BEGIN:VCALENDAR VERSION:2.0 PRODID:-//CERN//INDICO//EN BEGIN:VEVENT SUMMARY:Fluorinated Surfactants for Membrane-Protein Extraction DTSTART;VALUE=DATE-TIME:20210322T150000Z DTEND;VALUE=DATE-TIME:20210322T152000Z DTSTAMP;VALUE=DATE-TIME:20260614T225047Z UID:indico-contribution-397-6960@events.saip.org.za DESCRIPTION:Speakers: Kenechi Kanayo Onyia (University of Nigeria\, Nsukka )\nSurfactants carrying either fully or partially fluorinated alkyl chains are conventionally thought to be poor solubilisers of lipids and membrane proteins because of their lipophobicity. New fluorinated surfactants of d ifferent headgroups have been developed. We show that these compounds coul d substitute detergents' function without much interference with membrane proteins' functionality. Their self-assembly and solubilising properties w ere studied by the use of isothermal titration calorimetry (ITC)\, dynamic light scattering (DLS)\, and gel electrophoresis (SDS-PAGE). Micellisatio n was found to be mainly driven by entropy\, and the critical micellar con centration (CMC) decreased with increasing hydrocarbon chain length. Notab ly\, some of these surfactants solubilise lipid vesicles at room temperatu re and extract important membrane proteins directly from *Escherichia coli * membranes. Our findings demonstrated promising\, mild detergent activity for maltose-based fluorinated surfactants in membrane-protein extraction and applications compared to the lactose-based compounds.\n\nhttps://event s.saip.org.za/event/213/contributions/6960/ LOCATION:Zoom Conference URL:https://events.saip.org.za/event/213/contributions/6960/ END:VEVENT BEGIN:VEVENT SUMMARY:The characterization and crystallization of the TBR1 T-box domain in the presence and absence of the T-box Binding Element DTSTART;VALUE=DATE-TIME:20210322T144000Z DTEND;VALUE=DATE-TIME:20210322T150000Z DTSTAMP;VALUE=DATE-TIME:20260614T225047Z UID:indico-contribution-397-6956@events.saip.org.za DESCRIPTION:Speakers: Riyaadh Mayet (University of the Witwatersrand)\nTBR 1 is a neuron-specific transcription factor involved in multiple aspects o f cortical development\,and has recently emerged as a master regulator of genes implicated in Autism Spectrum Disorder (ASD).It is thus possible tha t aberrant molecular interactions with TBR1 could underlie the altered neu ro-molecular networks observed in Autism.\n\nCurrently there is no solved structure available of the TBR1 TBOX domain. In this study\, we aim to obt ain crystal structures of the TBR1 T-box domain in both the presence and a bsence of the T-box binding element\, with the hope of elucidating its DNA -binding mechanism. The structure may be solved by molecular replacement u sing TBX21. This will shed more light on how TBR1 regulates ASD-related ge nes and could explain how aberrant molecular interactions influence neurod evelopmental disorders.\n\nPreliminary structural characterization has bee n made by monitoring intrinsic tryptophan fluorescence and has revealed th at the protein is properly folded. The DNA-binding function has been confi rmed using an electrophoretic mobility shift assay. The DNA-binding proper ties were quantitatively assessed using fluorescence anisotropy and reveal ed a dissociation constant of 320 nM. Since the TBR1 T-box has been succes sfully characterized\, it is ready for crystal trials.\n\nhttps://events.s aip.org.za/event/213/contributions/6956/ LOCATION:Zoom Conference URL:https://events.saip.org.za/event/213/contributions/6956/ END:VEVENT BEGIN:VEVENT SUMMARY:Evolutionary cues in the physicochemical description of proteomes DTSTART;VALUE=DATE-TIME:20210322T142000Z DTEND;VALUE=DATE-TIME:20210322T144000Z DTSTAMP;VALUE=DATE-TIME:20260614T225047Z UID:indico-contribution-397-6953@events.saip.org.za DESCRIPTION:Speakers: Eloy Vallina (Stockholm University)\nWith the glarin g exception of highly conserved binding interfaces\, protein surfaces tend to be regarded as variable regions of hydrophilic character\, subjected o nly to soft evolutionary pressures. However\, in crowded cellular conditio ns\, electrostatic interactions between surfaces take on a critical role i n modulating protein interactivity\, with downstream consequences for prot ein stability\, mobility and solubility. In this context\, surface net cha rge density stands out as the single most important determinant of protein mobility inside the cell. Moreover\, in _E. coli_\, proteins organise aro und a moderately negative net charge density value\, which ensures cytosol -wide colloidal stability: molecules keep away and remain highly mobile mo st of the time\, but close-range interactions are allowed upon small therm al fluctuations. Our results show that\, across organisms\, the average va lue at which this Goldilocks situation is achieved varies\, often dependin g on niche and intracellular conditions: extreme lifestyles—archaeal hal ophiles and endosymbiotic bacteria— can be mapped to different net charg e density values. By combining net charge density with other simplistic ph ysicochemical observables\, derived from sequence data alone\, we can show that the profile of different organism groups changes consistently with t he taxonomical hierarchy. Thus\, we propose that previously unrecognised e volutionary cues can be revealed by inexpensive physicochemical profiling\ , and that these have the potential to contribute complementary informatio n to state-of-art phylogenetic inference.\n\nhttps://events.saip.org.za/ev ent/213/contributions/6953/ LOCATION:Zoom Conference URL:https://events.saip.org.za/event/213/contributions/6953/ END:VEVENT BEGIN:VEVENT SUMMARY:A Systematic Integration of Empirical and Computational Studies to Biophysically Describe Recombinant Nicotinate Mononucleotide Adenylyltran sferase (NaMNAT) From Klebsiella pneumonia DTSTART;VALUE=DATE-TIME:20210322T140000Z DTEND;VALUE=DATE-TIME:20210322T142000Z DTSTAMP;VALUE=DATE-TIME:20260614T225047Z UID:indico-contribution-397-6938@events.saip.org.za DESCRIPTION:Speakers: Olamide Jeje ()\nNicotinate mononucleotide adenylylt ransferase (NaMNAT) is an indispensable enzyme in the biosynthesis of pyri dine dinucleotides. Given the vital role of NAD+ in controlling key cellul ar processes\, NaMNAT represents an attractive target for the design of no vel broad-spectrum antibiotics to treat nosocomial infections associated w ith MDR Klebsiella Pneumonia. This study aims to characterize the biophysi cal structure of NaMNAT from K. Pneumonia (KpNaMNAT) using a systematic co mbination of experimental and computational approaches. Overexpression and purification were carried out using hexa-histidine tags in E. coli expres sion system and nickel ion-immobilized metal affinity chromatography. Acti vity studies using NMN substrate showed KpNaMNAT to demonstrate broad pH o ptima of 6.5-9.5 and preference for Mg2+. Structural characterisation reve aled KpNaMNAT as a monomer with predominate α-helices. ATP\, NMN\, and NA D+ all bind at the same site on KpNaMNAT\, but do not induce any significa nt conformational changes\, however\, ATP responds to Mg2+ more than the o ther ligands and the protein response in the presence of Mg2+. The data an d insight provided by this novel research would be useful as a molecular b asis for further evaluation of the enzymes for the design of structure-bas ed inhibitors with therapeutic potential.\n\nhttps://events.saip.org.za/ev ent/213/contributions/6938/ LOCATION:Zoom Conference URL:https://events.saip.org.za/event/213/contributions/6938/ END:VEVENT BEGIN:VEVENT SUMMARY:Fighting against COVID-19: A computational biophysics approach DTSTART;VALUE=DATE-TIME:20210322T134000Z DTEND;VALUE=DATE-TIME:20210322T140000Z DTSTAMP;VALUE=DATE-TIME:20260614T225047Z UID:indico-contribution-397-6926@events.saip.org.za DESCRIPTION:Speakers: Abdo Elfiky (Cairo University)\nPreviously it was re ported that cell-surface Glucose Regulated Protein 78 (CS-GRP78)\, also te rmed heat shock protein A5 (HSPA5)\, could be a possible route for SARS-Co V-2 internalization. The binding site on the spike protein of SARS-CoV-2\, which can recognize CS-GRP78\, was predicted in a previous study. The spi ke glycoprotein of the SARS-CoV-2 bear many conserved motifs to the previo usly determined human coronavirus strains such as HKU1\, 229E\, NL63\, OC4 3\, MERS-CoV\, and SARS-CoV. 2 However\, we would like to emphasize that u sing a simple bioinformatics approach can suggest a possible role of the G RP78 in cross immunization against COVID-19. Additionally\, different anti viral drugs have the potential to be SARS-CoV-2 inhibitors\, thus can be u sed against COVID-19. These drugs are tested in silico at the beginning of the pandemic\, and currently\, some are approved against COVID-19.\n \nRe cent Publications \n1. Ismail AM\, Elfiky AA. SARS-CoV-2 spike behavior in situ: a Cryo-EM images for a better understanding of the COVID-19 pande mic. Signal Transduction and Targeted Therapy. 2020\;5(1):252.\n2. Ibrahim IM\, Abdelmalek DH\, Elshahat ME\, Elfiky AA. COVID-19 spike-host cell re ceptor GRP78 binding site prediction. Journal of Infection. 2020\;80(5):55 4-62.\n3. Elfiky AA. SARS-CoV-2 Spike-Heat Shock Protein A5 (GRP78) recogn ition may be related to the immersed human coronaviruses. Frontiers in Pha rmacology. 2020\;11:1997.\n4. Elfiky AA\, Ibrahim IM\, Ismail AM\, Elsheme y WM. A possible role for GRP78 in cross vaccination against COVID-19. Jou rnal of Infection.\n5. Elfiky AA. Natural products may interfere with SARS -CoV-2 attachment to the host cell. Journal of Biomolecular Structure and Dynamics. 2020:1-10.\n\nhttps://events.saip.org.za/event/213/contributions /6926/ LOCATION:Zoom Conference URL:https://events.saip.org.za/event/213/contributions/6926/ END:VEVENT BEGIN:VEVENT SUMMARY:The nanoscale structure of the Octopus ink: Sepia melanin DTSTART;VALUE=DATE-TIME:20210322T132000Z DTEND;VALUE=DATE-TIME:20210322T134000Z DTSTAMP;VALUE=DATE-TIME:20260614T225047Z UID:indico-contribution-397-6923@events.saip.org.za DESCRIPTION:Speakers: Agnes Mbonyiryivuze (1African Centre of Excellence f or Innovative Teaching and Learning Mathematics and Science (ACEITLMS)\, U niversity of Rwanda-College of Education (UR-CE)\, Rwanda 2UNESCO-UNISA Af rica Chair in Nanosciences/Nanotechnology\, College of Graduate Studies\, University of South Africa\, Pretoria-South Africa 3Nanosciences African N etwork (NANOAFNET)\, iThemba LABS-National Research Foundation\, Cape Town \, South Africa)\nSepia melanin isolated from the ink sacs of Sepia offici nalis\, is commonly used as standard in many research activities on melani n such as photobiology and photoreactivity of skin pigments. Melanins are difficult to characterize because of their intractable chemical properties and the heterogeneity in their structural features. Melanin pigments\, in fact\, are composed of many different types of monomeric units that are c onnected through strong carbon-carbon bonds. Its high insolubility and und efined chemical entities are two obstacles in its complete characterizatio n. The morphological characterization and particle size distribution for s epia melanin by Scanning Electron Microscopy (SEM) on surface structure an d Transmission Electron Microscopy (TEM) to confirm the morphology obtaine d from SEM was done. Both results show that Sepia melanin is formed by man y aggregates agglomerated together. These aggregates are formed also by sm all spherical granules with different size distributions that have been de termined using image-J software. The small granule diameter obtained from different TEM and SEM micrographs were 100-200nm. EDS reveals that C and O were the most abundant in sepia melanin with concentration average concen trations of about 57% and 24% respectively. The major compositions of sepi a melanin are C\, O\, Na\, Cl\, while the minor are Mg\, Ca\, K\, S and N. From TEM micrograph at high resolution\, it was possible to measure the d istance between polymers layers of sepia melanin using image-J software an d it was 0.323 nm = 3.23 Å.\n\nhttps://events.saip.org.za/event/213/cont ributions/6923/ LOCATION:Zoom Conference URL:https://events.saip.org.za/event/213/contributions/6923/ END:VEVENT BEGIN:VEVENT SUMMARY:Theoretical comparison of real-time single-particle tracking techn iques DTSTART;VALUE=DATE-TIME:20210322T130000Z DTEND;VALUE=DATE-TIME:20210322T132000Z DTSTAMP;VALUE=DATE-TIME:20260614T225047Z UID:indico-contribution-397-6920@events.saip.org.za DESCRIPTION:Speakers: Bertus van Heerden (University of Pretoria)\nOne of the main challenges in studying single biomolecules in a native or near-na tive environment is their constant diffusion. An approach to solving this problem is real-time single particle tracking (SPT). In this study\, we us ed statistical calculations and dynamic simulations to compare the orbital \, Knight’s Tour and MINFLUX localization methods\, in the context of fl uorescence-based and interferometric scattering (iSCAT) approaches. While the Knight’s Tour method can track the fastest diffusion\, MINFLUX achie ves the greatest precision. The relative success of iSCAT vs fluorescence is strongly dependent on the particle size\, and the photophysical propert ies and density of the fluorophores.\n\nhttps://events.saip.org.za/event/2 13/contributions/6920/ LOCATION:Zoom Conference URL:https://events.saip.org.za/event/213/contributions/6920/ END:VEVENT END:VCALENDAR