Transferability of conformational dependent charges from protein simulations

We have studied the transferability of atomic charges for proteins, fitted to the quantum mechanical electrostatic potential and extensively averaged over a set of structures sampled by molecular dynamics (MD) and over all residues of the same kind in the protein sequence (xAvESP). Previously, such charges were obtained for one single protein (avidin). In this study, we use five additional proteins. The aim of this study is fourfold. First, we provide xAvESP charges for all amino acids, including amino- and carboxy-terminal variants of all, as well as alternative protonation states of His, Asp, Glu, Lys, Arg, Cys, and Tyr. Second, we show that the xAvESP charges averaged over the five new proteins are similar to charges obtained in the same way for avidin, with a correlation coefficient of 0.997. This shows that the charges are transferable and system-independent. Electrostatic proteinligand interaction energies calculated with charges obtained from different proteins differ by only 13 kJ/mol on average. The xAvESP charges correlate rather well with Amber charges (except for the N atom of amino-terminal residues that are erroneous in Amber), although they are obtained in a more general way. Third, the conformational dependence of the charges is significant and gives rise to quite large differences in energies. However, these differences are to a large extent screened by solvation effects. For example, the solvent-screened electrostatic interaction energy between the protein galectin-3 and five different ligands varies with the charge sets by less than 3 kJ/mol on average. Finally, we show that the xAvESP charges give a comparable root-mean-squared deviation as the Amber charges for the MD simulations of 18 proteinligand complexes, they give comparable or slightly worse backbone N?H order parameters for two galectin-3 complexes, but they give a better correlation between calculated and experimental affinities for the binding of seven biotin analogues to avidin and for nine inhibitors of factor Xa. (c) 2011 Wiley Periodicals, Inc. Int J Quantum Chem 112:17681785, 201

Effects of Non-Aerobic Maximal Effort Exercise on Fatigue in Deconditioned Men and Women with Multiple Sclerosis

Multiple Sclerosis (MS) is a neurodegenerative disease of unknown etiology affecting women more frequently than men. Mental and physical fatigue complaints are often the most disabling symptoms for an MS patient. Both are multifactorial, potentially exacerbated by aerobic exercise, may prevent sustained physical functioning, and significantly interfere with activities of daily living1. A multi-center study was designed to investigate the effects of non-aerobic maximal effort exercise (MEE) for deconditioned persons with MS, with the expectation of minimizing fatigue. The IsoPUMP (Neuromuscular Engineering; Nashville, TN), is a specialized exercise and strength-sensing machine, designed to allow individuals to safely perform and record their non-aerobic MEE sessions. The Modified Fatigue Impact Scale (MFIS) and Multiple Sclerosis Functional Composite (MSFC) are common, accepted methods used to measure fatigue and function. The MFIS is a 21-item questionnaire which assesses the subjects’ perception of physical, cognitive, and psychosocial aspects of fatigue over a four-week period2. Each of the 21 items are scored on a scale from 0 (never) to 4 (almost always), and the total MFIS score is calculated by summing the circled number for each item. Total scores can range from 0 to 84; higher scores indicating a greater impact of fatigue on the person. The MFIS has three distinct subscales: (1) physical, (2) cognitive, and (3) psychosocial. These subscales can be scored independently by summing the questions that pertain to each subscale2. The MFIS physical subscale score can range from 0 – 36 and the MFIS cognitive subscale score can range from 0 – 40. The MSFC combines clinical measures used to assess lower limb function (Timed 25-Foot Walk [25-FW]), upper limb function (9-Hole Peg Test [9-HPT]), and cognition (Paced Auditory Serial Addition Test [PASAT-3”])3. The 25-FW is a quantitative measure of lower extremity function. The 9-HPT is a quantitative measure of arm and hand function where a subject inserts and then removes 9 pegs from a board, using one hand at a time. The time is recorded for each hand with the dominant hand trial first and the non-dominant hand trial second. The final score is recorded as the mean time for both hands. The PASAT-3” is a measure of cognitive function, specifically assessing auditory information processing speed, short-term memory, flexibility, and calculation ability. Cognitive dysfunction affects half of all MS patients; slowing ability to reason, concentrate, and recall5. In this test subjects listen to a series of 61 spoken numbers separated by 3 seconds and must add each number to the prior number. Their final PASAT-3” score is the number of correct additions in the series, with 60 reflecting a perfect score. The MSFC is then evaluated by creating Z-scores for each component, which compare each outcome with the average outcome of the study population. The three Z-scores are then averaged to create an overall composite score (the MSFC score) which represents change over time for that population of MS subjects3

The Effect of Progressive Non-Aerobic High-Intensity Maximal Effort Exercise (MEE) on the Health-Related Quality of Life in Patients with Multiple Sclerosis

Background: Studies indicate that Multiple Sclerosis (MS) patients are less satisfied with the quality of their lives than healthy individuals in similar circumstances. Common symptoms experienced include fatigue, cognitive dysfunction, pain, spasticity, depression, bladder/bowel dysfunction and sexual dysfunction. Several pharmacological and non-pharmacological methods have been employed for such symptoms to try to increase quality of life and reduce the mortality rate. Non-pharmacological methods recommended for MS patients include lifestyle modifications, exercise programs and physical therapy. MS patients easily fatigue during aerobic exercise but a non-aerobic progressive maximal effort exercise (MEE) protocol consisting of a few short, duration isometric and eccentric leg press and whole body lunges was previously seen to increase strength without increasing fatigue. The IsoPUMP® (Neuromuscular Engineering, Nashville TN) exercise system permitted safe conduct and measurement of muscle strength and duration during each exercise repetition

An Analysis of Functional Status in Multiple Sclerosis Patients after Progressive Non-Aerobic High-Intensity Maximal Effort Exercise (MEE)

Background: Multiple Sclerosis (MS) is a disease with a wide-ranging impact on functional status. MS patient function has been assessed using Multiple Sclerosis Functional Composite Score (MSFCS). The MSFCS includes the standardized scores (Z-score) of three functional tests: the Paced Auditory Serial Addition Test (PASAT-3”) for cognitive function, 9-Hole Peg Test (9-HPT) for upper extremity function, and timed 25-foot walk (25-TW) for lower extremity function. One of the most common symptoms experienced by MS patients is severe fatigue, often brought on suddenly by aerobic exercise. Non-aerobic maximal effort exercise (MEE) is thought to increase strength without increasing fatigue. The IsoPUMP® (Neuromuscular Engineering; Nashville, TN) is a stationary exercise device designed for patient use to safely perform MEE leg presses and whole body lunges using isometric and eccentric exercises. The progressive functional changes of the MS patients were tracked using the MSFCs at specific intervals during the study

A Double-Blind, Placebo-Controlled, Randomized, Clinical Trial of the TLR-3 Agonist Rintatolimod in Severe Cases of Chronic Fatigue Syndrome

BACKGROUND: Chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) is a severely debilitating disease of unknown pathogenesis consisting of a variety of symptoms including severe fatigue. The objective of the study was to examine the efficacy and safety of a TLR-3 agonist, rintatolimod (Poly I: C(12)U), in patients with debilitating CFS/ME. METHODS AND FINDINGS: A Phase III prospective, double-blind, randomized, placebo-controlled trial comparing twice weekly IV rintatolimod versus placebo was conducted in 234 subjects with long-standing, debilitating CFS/ME at 12 sites. The primary endpoint was the intra-patient change from baseline at Week 40 in exercise tolerance (ET). Secondary endpoints included concomitant drug usage, the Karnofsky Performance Score (KPS), Activities of Daily Living (ADL), and Vitality Score (SF 36). Subjects receiving rintatolimod for 40 weeks improved intra-patient placebo-adjusted ET 21.3% (p = 0.047) from baseline in an intention-to-treat analysis. Correction for subjects with reduced dosing compliance increased placebo-adjusted ET improvement to 28% (p = 0.022). The improvement observed represents approximately twice the minimum considered medically significant by regulatory agencies. The rintatolimod cohort vs. placebo also reduced dependence on drugs commonly used by patients in an attempt to alleviate the symptoms of CFS/ME (p = 0.048). Placebo subjects crossed-over to receive rintatolimod demonstrated an intra-patient improvement in ET performance at 24 weeks of 39% (p = 0.04). Rintatolimod at 400 mg twice weekly was generally well-tolerated. CONCLUSIONS/SIGNIFICANCE: Rintatolimod produced objective improvement in ET and a reduction in CFS/ME related concomitant medication usage as well as other secondary outcomes. TRIAL REGISTRATION: ClinicalTrials.gov NCT00215800

Chemical Genetics Reveals an RGS/G-Protein Role in the Action of a Compound

We report here on a chemical genetic screen designed to address the mechanism of action of a small molecule. Small molecules that were active in models of urinary incontinence were tested on the nematode Caenorhabditis elegans, and the resulting phenotypes were used as readouts in a genetic screen to identify possible molecular targets. The mutations giving resistance to compound were found to affect members of the RGS protein/G-protein complex. Studies in mammalian systems confirmed that the small molecules inhibit muscarinic G-protein coupled receptor (GPCR) signaling involving G-αq (G-protein alpha subunit). Our studies suggest that the small molecules act at the level of the RGS/G-αq signaling complex, and define new mutations in both RGS and G-αq, including a unique hypo-adapation allele of G-αq. These findings suggest that therapeutics targeted to downstream components of GPCR signaling may be effective for treatment of diseases involving inappropriate receptor activation