Showing papers in "Advances in Protein Chemistry in 2013"

Proliferating cell nuclear antigen structure and interactions: too many partners for one dancer?

Abstract: PCNA is the DNA sliding clamp found in eukaryotes and archaebacteria. Sliding clamps were first described as processivity factors in DNA replication. They consist of multimeric, toroidal-shaped structures with pseudo-sixfold symmetry that encircle the DNA duplex and tether the replicative polymerases to the genomic template. Later, it was found that PCNA serves as a docking platform where other proteins dock to carry out different DNA metabolic processes. The structure of the bacterial clamp bound to a short primed DNA shows a tilted duplex in the central channel, which is lined by α-helices with net positive charges. Many of the proteins reported to interact with PCNA do so via the PCNA Interaction Protein sequence (PIP-box). The structures of several proteins and peptides bound to PCNA show a common binding mode, but it is still unknown how the many different partners compete for binding and exert their enzymatic and regulatory functions. Furthermore, the literature contains many reports on proteins that directly bind to PCNA as detected by different methods, but only few of the putative complexes have been examined in detail by quantitative analytical techniques or high-resolution structural methods. Some of the reported interactions are not observed in solution using the pure proteins, indicating that the direct interaction is nonexistent or very weak and is likely mediated by other factors. We review here the current knowledge on PCNA interactions from a structural point of view, with a focus on human proteins and highlighting the questions that remain to be answered.

Drug-DNA intercalation: from discovery to the molecular mechanism.

Abstract: The ability of small molecules to perturb the natural structure and dynamics of nucleic acids is intriguing and has potential applications in cancer therapeutics. Intercalation is a special binding mode where the planar aromatic moiety of a small molecule is inserted between a pair of base pairs, causing structural changes in the DNA and leading to its functional arrest. Enormous progress has been made to understand the nature of the intercalation process since its idealistic conception five decades ago. However, the biological functions were detected even earlier. In this review, we focus mainly on the acridine and anthracycline types of drugs and provide a brief overview of the development in the field through various experimental methods that led to our present understanding of the subject. Subsequently, we discuss the molecular mechanism of the intercalation process, free-energy landscapes, and kinetics that was revealed recently through detailed and rigorous computational studies.

Mammalian satellite DNA: a speaking dumb.

Abstract: The tandemly organized highly repetitive satellite DNA is the main DNA component of centromeric/pericentromeric constitutive heterochromatin. For almost a century, it was considered as "junk DNA," only a small portion of which is used for kinetochore formation. The current review summarizes recent data about satellite DNA transcription. The possible functions of the transcripts are discussed.

Computational approaches for predicting the binding sites and understanding the recognition mechanism of protein-DNA complexes.

Abstract: Protein-DNA recognition plays an important role in the regulation of gene expression. Understanding the influence of specific residues for protein-DNA interactions and the recognition mechanism of protein-DNA complexes is a challenging task in molecular and computational biology. Several computational approaches have been put forward to tackle these problems from different perspectives: (i) development of databases for the interactions between protein and DNA and binding specificity of protein-DNA complexes, (ii) structural analysis of protein-DNA complexes, (iii) discriminating DNA-binding proteins from amino acid sequence, (iv) prediction of DNA-binding sites and protein-DNA binding specificity using sequence and/or structural information, and (v) understanding the recognition mechanism of protein-DNA complexes. In this review, we focus on all these issues and extensively discuss the advancements on the development of comprehensive bioinformatics databases for protein-DNA interactions, efficient tools for identifying the binding sites, and plausible mechanisms for understanding the recognition of protein-DNA complexes. Further, the available online resources for understanding protein-DNA interactions are collectively listed, which will serve as ready-to-use information for the research community.

NMR studies on the dynamics of hydrogen bonds and ion pairs involving lysine side chains of proteins.

Abstract: Hydrogen bonds and ion pairs involving side chains play vital roles in protein functions such as molecular recognition and catalysis. Despite the wealth of structural information about hydrogen bonds and ion pairs at functionally crucial sites on proteins, the dynamics of these fundamental chemical interactions are not well understood largely due to the lack of suitable experimental tools in the past. NMR spectroscopy is a powerful tool for investigations of protein dynamics, but the vast majority of NMR methods had been applicable only to the backbone or methyl groups. Recently, a substantial progress has been made in the research on the dynamics of hydrogen bonds and ion pairs involving lysine side-chain NH3+ groups. Together with computational/theoretical approaches, the new NMR methods provide unique insights into the dynamics of hydrogen bonds and ion pairs involving lysine side chains. Here, the methodology and its applications are reviewed.

Structure and orientation of interfacial proteins determined by sum frequency generation vibrational spectroscopy: method and application.

Abstract: In situ and real-time characterization of molecular structures and orientation of proteins at interfaces is essential to understand the nature of interfacial protein interaction. Such work will undoubtedly provide important clues to control biointerface in a desired manner. Sum frequency generation vibrational spectroscopy (SFG-VS) has been demonstrated to be a powerful technique to study the interfacial structures and interactions at the molecular level. This paper first systematically introduced the methods for the calculation of the Raman polarizability tensor, infrared transition dipole moment, and SFG molecular hyperpolarizability tensor elements of proteins/peptides with the secondary structures of α-helix, 310-helix, antiparallel β-sheet, and parallel β-sheet, as well as the methodology to determine the orientation of interfacial protein secondary structures using SFG amide I spectra. After that, recent progresses on the determination of protein structure and orientation at different interfaces by SFG-VS were then reviewed, which provides a molecular-level understanding of the structures and interactions of interfacial proteins, specially understanding the nature of driving force behind such interactions. Although this review has focused on analysis of amide I spectra, it will be expected to offer a basic idea for the spectral analysis of amide III SFG signals and other complicated molecular systems such as RNA and DNA.

Chromatin Reorganization Through Mitosis

Abstract: Chromosome condensation is one of the major chromatin-remodeling events that occur during cell division. The changes in chromatin compaction and higher-order structure organization are essential requisites for ensuring a faithful transmission of the replicated genome to daughter cells. Although the observation of mitotic chromosome condensation has fascinated Scientists for a century, we are still far away from understanding how the process works from a molecular point of view. In this chapter, I will analyze our current understanding of chromatin condensation during mitosis with particular attention to the major molecular players that trigger and maintain this particular chromatin conformation. However, within the chromosome, not all regions of the chromatin are organized in the same manner. I will address separately the structure and functions of particular chromatin domains such as the centromere. Finally, the transition of the chromatin through mitosis represents just an interlude for gene expression between two cell cycles. How the transcriptional information that governs cell linage identity is transmitted from mother to daughter represents a big and interesting question. I will present how cells take care of the aspect ensuring that mitotic chromosome condensation and the block of transcription does not wipe out the cell identity.

X-ray absorption spectroscopy: a tool to investigate the local structure of metal-based anticancer compounds in vivo.

Abstract: This review gives a brief description of the theory and application of X-ray absorption spectroscopy (XAS) comprising both X-ray absorption near-edge structure and extended X-ray absorption fine structure, especially focusing onto the use in inorganic medicinal chemistry. The advantages and limitations of the methods are described and showcased through examples from studies on anticancer metal compounds. The strength of XAS and its relevance for the structural chemical characterization of metal-based compounds in vivo in native tissue samples is exemplified. The common data reduction and analysis strategies are presented and recent advances in the field and perspectives for the near future are given.

Protein functional dynamics in multiple timescales as studied by NMR spectroscopy.

Abstract: Protein functional dynamics are defined as the atomic thermal fluctuations or the segmental motions that are essential for the function of the biomolecule. NMR is a very versatile technique that allows obtaining quantitative information from these processes at atomic resolution. This review is focused on the use of 15N spin relaxation methods to study functional dynamics although the connections with other NMR methods and biophysical techniques will be briefly mentioned. In the first part of the chapter, methodological aspects will be considered, while a set of selected cases will be described in more detail in the second part.

Zinc Finger Proteins and the 3D Organization of Chromosomes

Abstract: Zinc finger domains are one of the most common structural motifs in eukaryotic cells, which employ the motif in some of their most important proteins (including TFIIIA, CTCF, and ZiF268). These DNA binding proteins contain up to 37 zinc finger domains connected by flexible linker regions. They have been shown to be important organizers of the 3D structure of chromosomes and as such are called the master weaver of the genome. Using NMR and numerical simulations, much progress has been made during the past few decades in understanding their various functions and their ways of binding to the DNA, but a large knowledge gap remains to be filled. One problem of the hitherto existing theoretical models of zinc finger protein DNA binding in this context is that they are aimed at describing specific binding. Furthermore, they exclusively focus on the microscopic details or approach the problem without considering such details at all. We present the Flexible Linker Model, which aims explicitly at describing nonspecific binding. It takes into account the most important effects of flexible linkers and allows a qualitative investigation of the effects of these linkers on the nonspecific binding affinity of zinc finger proteins to DNA. Our results indicate that the binding affinity is increased by the flexible linkers by several orders of magnitude. Moreover, they show that the binding map for proteins with more than one domain presents interesting structures, which have been neither observed nor described before, and can be interpreted to fit very well with existing theories of facilitated target location. The effect of the increased binding affinity is also in agreement with recent experiments that until now have lacked an explanation. We further explore the class of proteins with flexible linkers, which are unstructured until they bind. We have developed a methodology to characterize these flexible proteins. Employing the concept of barcodes, we propose a measure to compare such flexible proteins in terms of a similarity measure. This measure is validated by a comparison between a geometric similarity measure and the topological similarity measure that takes geometry as well as topology into account.

DNA Sequence Motif: A Jack of All Trades for ChIP-Seq Data

Abstract: Nowadays, chromatin immunoprecipitation followed by next-generation sequencing, often referred to as ChIP-Seq, has become an industry standard to study a landscape of DNA-protein interactions in vivo. ChIP-Seq captures highly specific protein-DNA interactions, such as transcription factors (TFs) bound to appropriate binding sites, and sparse patterns formed by different histone marks. In this review, we focus on DNA sequence analysis methods adequate for TF ChIP-Seq data. We discuss numerous tasks starting from basic DNA motif finding and motif discovery as is, further applied to explore various features of experimental data. We show how sequence analysis of ChIP-Seq data derives novel biological knowledge on multiple levels, from individual transcription factor binding sites to genome segments operating as regulatory modules. Finally, we provide an overview of existing software in the field.

Generation of ligand specificity and modes of oligomerization in β-prism I fold lectins.

Abstract: β-Prism I fold lectins constitute one of the five widely occurring structural classes of plant lectins. Each single domain subunit is made up of three Greek key motifs arranged in a threefold symmetric fashion. The threefold symmetry is not reflected in the sequence except in the case of the lectin from banana, a monocot, which carries two sugar-binding sites instead of the one in other lectins of known three-dimensional structure, all from dicots. This is believed to be a consequence of the different evolutionary paths followed by the lectin in monocots and dicots. The galactose-specific lectins among them have two chains produced by posttranslational proteolysis and contain three aromatic residues at the binding site. The extended binding sites of galactose- and mannose-specific lectins have been thoroughly characterized. Ligand binding at the sites involves both conformational selection and induced fit. Molecular plasticity of some of the lectins in the family has been characterized. The plasticity appears to be such as to promote variability in quaternary association which could be dimeric, tetrameric, or octameric. Structural and evolutionary reasons for the variability have been explored, and the relation of oligomerization to ligand binding and conformational selection investigated.

Protein-DNA electrostatics: toward a new paradigm for protein sliding

Abstract: 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.

Dynamics of modeled oligonucleosomes and the role of histone variant proteins in nucleosome organization.

Abstract: Elucidation of the structural dynamics of a nucleosome is of primary importance for understanding the molecular mechanisms that control the nucleosomal positioning. The presence of variant histone proteins in the nucleosome core raises the functional diversity of the nucleosomes in gene regulation and has the profound epigenetic consequences of great importance for understanding the fundamental issues like the assembly of variant nucleosomes, chromatin remodeling, histone posttranslational modifications, etc. Here, we report our observation of the dominant mechanisms of relaxation motions of the oligonucleosomes such as dimer, trimer, and tetramer (in the beads on a string model) with conventional core histones and role of variant histone H2A.Z in the chromatin dynamics using normal mode analysis. Analysis of the directionality of the global dynamics of the oligonucleosome reveals (i) the in-planar stretching as well as out-of-planar bending motions as the relaxation mechanisms of the oligonucleosome and (ii) the freedom of the individual nucleosome in expressing the combination of the above-mentioned motions as the global mode of dynamics. The highly dynamic N-termini of H3 and (H2A.Z-H2B) dimer evidence their participation in the transcriptionally active state. The key role of variant H2A.Z histone as a major source of vibrant motions via weaker intra- and intermolecular correlations is emphasized in this chapter.

Large tandem repeats make up the chromosome bar code: a hypothesis.

Abstract: Much of tandem repeats' functional nature in any genome remains enigmatic because there are only few tools available for dissecting and elucidating the functions of repeated DNA. The large tandem repeat arrays (satellite DNA) found in two mouse whole-genome shotgun assemblies were classified into 4 superfamilies, 8 families, and 62 subfamilies. With the simplified variant of chromosome positioning of different tandem repeats, we noticed the nonuniform distribution instead of the positions reported for mouse major and minor satellites. It is visible that each chromosome possesses a kind of unique code made up of different large tandem repeats. The reference genomes allow marking only internal tandem repeats, and even with such a limited data, the colored "bar code" made up of tandem repeats is visible. We suppose that tandem repeats bare the mechanism for chromosomes to recognize the regions to be associated. The associations, initially established via RNA, become fixed by histone modifications (the histone or chromatin code) and specific proteins. In such a way, associations, being at the beginning flexible and regulated, that is, adjustable, appear as irreversible and inheritable in cell generations. Tandem repeat multiformity tunes the developed nuclei 3D pattern by sequential steps of associations. Tandem repeats-based chromosome bar code could be the carrier of the genome structural information; that is, the order of precise tandem repeat association is the DNA morphogenetic program. Tandem repeats are the cores of the distinct 3D structures postulated in "gene gating" hypothesis.

Anomalous Protein–DNA Interactions Behind Neurological Disorders

Abstract: Aggregation, nuclear location, and nucleic acid interaction are common features shared by a number of proteins related to neurodegenerative diseases, including Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis, transmissible spongiform encephalopathy, Huntington’s disease, spinobulbar muscular atrophy, dentatorubro-pallidoluysian atrophy, and several spinocerebellar ataxias. β-Amyloid peptides, tau protein, α-synuclein, superoxide dismutase1, prion protein, huntingtin, atrophin1, androgen receptor, and several ataxins are proteins prone to becoming aggregated, to translocate inside cell nucleus, and to bind DNA. In this chapter, we review those common features suggesting that neurological diseases too may share a transcriptional disorder, making it an important contribution to the origin of the disease.

Conformational dynamics of single protein molecules studied by direct mechanical manipulation.

Abstract: Advances in single-molecule manipulation techniques have recently enabled researchers to study a growing array of biological processes in unprecedented detail. Individual molecules can now be manipulated with subnanometer precision along a simple and well-defined reaction coordinate, the molecular end-to-end distance, and their conformational changes can be monitored in real time with ever-improving time resolution. The behavior of biomolecules under tension continues to unravel at an accelerated pace and often in combination with computational studies that reveal the atomistic details of the process under investigation. In this chapter, we explain the basic principles of force spectroscopy techniques, with a focus on optical tweezers, and describe some of the theoretical models used to analyze and interpret single-molecule manipulation data. We then highlight some recent and exciting results that have emerged from this research field on protein folding and protein–ligand interactions.

Ligand docking simulations by generalized-ensemble algorithms.

Abstract: In protein chemistry and structural biology, conventional simulations in physical statistical mechanical ensembles, such as the canonical ensemble with fixed temperature and isobaric–isothermal ensemble with fixed temperature and pressure, face a great difficulty. This is because there exist a huge number of local-minimum-energy states in the system and the conventional simulations tend to get trapped in these states, giving wrong results. Generalized-ensemble algorithms are based on artificial unphysical ensembles and overcome the above difficulty by performing random walks in potential energy, volume, and other physical quantities or their corresponding conjugate parameters such as temperature and pressure. The advantage of generalized-ensemble simulations lies in the fact that they not only avoid getting trapped in states of energy local minima but also allow the calculations of physical quantities as functions of temperature or other parameters from a single simulation run. In this chapter, we review the generalized-ensemble algorithms. Some of their specific examples such as replica-exchange molecular dynamics and replica-exchange umbrella sampling are described in detail. Examples of their applications to drug design are presented.

Protein and water confined in nanometer-scale reverse micelles studied by near infrared, terahertz, and ultrafast visible spectroscopies.

Abstract: Protein-containing reverse (PCR) micelles are suitable systems to study the properties of proteins and waters in a cell-like environment. A model for determining the structural parameters of PCR micelles, such as the aqueous cavity size and molecule number of water within the reverse micelle, is presented. The model is based on an important hypothesis that the structural parameters of the protein-unfilled reverse micelle do not change after solubilization of protein. I describe a procedure using near infrared spectroscopy of OH stretching vibration band of water to verify the hypothesis. Further, the terahertz (THz) absorption spectrum of myoglobin is derived from THz time-domain spectroscopy of the PCR micellar solution, and the states of waters in reverse micelles with and without protein are discussed on the basis of the structural parameters. The last topic is on internal dynamics of PCR micelles on timescales from femtoseconds to nanoseconds studied by femtosecond time-resolved fluorescence spectroscopy.

Structural and dynamical aspects of HIV-1 protease and its role in drug resistance.

Abstract: Acquired immunodeficiency syndrome (AIDS) caused by the retrovirus human immunodeficiency virus (HIV) has become a major epidemic afflicting mankind. The Joint United Nations Program on HIV/AIDS (UNAIDS) projection shows the existence of millions of AIDS patients at the end of 2012. All the Food and Drug Administration (FDA)-approved drugs are getting ineffective due to resistance offered by the mutation-prone HIV. Hence, there is an urgent need for developing new drugs with greater potential. HIV life cycle is controlled by the activities of its essential proteins like glycoproteins (gp41 and gp120), HIV reverse transcriptase (HIV-RT), HIV integrase (HIV-IN), and HIV-1 protease (HIV-pr). This chapter focuses on the protein HIV-pr, which is important for the cleavage of Gag and Gag-Pol polyproteins to form mature, structural, and functional virions. The conformation and dynamics of the protein HIV-pr play a pivotal role in ligand binding and the catalytic process, which is affected by the rapid point mutations and various physiological parameters. The effect of the mutations and the varied simulation protocols on conformational dynamics and drug resistance of HIV-pr is discussed.

Detecting DNA-Protein Interactions in Living Cells-ChIP Approach

Abstract: DNA-binding proteins play a critical role in many major cellular processes. The immunoprecipitation of protein complexes with associated DNA fragments, termed chromatin immunoprecipitation or ChIP, allows for the analysis of the binding of protein factors in their natural environment. It evolved from a confirmation assay to a discovery tool that really changed our understanding of the biology of living cells. With the widespread use of next-generation high-throughput sequencing technologies, factor binding can not only be assessed in an unbiased and genome-wide manner but can also be predicted and linked to gene expression and chromatin structure. This review summarizes the current advances of the ChIP-based approaches to decipher gene regulatory and epigenetic network in the cells. The limitations of the method are discussed and the future ChIP-based developments are explored.

Studying biomacromolecules with two-dimensional infrared spectroscopy.

Abstract: Two-dimensional infrared (2DIR) spectroscopy is a rapidly developing nonlinear spectroscopy, which allows access to greater structural detail than traditional vibrational spectroscopies. The ability to gain extra structural insight is particularly relevant to the study of biomacromolecules, whose Fourier transform infrared (FTIR) spectra are often congested, due to the large number of vibrations. The subpicosecond timescale of the spectroscopy gives the opportunity to follow the fluctuations of a molecule in the time domain. Theoretical and experimental techniques are well developed for 2DIR, and they have already given insight into some of the fundamental aspects of the structure and dynamics of proteins and nucleic acids. This chapter reviews some of these recent studies and showcases the potential of the method.

Structure–Function Relationship of the Plant Photosynthetic Pigment–Protein Complex LHCII Studied with Molecular Spectroscopy Techniques

Abstract: LHCII, the largest plant photosynthetic pigment–protein complex of photosystem II, is a most abundant membrane protein in living organisms and comprises approximately half of the pool of chlorophyll molecules in the biosphere. The principal role of this pigment–protein complex is to collect sunlight quanta and transfer electronic excitations toward the reaction centers, where the primary photosynthetic electric charge separation reactions take place. The LHCII protein, as a major protein component of the photosynthetic membranes, modulates also the structural and dynamic properties of the lipid phase of the membranes. According to the recent concepts, one of the physiological roles of LHCII is also a protection of the photosynthetic apparatus against oxidative damage caused by illumination with high intensity light. Detailed examination of all those physiological functions of LHCII, in relation to the complex structure, was possible owing to the application of several molecular spectroscopy techniques. Some examples of such studies are presented in this chapter. The examples of application of steady-state and time-resolved fluorescence spectroscopy, Fourier-transform infrared absorption spectroscopy, and resonance Raman scattering spectroscopy are presented and discussed.

Enzyme active site interactions by Raman/FTIR, NMR, and Ab initio calculations

Abstract: Characterization of enzyme active site structure and interactions at high resolution is important for the understanding of the enzyme catalysis. Vibrational frequency and NMR chemical shift measurements of enzyme-bound ligands are often used for such purpose when X-ray structures are not available or when higher resolution active site structures are desired. This review is focused on how ab initio calculations may be integrated with vibrational and NMR chemical shift measurements to quantitatively determine high-resolution ligand structures (up to 0.001 A for bond length and 0.01 A for hydrogen bonding distance) and how interaction energies between bound ligand and its surroundings at the active site may be determined. Quantitative characterization of substrate ionic states, bond polarizations, tautomeric forms, conformational changes and its interactions with surroundings in enzyme complexes that mimic ground state or transition state can provide snapshots for visualizing the substrate structural evolution along enzyme-catalyzed reaction pathway. Our results have shown that the integration of spectroscopic studies with theoretical computation greatly enhances our ability to interpret experimental data and significantly increases the reliability of the theoretical analysis.

Combined use of optical spectroscopy and computational methods to study the binding and the photoinduced conformational modification of proteins when NMR and X-ray structural determinations are not an option.

Abstract: The functions of proteins depend on their interactions with various ligands and these interactions are controlled by the structure of the polypeptides. If one can manipulate the structure of proteins, their functions can in principle be modulated. The issue of protein structure–function relationship is not only a central problem in biophysics, but is becoming clear that the ability to “artificially” modify the structure of proteins could be relevant in fields beyond the biomedical area to provide, for instance, light responses in proteins which would not possess such properties in their native state. This chapter presents an overview of the combination of optical electronic and vibrational spectroscopy with various computational methods to investigate the binding between photoactive ligands and proteins.

Introduction: Biomolecular Spectroscopy: Advances from Integrating Experiments and Theory

Abstract: Biomolecular spectroscopy has undergone rapid growth as a result of the development of new instrumental techniques, building of massive synchrotron facilities, and also the progress in theoretical and computational methods able to explain and correlate the spectroscopic data to the underlying structure and interactions. Biomolecular spectroscopy involves very broad range of methods differing in the energy region of interest, the underlining phenomena, and the properties they explore (Cantor & Schimmel, 1980; van Holde, Jonson, & Ho, 2005). They provide versatile insight into biomolecular structure, functions, and mechanisms at multiple levels such as electronic structure and chemical bonding, revealing the mechanisms, understanding of the dynamics, binding, hydrogen bonding, etc. (Antoniou, Basner, Nunez, & Schwartz, 2006; Carey, 2006; Igumenova, Frederick, & Wand, 2006; Karabencheva & Christov, 2010; Solomon, 2006). Spectroscopic methods complement the results from crystallography, kinetics, mutagenesis, and computational methods (quantum chemistry, molecular dynamics combined quantum mechanics and molecular mechanics) and are used to validate and test computational models and findings (Hammes-Schiffer, 2013; Karabencheva & Christov, 2010; Manley, Rivalta, & Loria, 2013). In this thematic volume, the applications of most advanced spectroscopic methods and their synergy with computational methods for revealing biomolecular structure–function relationships are presented. Chapter 1 reviews the application of two-dimensional infrared (2DIR) spectroscopy for revealing the biomolecular fluctuations at sub-picosecond timescale. Chapter 2 is focused on applying the novel NMR approach for investigation of the dynamics of hydrogen bonding and salt bridges formed by the lysine side chains. The structure–function relationships in LHCII, the largest plant photosynthetic pigment–protein complex of photosystem II, by

Unconventional actin configurations step into the limelight.

Abstract: The existence of a cellular machinery that is based on the reversible polymerization of globular nucleotide-bound protomers into polar microfilaments is a persistent feature from prokaryotes to higher vertebrates. However, while in bacteria, actin-like proteins with such properties have evolved into a large family with divergent sequences and polymeric structures, eukaryotes express only a small number of highly conserved actins. Indeed, the sequence of actin is one of the best conserved among eukaryotes and yet actin carries out many different functions at distinct cellular sites. Because of the notorious conservation and lack of suitable tools to examine structural plasticity, the vast majority of studies on cellular actin functions consider mainly two structural states, G-actin and F-actin. However, there is more to the structural plasticity of actin than first meets the eye. On one hand, more than 200 actin-binding proteins shape the conformation of actin and thereby regulate functional diversity. On the other hand, unconventional actin conformations that differ from monomeric G-actin are stepping into the limelight. In addition, supramolecular actin structures that extend beyond classical F-actin are emerging. Herein, we recapitulate the current knowledge on the structure and conformations of monomeric actin and its polymerization into higher order structures, paying special attention to less known forms and their involvement in actin function.

Conformational Changes of Enzymes and DNA in Molecular Dynamics: Influenced by pH, Temperature, and Ligand

Abstract: Protein conformation, which has been a research hotspot for human diseases, is an important factor of protein properties. Recently, a series of approaches have been utilized to investigate the conformational changes under different conditions. Some of them have gained promising achievements, but it is still deficient in the detail researches at the atomic level. In this chapter, a series of computational examples of protein conformational changes under different pH environment, temperature, and ligand binding are described. We further show some useful methods, such as constant pH molecular dynamics simulations, molecular docking, and molecular mechanics Poisson-Boltzmann surface area/generalized Born surface area calculations. In comparison with the experimental results, the methods mentioned above are reasonable to detect and predict the interaction between residue and residue, residue and DNA, and residue and ligand. Additionally, some crucial interactions that cause protein conformational changes are discovered and discussed in this chapter. In summary, our work can give penetrating information to understand the pH-, temperature-, and ligand-induced conformational change mechanisms.