scholarly journals Dynamics of proteins in solution

2019 ◽  
Vol 52 ◽  
Author(s):  
Marco Grimaldo ◽  
Felix Roosen-Runge ◽  
Fajun Zhang ◽  
Frank Schreiber ◽  
Tilo Seydel
Keyword(s):  
Protein Dynamics ◽  
Protein Function ◽  
Center Of Mass ◽  
Mass Diffusion ◽  
Transport Processes ◽  
Side Chain ◽  
Neutron Spectroscopy ◽  
Length Scales ◽  
Comprehensive Picture ◽  
Mechanistic Understanding

AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.

scholarly journals Conformational dynamics is key to understanding loss-of-function of NQO1 cancer-associated polymorphisms and its correction by pharmacological ligands

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Encarnación Medina-Carmona ◽  
Rogelio J. Palomino-Morales ◽  
Julian E. Fuchs ◽  
Esperanza Padín-Gonzalez ◽  
Noel Mesa-Torres ◽  
...  
Keyword(s):  
Protein Dynamics ◽  
Protein Function ◽  
Conformational Dynamics ◽  
Loss Of Function ◽  
Quinone Oxidoreductase ◽  
Protein Levels ◽  
Terminal Domain ◽  
Directional Preference

Abstract Protein dynamics is essential to understand protein function and stability, even though is rarely investigated as the origin of loss-of-function due to genetic variations. Here, we use biochemical, biophysical, cell and computational biology tools to study two loss-of-function and cancer-associated polymorphisms (p.R139W and p.P187S) in human NAD(P)H quinone oxidoreductase 1 (NQO1), a FAD-dependent enzyme which activates cancer pro-drugs and stabilizes several oncosuppressors. We show that p.P187S strongly destabilizes the NQO1 dimer in vitro and increases the flexibility of the C-terminal domain, while a combination of FAD and the inhibitor dicoumarol overcome these alterations. Additionally, changes in global stability due to polymorphisms and ligand binding are linked to the dynamics of the dimer interface, whereas the low activity and affinity for FAD in p.P187S is caused by increased fluctuations at the FAD binding site. Importantly, NQO1 steady-state protein levels in cell cultures correlate primarily with the dynamics of the C-terminal domain, supporting a directional preference in NQO1 proteasomal degradation and the use of ligands binding to this domain to stabilize p.P187S in vivo. In conclusion, protein dynamics are fundamental to understanding loss-of-function in p.P187S and to develop new pharmacological therapies to rescue this function.

scholarly journals Leveraging protein dynamics to identify cancer mutational hotspots using 3D structures

2019 ◽  
Vol 116 (38) ◽  
pp. 18962-18970 ◽  
Author(s):  
Sushant Kumar ◽  
Declan Clarke ◽  
Mark B. Gerstein
Keyword(s):  
Protein Dynamics ◽  
Protein Function ◽  
Large Scale ◽  
Protein Structures ◽  
Structural Data ◽  
The Cancer Genome Atlas ◽  
Detection Methods ◽  
Hotspot Detection ◽  
Driver Genes ◽  
Mutational Hotspots

Large-scale exome sequencing of tumors has enabled the identification of cancer drivers using recurrence-based approaches. Some of these methods also employ 3D protein structures to identify mutational hotspots in cancer-associated genes. In determining such mutational clusters in structures, existing approaches overlook protein dynamics, despite its essential role in protein function. We present a framework to identify cancer driver genes using a dynamics-based search of mutational hotspot communities. Mutations are mapped to protein structures, which are partitioned into distinct residue communities. These communities are identified in a framework where residue–residue contact edges are weighted by correlated motions (as inferred by dynamics-based models). We then search for signals of positive selection among these residue communities to identify putative driver genes, while applying our method to the TCGA (The Cancer Genome Atlas) PanCancer Atlas missense mutation catalog. Overall, we predict 1 or more mutational hotspots within the resolved structures of proteins encoded by 434 genes. These genes were enriched among biological processes associated with tumor progression. Additionally, a comparison between our approach and existing cancer hotspot detection methods using structural data suggests that including protein dynamics significantly increases the sensitivity of driver detection.

LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor

2019 ◽  
Vol 21 (6) ◽  
pp. 2206-2218 ◽  
Author(s):  
Jing-Fang Yang ◽  
Fan Wang ◽  
Yu-Zong Chen ◽  
Ge-Fei Hao ◽  
Guang-Fu Yang
Keyword(s):  
Estrogen Receptor ◽  
Protein Dynamics ◽  
Protein Function ◽  
Inflammatory Diseases ◽  
Great Difficulty ◽  
Vital Role ◽  
Site Directed Mutagenesis ◽  
Bioinformatic Tools ◽  
Wide Range ◽  
User Friendly

Abstract Protein dynamics is central to all biological processes, including signal transduction, cellular regulation and biological catalysis. Among them, in-depth exploration of ligand-driven protein dynamics contributes to an optimal understanding of protein function, which is particularly relevant to drug discovery. Hence, a wide range of computational tools have been designed to investigate the important dynamic information in proteins. However, performing and analyzing protein dynamics is still challenging due to the complicated operation steps, giving rise to great difficulty, especially for nonexperts. Moreover, there is a lack of web protocol to provide online facility to investigate and visualize ligand-driven protein dynamics. To this end, in this study, we integrated several bioinformatic tools to develop a protocol, named Ligand and Receptor Molecular Dynamics (LARMD, http://chemyang.ccnu.edu.cn/ccb/server/LARMD/ and http://agroda.gzu.edu.cn:9999/ccb/server/LARMD/), for profiling ligand-driven protein dynamics. To be specific, estrogen receptor (ER) was used as a case to reveal ERβ-selective mechanism, which plays a vital role in the treatment of inflammatory diseases and many types of cancers in clinical practice. Two different residues (Ile373/Met421 and Met336/Leu384) in the pocket of ERβ/ERα were the significant determinants for selectivity, especially Met336 of ERβ. The helix H8, helix H11 and H7-H8 loop influenced the migration of selective agonist (WAY-244). These computational results were consistent with the experimental results. Therefore, LARMD provides a user-friendly online protocol to study the dynamic property of protein and to design new ligand or site-directed mutagenesis.

scholarly journals Recent advances in user-friendly computational tools to engineer protein function

2020 ◽  
Author(s):  
Carlos Eduardo Sequeiros-Borja ◽  
Bartłomiej Surpeta ◽  
Jan Brezovsky
Keyword(s):  
Protein Engineering ◽  
Protein Design ◽  
Protein Function ◽  
Transport Processes ◽  
Allosteric Communication ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions ◽  
User Friendly ◽  
Ligand Transport ◽  
Further Development

Abstract Progress in technology and algorithms throughout the past decade has transformed the field of protein design and engineering. Computational approaches have become well-engrained in the processes of tailoring proteins for various biotechnological applications. Many tools and methods are developed and upgraded each year to satisfy the increasing demands and challenges of protein engineering. To help protein engineers and bioinformaticians navigate this emerging wave of dedicated software, we have critically evaluated recent additions to the toolbox regarding their application for semi-rational and rational protein engineering. These newly developed tools identify and prioritize hotspots and analyze the effects of mutations for a variety of properties, comprising ligand binding, protein–protein and protein–nucleic acid interactions, and electrostatic potential. We also discuss notable progress to target elusive protein dynamics and associated properties like ligand-transport processes and allosteric communication. Finally, we discuss several challenges these tools face and provide our perspectives on the further development of readily applicable methods to guide protein engineering efforts.

Contribution of leucine 85 to the structure and function of Saccharomyces cerevisiae iso-1 cytochrome c

2001 ◽  
Vol 79 (4) ◽  
pp. 517-524 ◽  
Author(s):  
Jonathan C Parrish ◽  
J Guy Guillemette ◽  
Carmichael JA Wallace
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Electron Transfer ◽  
Electron Transport ◽  
Cytochrome C ◽  
Transport Processes ◽  
Complex Iii ◽  
Side Chain ◽  
Inner Mitochondrial Membrane ◽  
And Function ◽  
First Time

Cytochrome c is a small electron-transport protein whose major role is to transfer electrons between complex III (cytochrome reductase) and complex IV (cytochrome c oxidase) in the inner mitochondrial membrane of eukaryotes. Cytochrome c is used as a model for the examination of protein folding and structure and for the study of biological electron-transport processes. Amongst 96 cytochrome c sequences, residue 85 is generally conserved as either isoleucine or leucine. Spatially, the side chain is associated closely with that of the invariant residue Phe82, and this interaction may be important for optimal cytochrome c activity. The functional role of residue 85 has been examined using six site-directed mutants of Saccharomyces cerevisiae iso-1 cytochrome c, including, for the first time, kinetic data for electron transfer with the principle physiological partners. Results indicate two likely roles for the residue: first, heme crevice resistance to ligand exchange, sensitive to both the hydrophobicity and volume of the side chain; second, modulation of electron-transport activity through maintenance of the hydrophobic character of the protein in the vicinity of Phe82 and the exposed heme edge, and possibly of the ability of this region to facilitate redox-linked conformational change.Key words: protein engineering, cytochrome c, structure-function relations, electron transfer, hydrophobic packing.

Numerical modeling of multiple length scales in thermal transport processes

2014 ◽  
Vol 24 (4) ◽  
pp. 781-796 ◽  
Author(s):  
Yogesh Jaluria
Keyword(s):  
Numerical Modeling ◽  
Boundary Conditions ◽  
Time Scales ◽  
Transport Processes ◽  
Thermal Processes ◽  
Length Scales ◽  
Content Type ◽  
Multiple Length Scales ◽  
Wide Range ◽  
Simulation Results

Purpose – Multiple length and time scales arise in a wide variety of practical and fundamental problems. It is important to obtain accurate and validated numerical simulation results, considering the different scales that exist, in order to predict, design and optimize the behavior of practical thermal processes and systems. The purpose of this paper is to present modeling at the different length scales and then addresses the question of coupling the different models to obtain the overall model for the system or process. Design/methodology/approach – Both numerical and experimental methods to obtain results at the different length scales, particularly at micro and nanoscales, are considered. Even though the paper focusses on length scales, multiple time scales lead to similar concerns and are also considered. The two circumstances considered in detail are multiple length scales in different domains and those in the same domain. These two cases have to be modeled quite differently in order to obtain a model for the overall process or system. The basic considerations involved in such a modeling are discussed. A wide range of thermal processes are considered and the methods that may be used are presented. The models employed must be validated and the accuracy of the simulation results established if the simulation results are to be used for prediction, control and design. Findings – Of particular interest are concerns like verification and validation, imposition of appropriate boundary conditions, and modeling of complex, multimode transport phenomena in multiple scales. Additional effects such as viscous dissipation, surface tension, buoyancy and rarefaction that could arise and complicate the modeling are discussed. Uncertainties that arise in material properties and in boundary conditions are also important in design and optimization. Large variations in the geometry and coupled multiple regions are also discussed. Research limitations/implications – The paper is largely focussed on multiple-scale considerations in thermal processes. Both numerical modeling/simulation and experimentation are considered, with the latter being used for validation and physical insight. Practical implications – Several examples from materials processing, environmental flows and electronic systems, including data centers, are given to present the different techniques that may be used to achieve the desired level of accuracy and predictability. Originality/value – Present state of the art and future needs in this interesting and challenging area are discussed, providing the impetus for further work. Different methods for treating multiscale problems are presented.

scholarly journals Protein dynamics enables phosphorylation of buried residues in Cdk2/Cyclin A-bound p27

2020 ◽  
Author(s):  
João Henriques ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Protein Phosphorylation ◽  
Protein Dynamics ◽  
Single Molecule ◽  
Protein Function ◽  
Cell Cycle Progression ◽  
Conformational Dynamics ◽  
Protein Structures ◽  
Cyclin A ◽  
General Role ◽  
Wide Range

AbstractProteins carry out a wide range of functions that are tightly regulated in space and time. Protein phosphorylation is the most common post-translation modification of proteins and plays key roles in the regulation of many biological processes. The finding that many phosphorylated residues are not solvent exposed in the unphosphorylated state opens several questions for understanding the mechanism that underlies phosphorylation and how phosphorylation may affect protein structures. First, since kinases need access to the phosphorylated residue, how do such buried residues become modified? Second, once phosphorylated, what are the structural effects of phosphorylation of buried residues and do they lead to changed conformational dynamics. We have used the ternary complex between p27, Cdk2 and Cyclin A to study these questions using enhanced sampling molecular dynamics simulations. In line with previous NMR and single-molecule fluorescence experiments we observe transient exposure of Tyr88 in p27, even in its unphosphorylated state. Once Tyr88 is phosphorylated, we observe a coupling to a second site, thus making Tyr74 more easily exposed, and thereby the target for a second phosphorylation step. Our observations provide atomic details on how protein dynamics plays a role in modulating multi-site phosphorylation in p27, thus supplementing previous experimental observations. More generally, we discuss how the observed phenomenon of transient exposure of buried residues may play a more general role in regulating protein function.Significance StatementProtein phosphorylation is a common post-translation modification and is carried out by kinases. While many phosphorylation sites are located in disordered regions of proteins or in loops, a surprisingly large number of modification sites are buried inside folded domains. This observation led us to ask the question of how kinases gain access to such buried residues. We used the complex between p27, a regulator of cell cycle progression, and Cyclin-dependent kinase 2/Cyclin A to study this problem. We hypothesized that transient exposure of buried tyrosines in p27 to the solvent would make them accessible to kinases, explaining how buried residues get modified. We provide an atomic-level description of these dynamic processes revealing how protein dynamics plays a role in regulation.

scholarly journals The Periodic Transient Kinetics Method for Investigation of Kinetic Process Dynamics Under Realistic Conditions: Methanation as an Example

2021 ◽  
Author(s):  
Dominik Meyer ◽  
Jens Friedland ◽  
Jannik Schumacher ◽  
Robert Güttel
Keyword(s):  
Energy Storage ◽  
Transport Processes ◽  
Kinetic Process ◽  
Chemical Energy ◽  
Unsteady State ◽  
Transient Kinetics ◽  
Length Scales ◽  
Process Dynamics ◽  
Operation Conditions ◽  
Catalyzed Reactions

Due to rising interest for the integration of chemical energy storage into the electrical power grid, the unsteady-state operation of chemical reactors is gaining more and more attention with emphasis on heterogeneously catalyzed reactions. The transient response of those reactions is influenced by effects on different length scales, ranging from the active surface via the individual porous catalyst particle up to the full-scale reactor. The challenge, however, is to characterize unsteady-state effects under realistic operation conditions and to assign them to distinct transport processes. Therefore, the periodic transient kinetics (PTK) method is introduced, which allows for the separation of kinetic process dynamics at different length scales experimentally under realistic operation conditions. The methodology also provides the capability for statistical analysis of the experimental results and therefore improved reliability of the derived conclusions. Therefore, the PTK method provides the experimental basis for model-based derivation of reaction kinetics valid under dynamic conditions. The applicability of the methodology is demonstrated for the methanation reaction chosen as an example process for heterogeneously catalyzed reactions relevant for chemical energy storage purposes. <br>

scholarly journals Animal evolution coincides with a novel degree of freedom in exocytic transport processes

2019 ◽  
Author(s):  
Martin Kollmar ◽  
Tobias Welz ◽  
Felix Straub ◽  
Noura Alzahofi ◽  
Klas Hatje ◽  
...  
Keyword(s):  
Protein Function ◽  
Tissue Expression ◽  
Transport Processes ◽  
Degree Of Freedom ◽  
Rab Gtpase ◽  
Animal Evolution ◽  
Protein Activation ◽  
Vesicle Membranes ◽  
Genome Duplications ◽  
Membrane Tethering

AbstractExocytic transport of transmembrane receptors and secreted ligands provides the basis for cellular communication in animals. The RAB8/RAB3/RAB27 trafficking regulators function in transport processes towards the cell membrane. The small G-proteins recruit a diversity of effectors that mediate transport along microtubule and actin tracks, as well as membrane tethering and fusion. SPIRE actin nucleators organise local actin networks at exocytic vesicle membranes. By complex formation with class-5 myosins, vesicle transport track generation and motor protein activation are coordinated. Our phylogenetic analysis traced the onset of SPIRE function back to the origin of the Holozoa. We have identified SPIRE in the closest unicellular relatives of animals, the choanoflagellates, and the more distantly related ichthyosporeans. The discovery of a SPIRE-like protein encoding a KIND and tandem-WH2 domains in the amoebozoanPhysarum polycephalumsuggests that the SPIRE-type actin nucleation mechanism originated even earlier. Choanoflagellate SPIRE interacts with RAB8, the sole choanoflagellate representative of the metazoan RAB8/RAB3/RAB27 family. Major interactions including MYO5, FMN-subgroup formins and vesicle membranes are conserved between the choanoflagellate and mammalian SPIRE proteins and the choanoflagellateMonosiga brevicollisSPIRE protein can rescue mouse SPIRE1/2 function in melanosome transport. Genome duplications generated two mammalianSPIREgenes (SPIRE1andSPIRE2) and allowed for the separation of SPIRE protein function in terms of tissue expression and RAB GTPase binding. SPIRE1 is highest expressed in the nervous system and interacts with RAB27 and RAB8. SPIRE2 shows high expression in the digestive tract and specifically interacts with RAB8. We propose that at the dawn of the animal kingdom a new transport mechanism came into existence, which bridges microtubule tracks, detached vesicles and the cellular actin cytoskeleton by organising actin/myosin forces directly at exocytic vesicle membranes. The new degree of freedom in transport may reflect the increased demands of the sophisticated cellular communications in animals.

scholarly journals Real Time de novo Deposition of Centromeric Histone-associated Proteins Using the Auxin Inducible Degradation system

2018 ◽  
Author(s):  
Sebastian Hoffmann ◽  
Daniele Fachinetti
Keyword(s):  
Real Time ◽  
Protein Dynamics ◽  
Protein Function ◽  
Genome Engineering ◽  
De Novo ◽  
Protein Complexes ◽  
Versatile Tool ◽  
Associated Proteins ◽  
Endogenous Proteins ◽  
Set Up

i.Summary/AbstractMeasuring protein dynamics is essential to uncover protein function and to understand the formation of large protein complexes such as centromeres. Recently, genome engineering in human cells has improved our ability to study the function of endogenous proteins. By combining genome editing techniques with the Auxin Inducible Degradation (AID) system, we created a versatile tool to study protein dynamics. This system allows us to analyze both protein function and dynamics by enabling rapid protein depletion and re-expression in the same experimental set-up. Here, we focus on the dynamics of the centromeric histone-associated protein CENP-C, responsible for the formation of the kinetochore complex. Following rapid removal and re-activation of a fluorescent version of CENP-C by auxin treatment and removal, we could follow CENP-C de novo deposition at centromeric regions during different stages of the cell cycle. In conclusion, the auxin degradation system is a powerful tool to assess and quantify protein dynamics in real time.

Sign in / Sign up

Export Citation Format

Share Document