Fulyani, Faizah

English

In dit proefschrift heb ik de structuur en functie van GlnPQ, een ATP- bindingscassette (ABC) transporter, bepaald. GlnPQ heeft twee verschillende, met elkaar verbonden substraatbindende domeinen (SBDs), die aan het transmembraan domein van de transporter vast zitten. Ondanks het feit dat de substraatbindingsplaatsen van de verschillende SBDs in GlnPQ sterke overeenkomsten vertonen, is de affiniteit en de specificiteit voor de substraten verschillend. Sterker, de twee met elkaar verbonden substraatbindende domeinen hebben verschillende specificiteiten, wat het voor een cel mogelijk maakt om met één ABC transporter verschillende aminozuren op te nemen. Het tweede gedeelte van dit proefschrift bespreekt de competitie tussen substraten voor de opname via GlnPQ en de consequenties voor de groei van de bacterie Lactococcus lactis. We laten zien dat GlnPQ uit L. lactis een relatief hoge affiniteit en lage transportsnelheid voor asparagine heeft via substraatbindend domein 1 (SBD1), en dat het tegenovergestelde waar is voor glutamine. Het laatste gedeelte van dit proefschrift beschrijft een strategie voor het ontwikkelen van medicijnen tegen pathogene Gram-positieve bacteriën. De functionaliteit van GlnPQ is vereist voor de opname van moleculen die als stikstofbron kunnen fungeren. Daarnaast is de transporter betrokken bij de virulentie van pathogene bacteriën. Een belangrijk gegeven is dat er geen homologen van GlnPQ in mensen en zoogdieren zijn geïdentificeerd, wat deze transporter een potentiëel doelwit maakt om medicijnen tegen te ontwikkelen.The studies in this thesis are focused on an ATP-Binding Casette (ABC) transporter for amino acids, named GlnPQ. GlnPQ has two different substrate-binding domains (SBDs) arranged in tandem, fused to the transmembrane domain of the transporter. The first part of this thesis describes the structural and functional characterization of the SBDs of GlnPQ from non-pathogenic and pathogenic Gram-positive bacteria. Even though the binding sites of the SBDs of GlnPQ show high structural similarity, the affinity and specificity for substrates is very different. Moreover, the SBDs in the tandem have a different specificity, which allows a cell to accumulate different amino acids via a single ABC transporter. The second part of the thesis addresses the competition between substrates for import via GlnPQ and its consequences for growth of L. lactis. We demonstrate that GlnPQ from L. lactis has relatively high affinity and low rate of transport for asparagine via SBD1, and the opposite is true for glutamine. Consequently when the growth medium contains equimolar concentrations of asparagine and glutamine, uptake of glutamine via SBD1 is strongly inhibited by asparagine and the growth is slow. The growth could be restored by increasing the glutamine concentration. The final part of this thesis describes a strategy to develop drugs against pathogenic Gram-positive bacteria. GlnPQ is required for nitrogen source intake and the system has been implicated in virulence in pathogenic bacteria. Importantly, homologs of GlnPQ are not present in humans and mammals, and it is therefore a potential target for drug development

Proceedings - University of Groningen

   University of GroningenStructural and functional diversity of substrate-binding domains in ABC importersFulyani, FaizahIMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2015Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Fulyani, F. (2015). Structural and functional diversity of substrate-binding domains in ABC importers.University of Groningen.CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license.More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne-amendment.Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 11-12-2022   	 155	Acknowledgements	Alhamdulillahhirabbil´alamin.	All	praise	to	Allah	SWT	who	granted	me	the	courage,	capability	 and	opportunity	 to	 complete	my	PhD.	 It	 has	been	a	 long	 journey	with	hardship	and	many	turns.	I	have	received	a	lot	of	support,	guidance,	and	kindness	from	people	whom	I	met	throughout	this	 journey	and	for	that	 it	 is	a	pleasure	for	me	to	express	my	gratitude	for	them.	Firstly,	 I	would	 like	to	thank	my	supervisor	Prof.	Bert	Poolman	for	giving	me	the	opportunity	 to	 do	 the	 PhD	 in	 the	 Enzymology	 group.	 I	 highly	 appreciate	 your	supervision,	constant	support,	guidance,	and	encouragement	throughout	my	PhD.	I	admire	your	hard	work	and	your	fast	response	in	correcting	my	thesis.	Thank	you	very	much.		I	 also	 would	 like	 to	 express	 my	 gratitude	 to	 my	 co‐supervisor	 Prof.	 Dirk	 J.	Slotboom.	 Thank	 you	 for	 the	 countless	 times	when	 you	 helped	me	with	 various	kinds	 of	 things.	 You	 always	 have	 a	 minute	 for	 me	 and	 patiently	 answer	 to	 my	questions.	 I	 really	 appreciate	 it.	 My	 special	 thanks	 to	 the	 reading	 committee	members	Prof.	Jan	Kok,	Prof	Dick	Janssen	and	Prof.	Lutz	Schmitt.	I	would	like	to	thank	the	Beasiswa	Disertasi	Indonesia	program,	Lembaga	Pengelola	Dana	 Pendidikan	 (LPDP),	 Departemen	 Keuangan	 Indonesia	 for	 taking	 part	 in	providing	me	with	the	financial	support	to	finish	my	PhD	study.	Special	thanks	to	Ibu	Bunga	who	helped	me	a	lot	with	all	the	administration	process	in	applying	the	scholarship.		My	 sincere	 thanks	 to	 people	 that	 contributed	 in	 my	 PhD	 study.	 Mrs.	 Margriet,	thank	you	for	your	extremely	kindness	in	helping	me	with	various	kinds	of	things.	I	will	always	remember	you.	Albert,	you	are	a	crystallographer	savior,	thank	you	for	everything.	You	are	very	knowledgeable,	reliable,	and	kind!	I	wish	I	met	you	earlier	in	my	PhD	study.	To	Soren,	 thank	you	 for	your	effort	 in	providing	 the	molecular	docking	data.	To	Gea,	eventually	we	were	writing	several	papers	 together,	 thank	you	for	the	hard	work!	I	really	appreciate	it.	My	special	thanks	to	Dr.	Ruud	Scheek.	You	are	probably	the	most	sincere	and	the	wise	person	that	I	ever	met	during	my	stay	 here,	 thank	 you	 for	 helping	 me	 with	 the	 Mathematica	 software.	 I	 highly	appreciate	your	support.	156	I	would	 like	 to	 thank	my	paranymph	Sonja	 and	Raj.	 Sonja,	 I	 first	met	 you	 in	 the	crystallography	group.	We	both	worked	late	setting‐up	crystallization	plates	using	the	 mosquito	 robot.	 Back	 then	 you	 were	 still	 a	 visiting	 master	 student	 but	 you	showed	capable	of	hard	work.	I	was	surprised	that	you	could	speak	Indonesian	and	eventually	 we	 became	 good	 friends.	 Thank	 you	 so	 much	 for	 willing	 to	 be	 my	paranymph.	I	will	be	waiting	for	you	to	visit	me	in	Indonesia).			I	will	 take	 this	 opportunity	 to	 thank	 the	 former	Enzymology	members:	 Josy	 and	Roonie,	 Tejas,	 Jacek,	 Siva,	 Jeanette,	 Pranav,	 Nobina,	 Erik,	 Karin,	 Astri,	 Justyna,	Anton,	 Marysia,	 Petra,	 Whim,	 Duygu,	 Gemma,	 Nadia,	 Mac	 Donald,	 Akira,	 Inga,	Karlien,	 and	 Armagan.	 I	 was	 having	 good	 times	 in	 the	 group	 because	 of	 our	friendship	 and	 I	 shall	 remember	 all	 of	 our	memories.	 Special	 thanks	 to	Guus	 for	letting	me	work	with	his	ThiT	and	to	finally	see	how	beautiful	membrane	protein	crystals	could	look	like.	To	Andreja,	we	shared	many	difficult	times	together	during	membrane	 protein	 crystallizations.	 Thank	 you	 for	 your	 patience	 and	 your	 help	during	that	time.	I	wish	all	the	best	for	you	and	your	family.	My	 office	mates	 Franz,	 Raj,	 and	 Ruslan.	 It	 was	 funny	 how	 the	 three	 of	 us	 often	ended	working	overtime	or	working	during	the	weekend	together.	Thanks	guys	for	your	 support	 and	 kindness.	 Also	 thanks	 to	 the	 rest	 of	 Enzymology	 members:	Stephanie,	 Frans,	 Hendrik,	 Ria,	 Jonas,	 Arnold,	 and	 Weronika.	 Special	 thanks	 to	Lotteke	who	helped	me	with	the	Dutch	translation	of	my	thesis	summary.	For	Alia,	we	have	 been	 friends	 for	 almost	 13	 years.	 I	 think	we	 know	 each	other	best,	going	through	the	good	and	bad	times	but	 in	the	end	you	are	always	on	my	side,	 Thank	 you.	My	 life	 in	 Groningen	 is	 not	 complete	without	 all	 the	 friendship	from	 the	 big	 Indonesian	 communities.	 Thank	 you	 to	 all	 Kimia	 02	 (Susanti,	 Lia,	Robby,	Iqbal,	Eryth,	Nizar,	Wahono,	Rachma),	Florence,	Astri,	Yusuf,	Teh	Sri	dan	Ka	Muiz,	Ka	Fean,	Ka	Guntur	dan	Teh	Intan,	Ka	Amel	dan	Teh	Puti,	Ria	dan	Martijn,	Ka	Wangsa,	 Ka	 Iging	 dan	 Desti,	 Mba	 Tina,	 Bang	 Fani,	 Mba	 Lia	 dan	 Mas	 Yayok,	 Pa	Hengki,	 Keluarga	 Pak	 Asmoro,	 Auliya,	 Shabrina,	 dan	 Neily,	Mas	 Bayu,	 and	many	more	that	I	cannot	mention	here	one	by	one.	My	special	thanks	to	the	family	of	Mas	Chalid	 dan	 Mba	 Nona.	 Semoga	 Allah	 SWT	 senantiasa	memberikan	 balasan	 yang	berlipat	ganda	untuk	kebaikan	yang	Mbak	dan	Mas	berikan.	Kepada	Bude	Nunung,	Bude	terimaksih	banyak	untuk	keluangan	waktu	yang	Bude	berikan	kepada	Hanna.	Semoga	Allah	SWT	memudahkan	segala	urusan	Bude.		My	special	thanks	to	my	beloved	big	family	for	their	unconditional	love	and	care.	I	would	 not	 have	 made	 it	 this	 far	 without	 your	 support.	 Untuk	Mama	 dan	 Papa,	terimakasih	yang	tak	terhingga	atas	kepercayaan,	pengorbanan,	dan	doa	yang	tiada	hentinya	 untuk	 anak	 mu	 ini.	 Hanya	 Allah	 SWT	 lah	 sebaik‐baiknya	 yang	 dapat	157	memberikan	balasan	atas	jasa	Mama	dan	Papa.	Semoga	menjadi	amal	jariyah	yang	tiada	akan	terputus	untuk	Mama	dan	Papa.	Untuk	adikku	tersayang,	Wilda	Rahma	Fulyani,	Uni	doakan	 semua	yang	 terbaik	untuk	 Ida.	 	Untuk	Mama	dan	Papa	 (alm)	Semarang	terimakasih	tiada	terhingga	untuk	dukungan	dan	doa	nya.	Semoga	Allah	SWT	senantiasa	memberikan	rahmat	dan	ridhaNya.	Untuk	semua	keluarga	besarku	tersayang,	terimakasih	banyak.	Untuk	Tek	Ta	dan	keluarga	 ,	Paman	Uyung,	Ka	 ira,	dan	Uda	yang	 sering	direpotkan	mengantar	dan	menjemput	 	 Iis	di	Bandara	Soeta,	terimakasih.		Finally,	 my	 deepest	 gratitude	 to	 my	 husband	 Pandji	 Triadyaksa.	 Thank	 you	 for	making	me	a	better	and	much	stronger	person.	Without	your	support	 I	wouldn´t	have	 come	 this	 far.	 Somehow	 your	 sense	 of	 humor	 helped	me	 a	 lot	 through	 the	hardest	 time	 in	 my	 life.	 Semoga	 Allah	 SWT	 membalas	 segala	 jasa	 Mas	 dan	memudahkan	pula	perjuangan	S3	Mas.	For	my	beloved	daughter	Hanna,	thank	you	sweetheart,	you	always	give	Mama	the	strength	to	go	through	this	journey	and	you	are	the	best	gift	from	Allah	to	Mama	and	Ayah.		Now	it´s	time	to	close	this	PhD	chapter	and	open	a	new	chapter	in	my	life.	Alhamdulillahhirabbil´alamin				Groningen,	September	2015	Faizah	Fulyani	 

Structural and functional diversity of substrate-binding domains in ABC importers

https://pure.rug.nl/ws/files/25212179/Acknowledgements_.pdf

Structural and functional diversity of substrate-binding domains in ABC importers

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Proceedings - University of Groningen