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Emerging Concepts about the Role of Protein Motion in Enzyme Catalysis
Corresponding authors:
Sharon Hammes-Schiffer University of Illinois, Urbana−Champaign
Judith Klinman, University of California, Berkeley
Acc. Chem. Res., 2015, 48 (4), pp 899–899
DOI: 10.1021/acs.accounts.5b00113
More about authors:
The Hammers-Schiffer Research Group: http://hammes-schiffer-group.org/
The Klinman Group: http://www.cchem.berkeley.edu/jukgrp/klinman_group/Home.html
The Special Issue of Accounts of Chemical Research on Protein Motion in Catalysis addresses one of the most active and compelling areas of investigation regarding protein function: the relationship of motions within a protein to catalytic rate enhancement, allosteric control, and thermal adaptation. There is growing acceptance that our ability to understand and predict protein function must go beyond the static views obtained from traditional X-ray crystallography and incorporate both local and global protein conformational landscapes that can involve large segments of a protein and take place on time scales from femtosecond to millisecond. The fields of computation and experimentation, which at times have appeared in conflict, are increasingly providing synergistic pictures of protein behavior.
The most direct properties that can be studied are for the ground state protein alone or in complex with substrate or modulator ligands. The emerging importance of Markov state models and the computation or measurement of side chain entropy is facilitating the evaluation of interconverting ground state structures and the relative importance of surface versus buried protein motions. Advances in NMR have provided the ability to detect low population protein substates, as do room temperature Ringer X-ray studies. Monitoring the progression of the enzyme–substrate complexes toward the activated complex introduces additional challenges for achieving sufficient spatial and temporal resolution of functionally linked protein motions. A wide range of studies has supported the concept of modulation of reaction barrier width and height, as well as active site electrostatics, through protein motions. What is particularly exciting is that this concept, which originally emerged from the properties of room temperature electron and most recently hydrogen tunneling, has become apparent in many different classes of enzyme reactions.
Advances in methodology are critical to the growth within this field of inquiry. Well-established computational approaches that include mixed quantum mechanical/molecular mechanical (QM/MM) approaches, empirical valence bond (EVB) potentials, molecular dynamics free energy simulations, and transition path sampling methods are being expanded to address challenges such as sampling for much longer (i.e., microsecond) time scales and incorporating a growing number of atoms in the region treated quantum mechanically. The experimental toolkit has also gained traction, with the availability of techniques that can be monitored and evaluated as a function of perturbations that alter catalytic efficiency. In the picosecond to nanosecond time regime, changes to vibrational frequencies can be observed through the selective modification of amino acid side chains or the use of bound substrates with vibrational frequencies that lie outside of the protein envelope. Time-resolved fluorescence measurements continue to provide important insight into local motions that control the lifetime and emission wavelengths for appropriately placed chromophores. On the much longer time scale, seconds to hours, hydrogen–deuterium exchange is a well-validated tool to evaluate changes in local protein unfolding and its dependence on perturbations to the protein or environment. One critically needed time scale lies within the microsecond to millisecond regime, which is the one most generally implicated for the real time interconversion among multiple protein substates. Future methodological developments within this time regime will be a boon to the field of protein dynamics.
Unraveling the mysteries of protein motions and conformational sampling is also relevant to protein design efforts. Attempts at rational protein design have often focused on the structural aspects of ligand binding and enzyme catalysis. The recent discoveries and insights summarized in this special issue suggest that protein motion and conformational sampling should also be taken into account in protein design strategies. Thus, these concepts could have broad implications for drug design and for the design of more effective catalysts for biomedical and technological purposes.
The electronic version of this article is the complete one and can be found online at: http://pubs.acs.org/doi/full/10.1021/acs.accounts.5b00113
Image source: allacronyms.com, ACS
Imaging technologies from bench to bedside
Corresponding author: Ravinder Reddy krr@mail.med.upenn.edu
Author Affiliations
Center for Magnetic Resonance and Optical Imaging, Perelman School of Medicine, Department of Radiology, University of Pennsylvania
Journal of Translational Medicine 2015, 13:97 doi:10.1186/s12967-015-0449-5
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Editorial
The last few decades have seen tremendous advances in medicine that have enhanced understanding of pathophysiological processes at the cellular and molecular level, and led to the development of increasingly sophisticated diagnostic imaging technologies. Early detection of disease induced molecular and functional changes before induction of irreversible structural changes is key for optimal treatment efficacy. Non-invasive imaging modalities, such as positron emission tomography (PET) [1], single photon emission computed tomography (SPECT) [2], computed tomography (CT) [3], optical tomographic technologies [4], magnetic resonance imaging (MRI) [5], ultrasound (US) [6], and X-rays play a vital role in both the diagnosis and monitoring of disease in response to therapy. These techniques cover a broad range of spatio-temporal resolution and varying degrees of sensitivity and specificity to different molecular changes, and in many cases provide complementary information [7],[8]. Recently discovered molecular targets of various disease states, including oncology, neurodegenerative and neuropsychiatric, cardiovascular, and musculoskeletal pathologies, drive further developments in the imaging field to detect these new molecular markers. Ultimately, these technologies contribute to improved disease management and personalized patient care.
Standard-of-care medical imaging techniques such as X-rays, US, CT and MRI provide exquisite structural details of human anatomy. These methods are the first-line techniques in clinic for diagnosis and characterization of disease, based primarily on structure/morphology such as size, texture and tissue attenuation [8]. In addition to providing diagnostic information, the US modality has the additional benefit of use as a therapeutic tool [6],[7],[9].
Functional nuclear medicine techniques (PET and SPECT) provide a unique, non-invasive assessment of intracellular processes and enzyme trafficking, receptors and gene expression, and serve as the underpinnings of molecular medicine. These techniques provide non-invasive diagnostic information about biochemical and physiological process ranging from glucose metabolism to gene expression by evaluating the kinetics of short-lived radioisotope tracers. While many promising tracers have been synthesized that target a variety of metabolic pathways or specific markers 18F-fluorodeoxyglucose (FDG), a glucose analogue is the main radiotracer in clinical practice today. In addition, these functional nuclear medicine techniques are also being used in research and clinical settings to detect and evaluate Alzheimer’s disease, metabolic viability of cardiac tissues, in vivo gene expression, and in tracking of cancer metastasis to different organs [7],[8],[10]-[12].
MRI is one of the most powerful and versatile non-invasive techniques. The major advantage of MRI is that it provides high-resolution, three-dimensional images of tissue structure, as well as functional and metabolic information. Furthermore, MRI is performed in vivo without the use of any ionizing radiation, allowing for repeated study. Several advanced MRI methods have been introduced to monitor the structural [13], functional [14],[15] as well as biochemical changes in various diseases. Magnetic resonance spectroscopy (MRS), which provides the information about the biochemical signatures, is an additional important clinical research tool to assess and characterize disease pathophysiology [16],[17].
Using MRS, enriched metabolites (e.g. 13C enriched) can be used to probe endogenous reaction kinetics. Latest advances in chemical exchange saturation transfer (CEST) MRI show promise in detecting several endogenous metabolites and proteins with substantially enhanced sensitivity (at least an order of magnitude) compared to conventional MRS [18]-[25]. Recent developments in hyperpolarized imaging based on dynamic nuclear polarization (DNP) of 13C enriched pyruvate are yielding highly promising preclinical results [26],[27] exploring in vivo reactions in oncology and other disease conditions. Some very preliminary results showing the promise of these methods in addressing clinical problems in patients have been demonstrated [28].
Optical imaging is another emerging imaging modality with high potential for improving diseases diagnosis and treatment, which can be readily set up at the patient’s bedside or in the operating room [4],[29]-[31]. Optical imaging uses non-ionizing radiation and offers potentially to image organs, tissues as well as smaller structures including cells and molecules using their unique photon absorption or scattering profiles. It also differentiates between native soft tissue and tissue labeled with endogenous or exogenous probes based on their wavelength dependent photon absorption or scattering pattern [32]-[35]. Despite limitations in their spatial resolution, optical imaging methods offer capabilities for studying functional and molecular events in different pathophysiological conditions. There are several techniques in optical imaging that are currently being used both in research and clinical setting for evaluating various diseases and therapeutic responses [30],[36]-[38]. Potentially, optical imaging can also be combined with other imaging modalities to improve the patient’s clinical management.
PET, SPECT and near-infrared reflectance fluorescence optical imaging techniques have relatively high sensitivity and can detect compounds with concentrations in micro- to pico-molar range [7]. Despite the high sensitivity these methods are beset by a relatively low spatial resolution (5 to 10 mm in clinical setting). Also, in many cases the emitting ligands may lose the specificity. One issue with nuclear medicine techniques is the use of nuclear radiation, which precludes their repeat use in short time spans. On the other hand, MRI provides high spatial resolution (in hundreds of micrometers range), but is relatively insensitive, in comparison to nuclear medicine techniques mentioned above; it requires concentrations of metabolites to be detected to be in the millimolar range and few endogenous molecules or metabolites can be imaged [39].
A milestone in the field of diagnostic imaging is the emergence of integrated structural and functional modalities such as combined PET-CT and PET-MRI [40],[41]. These integrated modalities provide concurrent structural, molecular and functional information, improve the multimodal imaging correlations and ease the patient burden for multiple imaging sessions.
Combining these advanced imaging techniques will result in improved precision of the data that are intrinsically more sensitive to the underlying pathophysiology than the morphological features available in routine structural imaging. Over the years, all these powerful imaging techniques have been improving the way the diseases are diagnosed, therapeutic responses are monitored and dramatically enhancing the practice of medicine making it more prognostic, preventative and personalized. Despite these advances, many technological innovations in these imaging modalities are still in research setting. Transferring these technologies into clinical setting requires an intense collaborative effort between researchers in imaging physics, instrumentation, image processing, biologists, chemists, and regulatory bodies as well as clinicians from all branches of medicine. This journal section facilitates communication of advances in translating the imaging modalities from mere research tools to clinical setting. We welcome research articles from all the stakeholders in this field.
The electronic version of this article is the complete one and can be found online at: http://www.translational-medicine.com/content/13/1/97
Image source: National Institute of Biomedical Imaging and Bioengineering
Still 0 and 1? Check this out: Memory leads the way to better computing
Correspondence: H.-S. Philip Wong & Sayeef Salahuddin
H.-S. Philip Wong - Department of Electrical Engineering and the Stanford SystemX Alliance, Stanford University, Stanford, California 94305, USA
Sayeef Salahuddin - Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720, USA
Nature Nanotechnology 10, 191–194 (2015) doi:10.1038/nnano.2015.29
More about Authors:
http://web.stanford.edu/~hspwong/
https://www.eecs.berkeley.edu/Faculty/Homepages/salahuddin.html
Introduction
Current memory devices store information in the charge state of a capacitor; the presence or absence of charges represents logic 1's or 0's. Several technologies are emerging to build memory devices in which other mechanisms are used for information storage. They may allow the monolithic integration of memories and computation units in three-dimensional chips for future computing systems1. Among those promising candidates are spin-transfer-torque magnetic random access memory (STT-MRAM) devices, which store information in the magnetization of a nanoscale magnet. Other candidates that are approaching commercialization include phase change memory (PCM), metal oxide resistive random access memory (RRAM) and conductive bridge random access memory (CBRAM).
Today's computing systems use a hierarchy of volatile and non-volatile data storage devices to achieve an optimal trade-off between cost and performance2. The portion of the memory that is the closest to the processor core is accessed frequently, and therefore it requires the fastest operation speed possible; it is also the most expensive memory because of the large chip area required. Other levels in the memory hierarchy are optimized for storage capacity and speed (Fig. 1). The main memory is often located in a separate chip because it is fabricated with a different technology from that of the microprocessor.
For over 30 years, static random access memory (SRAM)3 and dynamic random access memory (DRAM)3 have been the workhorses of this memory hierarchy4. Both SRAM and DRAM are volatile memories — that is, they lose the stored information once the power is cut off. For non-volatile data storage, magnetic hard disk drives (HDDs) have been in use for over five decades5, 6, 7. Since the advent of portable electronic devices such as music players and mobile phones, however, solid-state non-volatile memory known as Flash memory8 has been introduced into the information storage hierarchy between the DRAM and the HDD. Flash has become the dominant data storage device for mobile electronics; increasingly, even enterprise-scale computing systems and cloud data storage systems are using Flash to complement the storage capabilities of HDD.
For complete FREE article for:
- Electrical manipulation of magnetism in ferromagnets
- Electrical control of magnetization in multiferroics
image source: Controlling size and helicity of a spin-vortex skyrmion