complexes or assemblies. These methods often combine fast analytical approaches with computationally expensive full atomic molecular dynamics (MD) simulations with the goal of rapidly sampling large and cooperative conformational changes at full atomic resolution. We present here a systematic comparison of the utility and limits of four such hybrid methods that have been introduced in recent years: MD with excited normal modes (MDeNM), collective modes-driven MD (CoMD), and elastic network model (ENM)-based generation, clustering, and relaxation of conformations (ClustENM) as well as its updated version integrated with MD simulations (ClustENMD).

Precise druggability of the PTH type 1 receptor.

Class B G protein-coupled receptors (GPCRs) are notoriously difficult to target by small molecules because their large orthosteric peptide-binding pocket embedded deep within the transmembrane domain limits the identification and development of nonpeptide small molecule ligands. Using the parathyroid hormone type 1 receptor (PTHR) as a prototypic class B GPCR target, and a combination of molecular dynamics simulations and elastic network model-based methods, we demonstrate that PTHR druggability can be effectively addressed. Here we found a key mechanical site that modulates the collective dynamics of the receptor and used this ensemble of PTHR conformers to identify selective small molecules with strong negative allosteric and biased properties for PTHR signaling in cell and PTH actions in vivo.

ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution.

Summary: Efficient sampling of conformational space is essential for elucidating functional/allosteric mechanisms of proteins and generating ensembles of conformers for docking applications. However, unbiased sampling is still a challenge especially for highly flexible and/or large systems. To address this challenge, we describe a new implementation of our computationally efficient algorithm ClustENMD that is integrated with ProDy and OpenMM softwares.

ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python.

Summary: ProDy, an integrated application programming interface developed for modelling and analysing protein dynamics, has significantly evolved in recent years in response to the growing data and needs of the computational biology community. We present major developments that led to ProDy 2.0: (i) improved interfacing with databases and parsing new file formats, (ii) SignDy for signature dynamics of protein families, (iii) CryoDy for collective dynamics of supramolecular systems using cryo-EM density maps and (iv) essential site scanning analysis for identifying sites essential to modulating global dynamics.

State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps.

The eukaryotic chaperonin TRiC/CCT plays a major role in assisting the folding of many proteins through an ATP-driven allosteric cycle. Recent structures elucidated by cryo-electron microscopy provide a broad view of the conformations visited at various stages of the chaperonin cycle, including a sequential activation of its subunits in response to nucleotide binding. But we lack a thorough mechanistic understanding of the structure-based dynamics and communication properties that underlie the TRiC/CCT machinery.

Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions.

Despite the wealth of methods developed for exploring the molecular basis of allostery in biomolecular systems, there is still a need for structure-based predictive tools that can efficiently detect susceptible sites for triggering allosteric responses. Toward this goal, we introduce here an elastic network model (ENM)-based method, Essential Site Scanning Analysis (ESSA). Essential sites are here defined as residues that would significantly alter the protein's global dynamics if bound to a ligand.

Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior.

Allosteric behavior is central to the function of many proteins, enabling molecular machinery, metabolism, signaling and regulation. Recent years have shown that the intrinsic dynamics of allosteric proteins defined by their 3-dimensional architecture or by the topology of inter-residue contacts favors cooperative motions that bear close similarity to structural changes they undergo during their allosteric actions. These conformational motions are usually driven by energetically favorable or soft modes at the low frequency end of the mode spectrum, and they are evolutionarily conserved among orthologs.

Protein-Ligand Complexes as Constrained Dynamical Systems.

This study focuses on how the low-frequency end of the vibrational spectrum related to the functional motions changes as a protein binds to a small ligand(s). Our recently proposed residue-specific (RESPEC) elastic network model provides a natural laboratory for this aim due to its systematic mixed coarse-graining approach and parametrization. Current analysis on a large data set of protein-ligand complexes reveals a universal curve enclosing the frequency distributions, which bears the features of previous computational and experimental studies.

RESPEC Incorporates Residue Specificity and the Ligand Effect into the Elastic Network Model.

RESPEC is a new framework that introduces residue specificity into elastic network modeling (ENM) to successfully render intact protein-ligand complexes as well as apo proteins. This framework establishes a broader application of coarse-graining idea via describing (i) a coarse-grained residue/node through its heavy atoms as virtual nodes, (ii) an effective B-factor for such a node, directly obtained from the experimental data, and (iii) a node-node interaction by a cumulative distance-dependent force constant. RESPEC improves the level of correlations with B-factors after optimizing the parameters of the model.

Moloney darn repair versus lichtenstein mesh hernioplasty for open inguinal hernia repair.

Purpose: To compare two tension-free techniques of inguinal hernia repair: the Moloney darn repair (MDR) and Lichtenstein mesh hernioplasty (LMH).

Methods: The subjects of this study were 651 patients from a total 732 who underwent open inguinal herniorrhaphy at our clinic between January 2000 and January 2006. We evaluated and compared analgesic requirement in the first 24 h, operative time, hospital stay, early postoperative complications, time until return to work, and recurrence, between patients who underwent MDR (group A) and patients who underwent LMH (group B).

[Infected urachal cyst].

The urachus is a vestigial remnant of the cloaca and allantois. It is usually obliterated at early postnatal life. When this obliteration is incomplete, in addition to congenital urachal anomalies such as patent urachus, umblical-urachal sinus, vesico-urachal diverticulum, and urachal cyst, acquired urachal pathologies as infections and neoplasms can emerge.